text:
MacVector and ChemDoodle web components news
MacVector Inc have released a free version of MacVector.
If you used a temporary trial license, then when the 21 days were up, MacVector would simply refuse to start unless you entered a new valid license code. With the release of MacVector 12.7 we have changed that behavior. Now, when the trial license (or any annual license) expires, MacVector will give you the option of continuing to work, but with reduced functionality. All of the functions in the Analyze menu become disabled, but you can still open, edit, save and print MacVector documents, or save MacVector files in other formats.
ichemlabs have announced the release of ChemDoodle Web Components 5.
ChemDoodle Web Components 5 is a massive update. The most notable addition is a Full Sketcher, for drawing multiple molecules, shapes and figures, in addition to the Single Molecule Sketcher already provided. iChemLabs Cloud services and the ChemDoodle JSON format have been updated and drastically improved. The entire codebase has been reoptimized and cleaned, doubling the performance in desktop browsers and more than quadrupling the performance in mobile browsers. All Canvases now handle managing multiple molecules and shapes. Many new additions have been added and dozens of bug fixes have been implemented. We will be unrolling our new proprietary options over the next month, but of course, everything is available for free today under the GPL license!
There is a tutorial for using ChemDoodle web components here.
The Modern Alchemist
I've been watching the Royal Institution Christmas lectures with my family, and ever they are brilliantly presented exploration of an area of science. This year it is the turn of Peter Wothers "The Modern Alchemist" to explain about the chemicals in the air we breath and the water we drink. Hopefully inspiring the next generation of scientists and hopefully convincing people that "chemicals" far from being man-made toxins are in fact essential for all human life.
If you have ever wanted to know what the reaction of caesium with fluorine is like then have a look at lecture two.
The lectures are televised on BBC 4 and are available on iPlayer
Further behind the scenes clips and more information is available on the Royal Institution website
The two most reactive elements in the Periodic Table. In preparation for the 2012 Christmas Lectures Dr Peter Wothers heads off to the University of Leicester to conduct an extraordinary experiment - reacting the most reactive metal in the periodic table (Caesium) with the most reactive non-metal (Fluorine). Due to the extreme reactivity of the two elements, Fluorine expert Professor Eric Hope is on hand to enable the experiment to be conducted safely in a unique set of apparatus. We believe this is the first time the reaction has been caught on camera.
Structure activity on an iPhone
An interesting post on Cheminformatics 2.0
the SAR Table app has a not-yet-released feature which allows the current set of structures and their activities ("responses") to be packed off to a webservice, which proceeds to construct a model based on structural features, then predicts values for any structures that don't have values for that particular property.
Mobile science is coming on in leaps and bounds.
There many more iPhone/iPad apps on the mobile science page.
Bookends Updated
The reference management application Bookends has been updated to version 11.3.4 (December 23, 2012)
Autofill ISBN from any Amazon source In preferences, select which Amazon site (US, UK, Japan, etc.) to use to autofill references using the ISBN. This was previously limited to Amazon US. Note that many sites do not provide summary information.
Automatically exclude author and title from a citation or footnote If the temporary citation begins with &, Bookends will exclude the author and title (or secondary title) in the final citation or footnote.
The font size delta for small caps has been changed to 3 points (from 2)
Search Web Of Science for grant number and funding agency
JSTOR parser in Bookends Browser was updated to deal with changes made by JSTOR
Perform a Spotlight boolean NOT search by putting a minus sign directly in front of a word For example, to search for an attached pdf written by Smith and not Jones, search for "Smith -Jones" (without the quote marks).
Bookends Browser will detect DOIs on the Web Of Science web site and allow you to import references and pdfs by clicking on the green icon If not already present, the Web Of Science web site will be added to the Bookends Browser bookmarks.
Keywords shown in a column in the list view will be separated with semicolons Previously, only the first keyword was shown.
Bug fixes Improved check for a valid PMID in the PMID field when doing an Autofill From Internet. Fixed a bug that prevented text in fields being edited from being saved if some of the Action pop-up menu commands were invoked. Fixed a bug that could result in incorrect author-date sorts in citation groups if the name and date was separated by a space. Fixed a bug that caused an error when renaming a Type in preferences when a format window displaying that Type was open. The Reveal In Finder contextual menu now works in the reference pane view of the library window. Fixed a bug that could cause an error when syncing pdfs with Bookends On Tap. Fixed a problem where trying to open a pdf in Preview using the right-click hierarchical menu could result in an error. Fixed an error that could occur when changing the pop-up menu to select different search options in the Find dialog. Fixed an error that was generated with exporting a tab-delimited text file with attachments. Fixed a bug where the pdf display pane was not updated properly when replicating a Book as a Book Chapter.
There is a page of reference management applications here.
BBEdit 10.5.1 Released
BBEdit 10.5.1 is a focused maintenance update which includes fixes for reported issues. This release consists entirely of fixes for reported issues, and contains no new features, nor changes to existing features.
They include
Fixed crash which would occur after using the "Other..." menu item to choose an alternate file in the Markup Builder panel, then cancelling the file dialog, and then immediately dismissing the markup panel. On a Thursday.
NEXT to Mac OS X
An interesting piece on Ars Technica
The legacy of NeXT lives on in OS X NeXTSTEP technologies still fuel Macs, iPhones, and iPads 16 years later.
Readers might also enjoy this video
Gene Backlin: NeXT to X: A Trip Down Memory Lane
Data Extractor Updated
Data Extractor solves the problem that often advanced users have, the necessity to extract data available in text format on one or more files (often thousands and thousands of files) , and moving them inside a table or a database in an ordered and structured form with fields and records for archiving and successive processing. Data extractor can parse thousands and thousands of file in few seconds and collect all the data inside these files using simple instructions on how to recognise data, how to extract them and where to put these data inside Data Extractor tables, ready to be exported
Included on the page of data analysis tools
Datasets are ubiquitous in chemistry research and education. For fields involving organic chemistry, these datasets often take the form of Structure data files (SD files). Although an assortment of tools can present SD files on desktops and laptops, few options exist for doing so on increasingly-useful tablets and phones StructureMate™, aims to bring chemical structure dataset analysis and visualisation to a much wider range of devices. This Universal app runs on both the iPad/iPad Mini and iPhone/iPod Touch families, with custom-built interface for each.
There many more iPhone/iPad apps on the mobile science page.
Using ChemBioDraw with MOE
As I mentioned in my recent review of MOE 2012 there is now support for using Marvin as an external 2D chemical drawing package, but what happens if you want to use another drawing package? Well that is where Applescript comes to the rescue, using Applescript support for shell scripts and one line of SVL (scientific vector language) we can use ChemBioDraw as the external editor. Full details of the script are here.
The Applescript section contains more tutorials, scripts and resources.
A Review of MOE 2012
I've just finished a review of the latest version of MOE from the Chemical Computing Group.
There are a number of new features that will be of particular interest to Mac users and I've included a few tips for using Marvin as the external 2D chemical drawing package.
There is a collection of software reviews here.
Chemcomp release PSILO version 2012.11
The Chemical Computing Group have announced the release of PSILO version 2012.11. PSILO is a protein structure database and visualization system that provides an easily accessible, consolidated repository for macromolecular and protein-ligand information. Some key features in PSILO include:
- 3D Interaction Query
- Pocket Similarity Search
- Project Standard Orientation
New and enhanced features in PSILO 2012.11 include: domain motif search, nonredundant BLAST summary report, automatic GPCR annotation and Interactive protein:ligand interaction diagrams. PSILO offers research organizations a means to systematically track, register and search both experimental and computational macromolecular data. A web-browser interface facilitates searching and accessing public and private data
DIRAC 12 Released
New features in DIRAC12 (released 12/12/12) Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations
- 2-component relativistic Effective Core Potentials (ECPs)
- London Atomic Orbitals (LAOs) at the DFT level
- Simple magnetic balance for NMR shieldings
- LAO current densities
- Overlap diagnostic for TD-DFT calculations of excitation energies
- Pipek-Mezey localization by trust-region optimization
- Long-range MP2/short-range DFT
- Atomic start guess for SCF calculations
- MP2 natural orbitals
- Complex/Damped DFT response module
- New Lanczos algorithm for relativistic Algebraic Diagrammatic Construction (ADC)
iNMR 5.2.4 released
The latest Mac version of iNMR is 5.2.4, released today. Due to popular demand it restores the slider for zero-order phase correction, which reappears side-by-side with the knob that has been in its place for a whole year. Their function is equivalent. This seems to be a case where it's better to have redundant controls.
Maple 16.02 released
Maple 16.02, a maintenance update, is available to all users running Maple 16. This update contains enhancements to many areas, including:
- Maple 16 now works on Macintosh OS X 10.8
Connectivity features have been extended to include: MATLAB® 2012b and Microsoft Visual Studio 2012
Physics. Enhancements were made to several areas of the Physics package, including
- Algebraic manipulations of dot products of quantum operators (possibly tensorial) and eigenstates
- Algebraic simplification taking into account commutation/anticommutation rules
- Simplification of tensor products involving the sum rule for repeated indices in the presence of symmetric and antisymmetric tensors
- Dagger, Commutator, AntiCommutator, Bracket
- Normal forms of products of quantum operators
- Saving and loading Physics setup across sessions
- Allowing selective partial clearing of setting using Setup(clear, <…>)
Copying and pasting of textbook display (typesetting = extended)
Enhancements were made to memory management/garbage collection.
- Improvements were made to the display of data tables and to custom palettes.
I've updated the page of data analysis tools
KNIME 2.7 released
KNIME 2.7 has been released.
KNIME now runs on Java 7 for Windows and Linux systems (Mac stays on Java 6) Eclipse update 3.7 increases stability on Mac and some Linux systems. BIRT 3.7 brings Open Office support among other new features
JFreeChart nodes have now more setting options in the "General Plot Options" tab of their configuration window.
In R-> Local there are a number of new nodes to import:
- "Table to R" can read a KNIME table into R and output the R workspace.
- "R to Table" takes an R workspace and outputs a KNIME table.
- "R +Data to R" takes an R workspace and optional data input and outputs an R workspace.
- "R to R-View" takes an R workspace and outputs a KNIME view
There is a KNIME tutorial here
An intro to Open Babel
Noel O'Boyle has written a brilliant introduction to OpenBabel.
Tableau Mobile
A few days ago I mention Spotfire for the iPad and a couple of readers sent in details of similar applications.
Tableau mobile is an iPad front-end to an analytics server. Create interactive reports and dashboards in Tableau Desktop then publish them to Tableau Server for secure access on your desktop, or on the web or with your iPad.
Similarly SAP BusinessObjects Mobile connects to the SAP BusinessObjects Business Intelligence platform.
BBEdit 10.5 released
BBEdit has been updated to version 10.5.
I'm a great fan of BBEdit I've been using it as long as I've been using a Mac and it is my "swiss army knife" when it comes to opening unusual file types. It is also a great tool for programming, scripting and creating html pages (including Markdown). Version 10.5 is a significant feature update which includes support for Macs with the high-resolution "Retina" displays, assorted new features, and fixes for reported issues.
The full release notes are here.
The release notes are always worth a read since they do reflect the humour of the BBEdit team, I've included a couple of the notes below.
When creating a new HTML document (from the dialog or from a template), there's a new substitution available: #LOCALE#. This is the "short" locale code corresponding to the "Language" setting in the dialog box, e.g. en, de, x-klingon, and the like…..
The "Show Clipboard" command on the Edit menu has been retired. It now lives on a farm upstate.
App state restoration has an indeterminate progress dialog, hopefully hinting that "No, we're not hung; we're busy".
The "current process" indicator in shell worksheets now has a spinny thing so that you know something's running, and a clicky thing if you want to stop the running thing indicated by the spinny thing.
I posted a selection of other Markdown editors here and there is more info on programming tools.
SMARTCyp Updated
SMARTCyp 2.3 has been released with some additional improvements including: Improved energies for N-oxidations Empirical correction for unlikely N-oxidations of tertiary alkylamines A filtering functionality for excluding compounds with very low activation barriers to CYP-mediated oxidations A smiles string can now be input directly on the command line using the -smiles flag. Available as usual at http://www.farma.ku.dk/smartcyp The science behind the improved N-oxidations and the empirical correction has also been published in a paper in Angewandte Chemie: DOI
Website Stats
As we come to the end of the year I thought I'd have a look at the website stats.
The site is currently averaging over 20,000 hits per month and around 35% are returning visitors, this compares with around 15,000 hits last year and just under 30% returning visitors. The majority of readers are Mac users (61%) but there are also a number of Windows users (26%), the big change has been with mobile usage which has doubled to around 10% nearly all iOS.
The geographic coverage has expended with the US and UK now accounting for 40% (last year it was 55%), in total 118 different countries are represented in the web logs.
The top search terms were emolecules, Spotlight, Chemdoodle and Vortex.
The top pages were (ignoring the home page)
Mobile Science
Comparison of Chemical Drawing packages
Chemdoodle 5 Review
Clipboard Managers
Data Analysis Tools
The most popular blog posts this year were
Review of ChemDoodle 5
Elemental for iPad
Chemical Drawing Packages
The most popular blog post of all time remains Siri knows chemistry
Spotfire for iPad
Spotfire for the iPad requires access to a TIBCO Spotfire Web Player Server. By default, the app is connected to our public demo gallery so you can start experiencing data in Spotfire immediately. After that, you can connect to your internal server, or you can connect to public servers and explore Spotfire analytical tools.
Now added to the mobile science page.
iOS marketshare on the rise again
The November marketshare results from Net Applications are out and again we see the rise in mobile browsing. From around 6% twelve months ago we have seen a steady rise to over 10% in November 2012 and I'd expect to see a continued rise over Christmas. After a small dip in October, presumably due to consumers waiting for updates, iOS has started to rise again at the expense of Java ME, Blackberry and Symbian which had a combined market share of 30% twelve months ago and have now fallen to a combined share of less than 10%.
On the desktop Windows (91%) continues to drift downwards with no evidence that Windows 8 has lifted the PC market, Mac OSX continues to rise slowly and now stands at 7.3%, the highest level since Net Applications began recording.
Samsung printer vulnerability
A recent report highlights a potentially critical vulnerability. Samsung printers (as well as some Dell printers manufactured by Samsung) contain a hardcoded SNMP full read-write community string that remains active even when SNMP is disabled in the printer management utility.
A remote, unauthenticated attacker could access an affected device with administrative read/write privileges. Secondary impacts include: the ability to make changes to the device configuration, access to sensitive information (e.g., device and network information, credentials, and information passed to the printer), and possibility the ability to leverage further attacks through arbitrary code execution.
I was recently asked about security software to protect desktop and iOS devices, perhaps as we move into an age where we all have many devices, printers, games consoles, TVs, media centres etc. security software vendors need to widen their remit.
Mathematica 9 is released
Wolfram have announced the release of Mathematica 9 with a host of new features
Optimize your workflow with the Wolfram Predictive Interface The Wolfram Predictive Interface makes it easy to find and use the power of Mathematica 9. The Input Assistant's context-sensitive autocompletion and dynamic highlighting help you discover and enter commands, and the next-computation Suggestions Bar offers optimized suggestions for what to do next. It's the next step in our ongoing Compute-as-You-Think initiative that began with free-form linguistic input.
Examine social networks with built-in links to social media Mathematica 9 introduces a full suite of social network analysis features including community detection, cohesive groups, and centrality measures, plus built-in links to Facebook, LinkedIn, Twitter, and more. It also adds new capabilities for network flows and new graph distributions.
Work with systemwide support for units Mathematica 9 introduces a new unit system containing more than 4,500 different units, all integrated with Wolfram|Alpha's sophisticated unit interpretation system. From unit conversion to dimensional analysis, Mathematica provides you with all the tools you need to work with, and extract properties from, units and quantities.
Use survival analysis, random processes, and other expanded capabilities in data science and visualization Mathematica offers more statistical distributions than any other system, including specialized coverage of finance, medicine, and engineering. Mathematica 9 adds survival and reliability analysis; full support for random processes including queues, time series, and stochastic differential equations; a complete set of customizable gauges for dashboards and reports; and systemwide support for automatic legends for plots and charts.
Integrate R code into your Mathematica workflow Mathematica 9 offers built-in ways to integrate R code into your Mathematica workflow, allowing data exchange between Mathematica and R and execution of R code from within Mathematica. With RLink, R users can use thousands of functions from across the full Mathematica system.
Deploy interactive documents with enhanced capabilities Instantly create documents in the Computable Document Format (CDF) to present interactive charts of results, show dynamic models, or prototype your next application, and deploy them to the web or desktop. With Mathematica Enterprise Edition, you can deploy CDFs with live data and other enhanced features.
Perform powerful 3D volumetric and out-of-core image processing Mathematica 9 scales up performance to very large 2D- and 3D-volumetric images using out-of-core technology, and builds in a hardware-accelerated rendering engine for 3D images and volumes. Mathematica 9 also adds feature tracking, face detection, image enhancements, and other highly optimized algorithms to perform comprehensive image analysis.
Use integrated analog and digital signal processing Filter and analyze sound, images, and multidimensional data with Mathematica 9's signal processing capabilities. Instantly design and deploy interactive filters and simulate them with Wolfram SystemModeler.
Visualize with new customizable gauges and built-in legends Mathematica 9 adds a complete set of customizable interactive gauges for dashboards and reports, with built-in support for units. Systemwide support for automatic legends for plots and charts means legends with any style or layout can be added to arbitrary content.
I've updated the page of data analysis tools
Wizard Pro 1.1.1
Wizard Pro has been updated this release fixes a critical bug that prevented saved multivariate models from opening on Mountain Lion. Wizard Pro is $199.99 for Mac OS X 10.6 through 10.8 and is only available in the Mac App Store. Wizard Pro is a multivariate statistics program for data analysis and exploration. The software keeps all work (tables, results, predictions) in a single document with an iTunes-like navigator and provides "interactive interfaces" for querying data. It includes basic statistics tests, regression models and results, stacking and joining of tables, indicator variables with custom logic, and more.
There is a page of data analysis tools here.
FiercePharma are obviously on a recruitment drive, I have to confess I'm already a subscriber. Makes an interesting read over the early morning cup of coffee.
Anyway a chance to win an iPad mini….
Applescript Pages
I did a little housekeeping on the Applescript pages, many thanks to those readers who reported bad links etc. it is much appreciated.
MOE 2012.10 released
Integrated Protein Engineering Applications
- Residue scanning to identify critical residues for affinity
- Search for optimal mutations to modulate thermostability
- Predict hydrophobic and electrostatic hot spots with the protein Patch Analyzer
Domain Motif Searching
- Compare protein domains based on secondary structure elements
- Search proteins for secondary structure sub-geometries
- Identify similarities independent of sequence
Amber12:EHT: New Force Field for Biopolymers and Small Molecules
- Amber12 parameters for proteins and nucleic acids
- Extended Hückel Theory parameterization of small molecules
- More precise treatment of resonance and substituent effects
Reaction-based Library Enumeration and Screening
- New reaction engine combined with library enumeration or sampling
- Sketch reactions or core/R-group libraries
- Screen products with 2D or 3D filters (educts & products)
Usability Enhancements
- Docked System Manager with control over surfaces
- Undo, redo, keyboard shortcuts, configurable mouse, drag & drop, etc.
- 2D sketcher integration with MOE Window
MacVector 12.7 is released
MacVector 12.7 is now available for download for all active users. Be sure to check out the new unique Cloning Clipboard window that simplifies creating new constructs
There is a new window available called the Cloning Clipboard that maintains a history of the DNA fragments created each time you use the Digest function. For example, if you select two restriction enzymes in a Map tab, then click on the Digest button, the fragment between the sites gets placed on the Cloning Clipboard. You can then join fragments together directly on the Cloning Clipboard by clicking on one end of a fragment and dragging to a different end
Marvin for JavaScript released
They are looking for input to prioritise future developments.
There are more chemical editors here.
Addded TOPCAT to data analysis tools
I've added TOPCAT to the list of data analysis tools.
TOPCAT is an interactive graphical viewer and editor for tabular data. Its aim is to provide most of the facilities that astronomers need for analysis and manipulation of source catalogues and other tables, though it can be used for non-astronomical data as well. It understands a number of different astronomically important formats (including FITS and VOTable) and more formats can be added. It offers a variety of ways to view and analyse tables, including a browser for the cell data themselves, viewers for information about table and column metadata, and facilities for 1-, 2-, 3- and higher-dimensional visualisation, calculating statistics and joining tables using flexible matching algorithms
I also noticed that Venuz has been updated
Veusz is a GUI scientific plotting and graphing package written in Python. It is designed to produce publication-ready Postscript or PDF output. SVG, EMF and bitmap export formats are also supported. The program runs under Unix/Linux, Windows or Mac OS X, and binaries are provided. Data can be read from text, CSV or FITS files, and data can be manipulated or examined from within the application
BioGPS free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.
Now added to the mobile science page.
Deprecation of ChemWriter Structure Paste Via Java Plugin
Serious problems with the security of the java browser plugin, together with a series of ongoing (and unresolved) stability issues mean that this developer is looking elsewhere.
Given the nature of the newly-disclosed Java Plugin security exploits and ongoing stability issues, ChemWriter's clipboard paste functionality will likely be removed altogether in a future release. Those currently using this feature are encouraged to find an alternative.
Added MathMagic
PublishPlot has been updated
PublishPlot has been updated and is now available from the Mac App store, it is a very handy tool for creating publication quality plots from any text based table of data.
PublishPlot is scriptable using either Applescript or Python.
New in version 1.1 is a tool bar to display x,y location when hovering over a plot, new fitting options and the ability to apply mathematical transforms to any two curves. There are also new export functions and bug fixes.
PublishPlot is included on the page of data analysis tools
Cheminformatics tools
A great collection of freeware tools provided by Michel Petitjean
- ARMS: Spatial Alignment with the RMS (Root Mean Square) method. (fixed pairwise correspondence)
- ASV: Analytical calculation of van der Waals surfaces and volumes. (or any union of spheres)
- CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. (pairwise correspondence computed)
- CYL: Minimal radius enclosing cylinder. Minimal radius circumscribed cylinder.
- DIVCF: Selects by clustering major conformations of a molecule in a set of its conformers.
- DOG: Docking Geometrically two molecules. (fixed pairwise correspondence)
- GRD: Computation of the Radius and Diameter of a molecular graph. (computes also the topological shape index)
- MCG: Optimal Partition (classification): numerical variables and non-euclidean spaces. The number of classes is computed.
- POP: Optimal Partition (classification): categorical variables. The number of classes is computed.
- POSE: Computes the RMSD between two ligand poses. No rotation translation is performed.
- QCM: Quantitative Chirality Measure of a conformer (graph automorphisms enumeration included)
- RADI: Computation of the Radius and Diameter of a spatial set. (computes also various other geometrical parameters)
Molegro Virtual Docker
CLC bio is pleased to announce a new release of Molegro Virtual Docker , an integrated platform for computational drug design available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality protein-ligand docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity.
New features in version 5.5:
A new 'Energy Maps' tool provides volumetric visualization of protein force fields. This makes it possible to understand why a compound interacts with a given receptor, and may provide insights on how to improve the binding.
We also added a new execution mode in the Docking Wizard: 'Run Docking in Multiple Processes'. This makes it possible to run medium sized jobs on a local machine, while utilizing multiple CPU cores and even multiple GPU graphics cards. For large jobs on multiple machines, Molegro Virtual Grid should still be used.
The ray-tracer has been improved to more closely match the live 3D view output. This makes it possible to create high resolution renderings of the 3D view.
MagicPlot Viewer
Sometimes you just need to have a quick look at a data file and Magic Plot Viewer offers the means to do this.
- Supports text files with different structure
- Auto detection of column delimiter and decimal separator
- Multiple columns for X and Y can be set
- All MagicPlot data navigation tools (zoom, hand, scrolling...)
- Equal scale for all thumbnails can be set
- Shows data point coordinates in status bar
- Quick export and printing of plots
- Additional support of image files (PNG, GIF, JPEG, BMP)
- Fullscreen mode
Added to the data analysis tools page
EventScripts is a simple application for triggering AppleScripts or shell scripts whenever certain events occur.
The listing of events a quite comprehensive and includes such things as Volumes mounted or unmounted, computer wakes, screenshot taken application launched etc.
Now added to the Applescript Resources Page.
UK Many-Core developer conference 2012 (UKMAC 2012)
Based on the weblogs there appears to be significant interest in GPU accelerated scientific applications so I thought I'd highlight this meeting that was mentioned to me.
UK Many-Core developer conference 2012 (UKMAC 2012)
Registration now open Only a limited number of spaces are available, so please register early (£70 for the conference only, £99.50 including the conference dinner). The UK Many-Core developer conference 2012 (UKMAC 2012) conference follows on from the UK GPU developer conference and is now in its fourth year. Previous conferences have been held at Oxford, Cambridge and Imperial College.
Papers is now officially part of Springer Science+Business media
Papers has rapidly become the application that in many ways has set the standard for reference management, winning Apple design awards for the iTunes like interface for organising your scientific references. Papers radically improved the way researchers handle their scientific literature by centralising search, downloads and organising references and documents in one tool, functioning as a personal library for research. The literature can be cited in the word processing software of choice, and can be shared with colleagues.The small team at Mekentosj rapidly gained recognition for their carefully thought out design, and as they expanded into Windows and iOS versions I guess it was clear that the team was becoming stretched, with difficult choices having to be made as to which new features could be implemented in the next release.
It seems an opportunity arose for the team to get additional support and resources from Springer and the acquisition of Mekentosj was the logical step.
The fit was a natural one, and we believe that by becoming part of Springer we will be able to offer our users so much more: we can take Papers to the next level, but much faster than on our own. Backed by the second largest scientific publisher we will be able to add features quicker, react faster, provide better support, and open up a realm of new possibilities.
For those that might be worried about the future of Papers.
The Mekentosj team will remain in charge of Papers, and continue to develop Papers for each of the platforms we currently support: Mac, PC, and iOS. We will continue to bring you updates, new features, and support. All with the same dedication and excitement you are used to getting from us
What is going to happen to the other Mekentosj apps like 4Peaks, EnzymeX, etc?
The Mekentosj molecular biology apps like 4Peaks, EnzymeX, iRNAi, LabAssistant, etc. will not become part of Springer and have moved to a new home. They will also remain free. Unfortunately, as has been the case for a while, Papers takes up all our time so we can't promise any updates soon.
There are press releases here and here and a Q&A here.
There is a listing of reference management applications for Mac here.
A review of ChemDoodle 5
I've just completed a review of ChemDoodle 5, this is a very good upgrade that focuses on improving workflow, but also adds several really useful new features.
There is a collection of software reviews here.
Xcode updated
With the release of the iPad mini Xcode has been updated to version 4.5.2 this update includes:-
Support for iPad mini and iPad with Retina display (4th generation).
Additional bug fixes and stability improvements.
Xcode 4.5 includes
- SDKs for OS X 10.8 Mountain Lion and iOS 6.
- Auto Layout now supported on both OS X and iOS.
- New localization workflow can share a single base .xib or .storyboard file for multiple locales.
- OpenGL debugger for iOS analyzes performance and suggests improvements.
- Debugger watchpoints can be set when running on a connected iOS device.
- Objective-C @synthesize command is generated by default when using properties.
- Objective-C adds literal syntax for numbers, arrays, dictionaries, and expressions.
- Xcode 4.5 runs on both OS X Lion and OS X Mountain Lion.
- Enhanced for the MacBook Pro with Retina display.
Calm before the storm?
The latest Marketshare data from Net applications shows little change from last month but with the announcements from Apple, Google and Microsoft this month it will be interesting to see what the impact is next month and the run up to Christmas.
One small milestone was reached, mobile browsing now accounts for more than 10% share. With the release of new devices including the iPad mini expect that to increase.
OpenEye Toolkits have been released
OpenEye is pleased to announce that the OpenEye Toolkits v2012.Oct have been released. This release includes the C++, Python, and .NET versions of the Toolkits
C++ examples build system changed to CMake for all supported platforms: Linux, Windows, and OSX.
This is a new release of the OpenEye Toolkits with versions of the following libraries:
OEChem TK:1.9.0
OEDepict TK:2.0.4
OEDocking TK:1.1.3
Grapheme TK:1.0.4
GraphSim TK:2.0.3
Grid TK:1.4.1
Lexichem TK:2.2.0
MolProp TK:2.1.4
Omega TK:2.5.0
Quacpac TK:1.6.0
Shape TK:1.8.3
Spicoli TK:1.1.3
Szybki TK:1.7.2
Zap TK:2.1.4
Details of the changes to the individual libraries are here
GPU accelerated applications in science
Last week I highlighted a couple of GPU accelerated applications and based on the number of views of the page I thought it might be worth looking to see how many GPU accelerated science applications are available.
It should be noted from the start that there are two main programming frameworks for writing programs that can execute on the GPU. OpenCL originally developed by Apple is an open-source initiative supported by a wide variety of graphics card vendors. The other major implementation is CUDA developed by Nvidia and is specific for Nvidia graphics units. Whilst it is true that for several years CUDA gave higher performance recent developments with OpenCL have probably closed the gap. "A Comprehensive Performance Comparison of CUDA and OpenCL" DOI.
I've compiled a listing of GPU-accelerated science applications here.
FileMaker Pro Update
I see FileMaker Pro has been updated to 12.0v3. For my point of view it is nice they have sorted out the issues with plugins, full details are here http://help.filemaker.com/app/answers/detail/a_id/11239.
Download from here http://www.filemaker.com/support/downloads/
More GPU accelerated applications
After posting about Lumo which accelerates the visualization of molecular orbitals from electronic structure calculations by harnessing the power of the gGPU, I received the following email which describes more GPU accelerated applications.
New Molecular Dynamics Benchmark Reports Oct 2012 are now available to compare CPU vs GPU & NVIDIAs New Kepler GPU Performance.
These reports are intended to assist computational chemistry researchers and IT managers to discover acceleration achieved by running MD applications on GPU based computing solutions.
Download Benchmark Reports - www.nvidia.com/GPUTestDrive
AMBER, GROMACS, LAMMPS, NAMD reports provide: a. Benchmark data on latest GPU architectures b. Hardware recommendations
Also, if you are looking to try GPUs: Sign up for a FREE GPU Test Drive on a remote cluster with AMBER, GROMACS, LAMMPS and NAMD preinstalled - www.nvidia.com/GPUTestDrive
iBooks update
iBooks Author has been updated. This release brings creation of portrait-only books, embedding of custom fonts into books, a new Scrolling Sidebar and Pop-Over widgets, and also support for mathematical expressions with new native equation editing using both LaTeX and MathML notation, which could be very useful for creating science text books. iBooks Author is free for Mac OS X 10.7.4 and up and is only available in the Mac App Store.
Lumo:- Molecular Orbital Visualisation
I've recently noticed an increasing interest in harnessing the computational power of the graphics card to accelerate scientfic calculations.
The latest application is Lumo which accelerates the visualization of molecular orbitals from electronic structure calculations by harnessing the power of the graphics processing unit in modern macs. Lumo currently reads formatted checkpoint calculations from Gaussian03/09 calculations and there is preliminary support for Orca output files. Lumo was designed to speed up the slow part of looking at molecular orbitals and making molecular orbital diagrams. Lumo eliminates several steps along the process by reading in the output of programs like Gaussian, quickly visualizing the orbitals, and creating pictures of the essential orbitals in seconds.
Lumo requires Mac OS 10.6 or higher, 64-bit processor, and an OpenCL capable compute device. Lumo is routinely run on MacBook Pros and MacBook Airs. For analysis of larger systems, it is recommended to have at least 4GB of system RAM.
There is a movie of Lumo in action on the website
Reference Managers Update
I've just noticed that a couple of the reference management applications have been updated.
Bookends is now up to version 11.3.3 with a number of bug fixes and new features including, Web of Science searches restored, autofill fields from internet, when tying to find a pdf online, if Bookends can't resolve the ip address it will skip to the next selected reference rather than showing an error dialog. There have also been some text formatting improvements.
DevonThink The maintenance release facilitates scanning documents with multiple pages using the new scanning feature of DEVONthink, which is also available in the Personal and Pro editions, and adds support for OS X 10.8's Calendar and Reminders applications to DEVONthink Pro and up. Scanning to PDF or TIFF reveals a convenient "Combine into single document" option which, when checked, directly collects all scanned pages into a new document
Papers2 Recent papers search for Authors and Periodicals,Auto-complete of authors and sources in the inspector,Editing of multiple papers at once and duplicate merging of papers,Merge and split any duplicate or incorrectly merged sources,Displaying and navigation of notes and highlights in the inspector,Addition of tools to allow page rotation and hiding a PDF coverpage,Creating of collection hierarchies upon import of folders,Return of column mode for search results in the search section,Support for inserting footnotes in Microsoft Word,Improved Papers for iOS syncing.
Readcube A collapsible left-side panel: After many requests, we've finally added a button to hide the side panel, giving you extra screen real estate for reading your articles. A few new options in preferences including an option to disable the ReadCube helper app and an option to alphabetize your lists. And the ability to send articles users find with their browser straight to ReadCube.
Zotero 220.127.116.11 was released for Zotero Standalone for Mac OS X only.
Also Sente is beta testing a new synchronisation feature between desktop and iPad.
Mendeley 1.7 has been released as a preview. Probably the most important feature is the Mac Word plugin has been updated for Word 2011 on Mac. The updated plugin has a more obvious UI for inserting citations and bibliographies. It is also much faster when refreshing medium to large bibliographies.
There is a comprehensive list of reference management apps for the Mac here.
Added pycifrw to spectroscopy page
PyCIFRW provides support for reading and writing CIF (Crystallographic Information Framework) files using Python. PyCIFRW is written entirely in Python. While this makes parsing of large CIF files rather slow, it will run wherever Python runs.
Now added to the spectroscopy page
AppleScriptObjC Explored 4th edition
The fourth edition of AppleScriptObjC Explored, the indispensable reference to AppleScriptObjC, is now available, this guide written by Shane Stanley is absolutely essential for anyone wanting to access the Cocoa frameworks from Applescript.
Since the release of the third edition there have been significant changes to Xcode, and subsequently how applications are developed. Unfortunately, but inevitably, things have become a bit more complicated.
The new edition covers the changes that have been introduced in Xcode 4.4 and later, as well as in OS X 10.8, plus other new material and projects.
Changes include new projects covering drag-and-drop in tables and making an application scriptable, plus an expanded Xcode section with a subsection on mastering build settings. There are also several new chapters in the Reference section. Code for more than 25 projects is included.
The price is $29.95 and there are upgrade options for previous purchasers.
A really great book I've added to the AppleScript resources page.
Marvin Updated
Marvin from ChemAxon has been updated to version 5.11
New features and improvements
- Image I/O
- Recently added rendering options are now available to be set from MolPrinter API (Absolute label visibility, Peptide display type, R-group visibility, Any bond style, Lone pair rendering style, Charge rendering style). Documentation
- MSketch GUI
- A new "imageImportServiceURL=[URL]" program argument was added to the MarvinSketch application.
- MSketch applet
- A new "imageImportServiceURL" was added as an applet parameter.
- Graphical object handling
- When an MMidPoint object was set as an end point for an MPolyLine, getting the MMidPoint location caused a StackOverFlowError.
- Import/Export
- Document to Structure (d2s)
- Names broken over two lines with a hyphen (-) are now recognized.
- Names followed by a superscript text, for instance, a reference or footnote number (e.g., "aspirin11") are now recognized.
- Name to Structure (n2s)
- In some cases, such as "4-methylthiophenylmethyl", there is an ambiguity whether "thiophenyl" refers to a compound derived from thiophene or thiophenol. Name to Structure now gives priority to the thiophenol related compound interpretation; though, "thiophenyl" by itself will still be supported as thiophene derivatives.
- Painting
- If R-group visibility was turned off and any of the bonds had label(s) to paint, an ArrayIndexOutOfBounds exception was thrown.
- Image I/O
- Display parameters of charge, lone pair, peptide could not be set for molexporter. The default values were charge "in a circle", lone pair "as line", peptide "three letter format". Image copy also used these values.
- Import/Export
- Aliphatic query properties of atoms with query string were not read from MDL formats.
- After importing Extended MOL files that contain superatom S-groups the orientation of S-groups could be changed.
- Atom containing both aliphatic and unsaturated query properties were exported incorrectly to MDL formats.
- SDF import returned structure with incorrect S-group embedding.
- SMILES T* option did not export all SDF fields, but only those which appeared in the first molecule.
- Molecule Representation
- S-groups
- Two superatom S-groups being each others' parents caused infinite loop. In these cases, now java.lang.IllegalStateException is thrown.
- Valence Check
- Phosphorous atom in hexafluorophosphate was not accepted by Valence Check. Forum topic, Forum topic
- Stereochemistry
- Cloning of BicyclostereoDescriptor in RxnMolecules threw java.lang.ArrayIndexOutOfBoundException.
- Clean 2D
- Terminal methyl-group in phosphate-ester was cleaned incorrectly.
- Clean2D could not handle condensed adamantane derivatives. Forum topic
- Calculations
- Other (HBDA, Huckel Analysis, ...)
- The --pH command line option did not work in hydrogen bond acceptor-donor calculation.
- Structure Checker
- If fixer action was not defined, default fixer was not applied in structurechecker command line tool.
A collection of mobile science apps
Labguru for iPad is a companion app to the Labguru web application. The app enables Labguru users to conduct and update their experiments from the lab bench. The app makes it possible to run and track multiple experiments, record notes and results while performing an experiment, and to sync the data with the Labguru web application.
My Lab, your iPAD is now a lab notebook, protocols organizer, lab inventory and much more. My lab was conceptualized and developed under the scientific expertise of Mahendra Rao MD PhD and Hue Medscience. My lab is a customizable app that lets you keep your lab data private and enables sharing of the content you want enabling full control of your files. My Lab also includes direct access to Dropbox to store your files for easy access from anywhere
BioTechniques The International Journal of Life Science Methods – Now on Your Mobile Device BioTechniques provides open access to high-quality, peer-reviewed papers on laboratory techniques and protocols. Now in its 52nd volume, BioTechniques has over 80,000 print subscribers worldwide.
Oracle Oracle Business Intelligence Mobile for Apple iPad and Apple iPhone is a mobile analytics application that allows users to view, analyze and take action on Oracle Business Intelligence content.
The Journal of Cell Biology app allows immediate access to full-text articles. The original international cell biology journal, JCB now travels wherever you do. You can read full-text articles anywhere at anytime, even without a network connection. The app, designed for easy reading and browsing on any iOS device
Life Technologies Protocols App provides quick, convenient access to popular Applied Biosystems or Invitrogen product protocols. Each protocol is presented with concise step-by-step instructions, along with easy access to the complete product manual
PNAS, the official journal of the US National Academy of Sciences, is an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences. The journal is published daily online in PNAS Early Edition and weekly in print. Easily access the PNAS table of contents and full text articles directly from your mobile device.
Mol Biology Get all the latest research findings from Molecular Microbiology, including articles yet to be published in an issue. Our iPad-optimised design provides the best browsing experience possible. With a few simple clicks you can quickly and easily move between articles, images and more.
MIQE - qPCR helps you in reviewing scientific works and checking your own experiments, when qPCR is involved. Check your project's compliance to MIQE in minutes, have all required references to hand, and follow qPCR events and new
Cell Imaging HD This mobile app is designed to help you find fluorescent dyes, reagents and protocols for cell biology related fluorescence microscopy applications.
BioLegend Tools , this application provides you with important information about your mouse and human CD Molecules, Cytokines and Chemokines. It also includes BioLegend pathway posters, an antibody usage calculator, and a lab timer.
There is an extensive collection of apps for science on the mobile science page.
15 mobile apps in Life Sciences
Last October when FierceBiotech IT rounded up the top apps in life sciences, the industry was just coming to terms with the potential of mobile devices. Now life science software providers are waking up to the fact that mobile is more than an opportunity, it is a necessity. It is increasingly hard to envisage a successful software company that lacks a mobile strategy.
Read more: 15 mobile apps in Life Sciences - 2012 - FierceBiotechIT
There is an extensive collection of apps for science on the mobile science page.
MolSoft updates
MolSoft have also released a new version of the free desktop molecular viewer ICM-Browser and the ActiveICM plugin for viewing fully interactive molecules in web browsers.
TB Mobile app
The TB Mobile app presents over 700 small molecules structures screened versus Mtb and their targets. This data is only available in Collaborative Drug Discovery, Inc. (CDD). To which has been added published data on target, essentiality, links to literature (PubMed), genes (tbdb.org), pathways (TBCyc, which provides a pathway-based visualization of the entire cellular biochemical network) and human homolog information. The structures, names and miscellaneous data for these drugs are stored within the app, and made available for browsing. The drugs can be filtered, searched by name or structure, and viewed in 2D. There are several functions for making use of the data. The app therefore merges cheminformatics and bioinformatics information.
Now added to the mobile science page.
AppleScript Library
I've just come across this fantastic AppleScript Library a collection of invaluable scripts and routines to make up for missing standard functionality. Currently there are libraries available for string manipulation, a files and folders library, iWork, a URL library and a number library.
A really great resource I've added to the AppleScript resources page.
ChemDoodle 5 is now available
ChemDoodle 5 includes significant new features and improvements, including:
- Round-trip editing on Windows via OLE. (Round-trip editing is already provided on Mac OS X)
- Round-trip editing on Linux!
- A revamped shape system for much easier and more precise manipulation of shapes, especially in crowded figures. Also a new quick colors button to now quickly change colours of objects.
- Bezier curves for complex shapes and mechanisms.
- Fragmentation tools.
- More functions for handling chemical data on the clipboard.
- File chooser previews.
- 77 new glassware templates!
- Hundreds of other features and improvements.
Upgrade pricing options are available.
Open Eventory has been updated
Open Eventory has been updated
2012-09-28: - updated Ketcher molecular structure editor, now also supports reaction equations - added DrugBank for structure-to-CAS and substance data search - fixed a bug that prevented merging of literature datasets - advert in navigation panel no longer covers functionality on smaller screens - added SDF export (experimental) - import of existing substance data is now possible (if you have data not within the online catalogs)
Open enventory is an integrated laboratory journal with a literature database and inventory program.
Absoft Fortran compiler update
News for all you Fortran programmers out there.
Absoft Corporation announced immediate availability of new Pro Fortran 2013 for Mac OS
Primary new features of Absoft Pro Fortran 2013 include: - Compatible with Mountain Lion and X code command line toolset - New AVX optimizations improve application speed up to 10% - Many additional F2008 extension supported - Upgraded ATools/GUI environment simplifies application development - New AWE (Absoft Window Environment) spreadsheet feature allows graphical display of 2D arrays - Absoft HPC Scientific and Engineering numerical library included at no additional charge - Compatible with IMSL v7.0, & 6.0 and NAG 23 numerical libraries - Additional product details http://www.absoft.com/AbsoftMacIntelCompiler.htm
Pricing: $299 academic, $699 commercial. IMSL 32/64-bit bundle an available option
iNMR Updated
iNMR has been updated to version 5.2. This version supports Mac OS X 10.6. 10.7 and 10.8.
I've also updated the spectroscopy page.
A Quick Review of ChemBioDraw 13
This version of ChemBioDraw released in August 2012 is the first release since Cambridgesoft became part of Perkin-Elmer and there are a significant number of changes. This is the first version to be released since the introduction of Mac OS X 10.7 and 10.8 and both are now officially supported. In addition the ChemDraw plugin is now supported in 64 bit mode and Microsoft Office 2011 is supported. I've written a brief review here.
Viewing Docking results in Vortex using Astex Viewer
I recently wrote a review of ForgeV10 from Cresset in which I actually imported the results into Vortex to do the analysis. There were however two issues with doing this, firstly interpretation of the 3D structures is sometimes difficult, this can be resolved by creating a 2D rendering of the structure. The other issue is trying to interpret the docking pose whilst looking at the analysis of the results in say a Vortex scatter plot.
I've been working with Mike Hartshorn and the people at Dotmatics who have incorporated OpenAstexViewer (a 3D molecule viewer) into the application you can read the full article here..
Chocolat has been updated
Chocolat is a text editor for Mac OS X, that combines native Cocoa with powerful text editing tools.
1.3.2 Feature – Image previews Feature – Hide line numbers Feature – Drag to reorder active files Feature – Subword movement using alt-ctrl-left/right (or ctrl-left/right you have that system shortcut disabled in System Preferences) Bug – Code completion moves above current line if clipped by bottom of screen Bug – Allow tabbing into document from find bar replace field
Operating systems market share
The latest monthly market share data is available from Net Applications and Mac OS X continues to show a steady rise now up to 7.16% (a rise of 0.3%). Adoption of Mac OS X 10.8 is now over 25% of the Mac OS X version share and steadily increasing.
In the mobile/tablet space iOS continues to dominate (63.48%) this represents just under 10% of the online presence with desktop/laptop still at 90%.
Canonical SMILES
I'm a great fan of SMILES notation (simplified molecular-input line-entry system) as a compact means of storing chemical structures, and whilst there are many tools for creating SMILES strings they often give different (but acceptable) results. Various algorithms for generating Canonical SMILES have been developed, including those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT, Chemical Computing Group, MolSoft LLC, all use proprietary code. In the latest issue of Journal of Cheminformatics Noel O'Boyle describes the development of Universal SMILES and Inchified SMILES as implemented in Open Babel an open source cheminformatics toolkit. DOI
Wizard Pro
I've just added Wizard Pro to the page of data analysis tools.
Wizard Pro can Import spreadsheets and CSV, plus files from SPSS: .sav, .por, and .sps files, Stata: .dta and .dct files, R: .RData files. EExport data as CSV and JSON, plus files for SPSS: .sav binary files, Stata: .dta binary filesR: .RData binary files. It can generate regression commands suitable for verifying results in SPSS, Stata, and R, It is fully multi-core — regressions run instantly and supports millions of rows and thousands of columns — no hard limits.
Xcode 4.5 available from AppStore
Xcode 4.5, was released on 19th September and is available free from the Mac App Store. Xcode is Apple's development environment. According to the release notes, Version 4.5 includes:
SDKs for OS X 10.8 Mountain Lion and iOS 6.
Auto Layout now supported on both OS X and iOS.
New localization workflow can share a single base .xib or .storyboard file for multiple locales.
OpenGL debugger for iOS analyzes performance and suggests improvements.
Debugger watchpoints can be set when running on a connected iOS device.
Objective-C @synthesize command is generated by default when using properties.
Objective-C adds literal syntax for numbers, arrays, dictionaries, and expressions.
Xcode 4.5 runs on both OS X Lion and OS X Mountain Lion.
Enhanced for the MacBook Pro with Retina display.
Additional bug fixes and stability improvements.
SPRESImobile 2.0 now available: full reaction searching SPRESImobile 2.0 now available: full reaction searching
The SPRESImobile app provides access to InfoChem's SPRESI database. It runs on Apple iOS devices (iPhones, iPods and iPads) and is free on the iTunes AppStore. The latest version extends the search capabilities to include searching by reaction: various types of exact, substructure and similarity searches can be performed. Furthermore, it is now possible for existing customers of SPRESI to provide their user credentials within the app, which unlocks the entirety of the database content, rather than the default curated ChemReact subset that is made available to all.
More apps are on the mobile science page
SparkV10 released by Cresset
Cresset have announced the formal release of sparkV10 the replacement for FieldStere.
- Updated molecular mechanics force field that uses a single analogue nitrogen atom and updates the field patterns for many functional groups including aromatic halides
- Added capability to read protein excluded volumes from pdb files
- Added new cluster algorithms for clustering of results
- Added option to edit reference molecules in the molecular editor
- Added capability to manage columns in the results table
- New optional module for scoring results using StarDrop models, this does not require access to a StarDrop server, simply place StarDrop model files in a directory and they automatically get used if you have the right license. The standard ADMET models that Optibrium have created are supplied but it works equally well with any models created by StarDrop.
- Added fragment import option in database generator
- Added capability to rescore all results against a 3D QSAR model using Forge or Torch
- Added capability to search databases for a particular fragment or substructure
- Added option to delete entire clusters from results
- Added depth cue to 3D window
- Added a GUI interface for selecting a portion of a molecule and writing command line arguments
- Cleaner GUI with improved buttons
Users should note:-
SparkV10 completely replaces Cresset's previous "FieldStere" application. If FieldStere is currently installed then it is recommended to uninstall the binary to avoid confusion over which application should be used to open FieldStere project files
Vida Updated by OpenEye
VIDA v4.2.0 has been released. This is an important update that offers many significant new features, is built on the most recent OpenEye Toolkits, and adds support for the Ubuntu platform. Among these new features is the ability to perform "telemodeling" by sharing interactive VIDA sessions over a network between multiple users at different locations. In addition, vast improvements have been made to the rendering engine to provide more vivid and realistic 3D graphics. The user interface has also been further streamlined for a more intuitive user experience and the new ability to export files as PDF documents enhances the off-line user experience as well. VIDA is available for download now. Existing licenses will continue to work. If a new license is needed, please contact your account manager or email email@example.com to request one.
Scripting Vortex 10
I've just added a new tutorial on scripting Vortex, starting to add user interaction.
Added Motofit to alphabetical listing
Motofit co-refines Neutron and X-ray reflectometry data, using the Abeles matrix / Parratt recursion and least squares fitting (Genetic algorithm or Levenberg Marquardt). It works in the IGOR Pro environment (TM Wavemetrics).
AFITT v2.2.0 has been released
OpenEye have announced that AFITT v2.2.0 has been released. This is the first release of the AFITT GUI that fully supports fragment and cocktail fitting to crystallographic data. In addition, poses fit to density can be re-ranked based on various docking scores (PLP, Chemscore) as well as the Real Space Correlation Coefficient (RSCC). This is particularly useful when analyzing highly symmetric ligands that can be fit to density equally well with multiple poses.
AFITT is an application designed to help crystallographers fit ligands to observed data. Ligands are placed in density and optimized in real-space limiting molecular strain thereby producing excellent matches to density while preserving known chemistry
Avogadro Updated
Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Windows, Linux and Mac OS X. The source code source is available under the GNU GPLv2.
This release highlights a great deal of new features, including a built-in crystal library, crystallographic editing, building slabs / surfaces with arbitrary Miller planes, support for Abinit (and soon Quantum Espresso), searching for IUPAC names in PubChem, custom atomic colors and radii, and much more.
See the Release Notes: http://avogadro.openmolecules.net/wiki/Avogadro_1.1.0
What does Avogadro do?
- An intuitive "builder," including common fragments, downloading directly from PDB or PubChem, and peptide sequences
- Innovative "auto-optimize" tool which allows you to continue to build and modify, during molecular mechanics optimization
- Interfaces to many common computational packages
- Designed to help both educational users and advanced research
- Plugins that allow Avogadro to be extended and customized
- Well defined public API, library and Python bindings for development
- Embedded Python interpreter
- Translations available in 19+ languages
For more information: http://avogadro.openmolecules.net/wiki/
Vortex script exchange
Vortex is an advanced data analysis package that understands chemistry, the capabilities of Vortex can be extended by the use of scripts. I've now created Vortex script exchange that users can use to download or share scripts.
There are also a series of scripting tutorials here to provide a starting point for creating new scripts.
Hopefully these scripts will be valuable to you.
Matlab R2012b released
A new version of Matlab has been released.
MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java™.
Markdown Editors
Just added Mou to the list of Markdown Editors, Mou offers syntax highlighting, live preview, sync scroll, fullscreen mode, auto save, powerful actions to allow rapid code inclusion, auto pair, custom themes (for those who like to write with green letters on a back background) and CSS, HTML and PDF export, enhanced CJK support. It also supports a variety of Asian languages, and auto-completion but I think only for English.
Scripting Vortex 9
I recently wrote a review of ForgeV10 in which I imported the results into Vortex for analysis. This works fine the only issue being the resulting structures are 3D which makes interpretation of the structure sometimes difficult to discern, this script uses OpenBabel to create SMILES which can be rendered as 2D images.
Review of ForgeV10
This is a review of ForgeV10 the latest offering from Cresset, whilst a new product those familiar with FieldAlign and FieldTemplater will recognise much of the functionality. ForgeV10 allows the scientist to use Cresset's proprietary electrostatic and physicochemical fields to align, score and compare diverse molecules. It allows the user to build field based pharmacophores to understand structure activity and then use the template to undertake a virtual screen to identify novel scaffolds.
There is a compilation of software reviews here.
Equalizer 1.4 released
Equalizer is the standard framework to create and deploy parallel, scalable 3D applications. This modular release includes Collage 0.6, a cross-platform C++ library for building heterogenous, distributed applications, GPU-SD 1.4, a C++ library and daemon for the discovery and announcement of graphics processing units using zeroconf networking and Lunchbox 1.4, a C++ library for multi-threaded programming. All software packages are available for free for commercial and non-commercial use under the LGPL open source license.
Equalizer 1.4 is a feature release extending the 1.0 API, introducing major new features, most notably asynchronous readbacks, region of interest and thread affinity for increased performance during scalable rendering. It culminates over seven years of development and decades of experience into a feature-rich, high-performance and mature parallel rendering framework and related high-performance C++ libraries.
Equalizer enables software developers to easily build interactive and scalable visualization applications, which optimally combine multiple graphics cards, processors and computers to scale the rendering performance, visual quality and display size.
ChemDoodle mobile updated
ChemDoodle mobile has just been updated
ChemDoodle Mobile is a calculator for drawn organic structures. There are four main windows: Draw, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The Calculate page calculates properties and the Spectra page simulates NMR spectra. All spectra are interactive. The Help page contains a detailed help guide.
Calculations 1. Molecular Formula 2. Molecular Mass 3. Monoisotopic Mass 4. Degree of Unsaturation 5. Hydrogen Bond Acceptors 6. Hydrogen Bond Donors 7. Average Molecular Polarizability 8. Molar Refractivity 9. Polar Surface Area 10. logP Spectra 1. Mass Parent Peak (Isotopic Distribution) 2. 1H NMR 3. 13C NMR
There are more apps on the mobile science page
iOS and OS X Graphing Library
iOS and OS X Graphing Library Free For Development
VVI today announced the availability of it's graphing library for iPhone, iPad, iPod touch and Macs. Version 10.8.3 of the graphing libraries and frameworks, aka Vvidget Code, brings the following achievements:
- Supports deployment to OS X versions 10.6 to 10.8 (Macs) and iOS versions 4.3 to 5.1 (iPhone, iPad and iPod Touch).
- Supports development on OS X versions 10.6 to 10.8 and Xcode 3.2 to 4.4.1.
- Uses native API on deployment platforms for the fastest and most robust possible implementation. That is, Cocoa Touch for the iPhone, iPad and iPod Touch and Cocoa for the Mac.
- Use for development is free.
- Eleven Vvidget-based applications available from VVI on the iTunes App Store for iPhone, iPad and iPod Touch and on the Mac App Store demonstrate Vvidget Code in actual situations.
- Applications based upon Vvidget Code are free-standing and require no additional installs. Vvidget Code itself can be installed using package installers or shared using free-standing Xcode projects.
- Download and install instructions are at: Download And Install Vvidget Code
Please email firstname.lastname@example.com for additional information.
Added Screening Assistant to alphabetical listing
Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering.
A recent publication describes it in detail. Mining Chemical Libraries with "Screening Assistant 2, Vincent Le Guilloux, Alban Arrault, Lionel Colliandre, Stéphane Bourg, Philippe Vayer and Luc Morin-Allory. DOI
Latest Market Share Data
Net Applications have published the August data for Net market share. For the first time since Net Applications began collecting data the Mac share has topped 7% (7.13%), looking at the different versions of the Mac operating system 10.7 has 34%, 10.6 has 33% and 10.8 (Mountain Lion) has 20% after being available for barely a month.
In the mobile arena there has been little change over the last three months with iOS accounting for 66% and Android 21%, JavaME, Blackberry and Symbian continue to slowly decline.
Java security update
Oracle Security Alert for CVE-2012-4681
Description This Security Alert addresses security issues CVE-2012-4681 (US-CERT Alert TA12-240A and Vulnerability Note VU#636312) and two other vulnerabilities affecting Java running in web browsers on desktops. These vulnerabilities are not applicable to Java running on servers or standalone Java desktop applications. They also do not affect Oracle server-based software. These vulnerabilities may be remotely exploitable without authentication, i.e., they may be exploited over a network without the need for a username and password. To be successfully exploited, an unsuspecting user running an affected release in a browser will need to visit a malicious web page that leverages this vulnerability. Successful exploits can impact the availability, integrity, and confidentiality of the user's system. In addition, this Security Alert includes a security-in-depth fix in the AWT subcomponent of the Java Runtime Environment. Due to the severity of these vulnerabilities, the public disclosure of technical details and the reported exploitation of CVE-2012-4681 "in the wild," Oracle strongly recommends that customers apply the updates provided by this Security Alert as soon as possible.
Download for the update is here
I've just added PublishPlot to the page of data analysis tools.
PublishPlot Features
- Quickly convert any table of data into a plot
- Customize all features of the plot
- Easily scale the plot to any size while conserving relative sizes of plot features
- Annotate the plot with labels and arrows
- Add error bars
- Do simple data transformations including fits and spline interpolations
- Plot arbitrary functions of x
- Edit data in PublishPlot by simple plain-text editing methods
- Export a plot to a PDF file (or simply drag it to your desktop or to another application)
- Create and transform plots using AppleScripts or Python scripts
Markdown Editors
I use markdown extensively on my websites, "Markdown" is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I tend to regard BBEdit as the "gold standard" but I keep an eye out for other markdown editors.
I've previously mentioned Markdown Pro which has been recently updated, this two pane editor allows you to write your document in one pane whilst giving you an instant preview of how the document will look. Markdown Pro now lets you add custom templates to the in built selection of templates. The application was built for Mac OS X so takes advantage of many Mac OS features.
I've also heard good things about Marked it also has two panes and it will update a preview as you work (with several high-quality themes to choose from, or design your own), refreshing every time you save. It can even automatically scroll the preview to where you're currently editing in your document. With one click you can copy HTML for posting online or including in web pages, copy rich text, save a PDF or print your work. Marked includes tools for handling page breaks, titles, table of contents and much more.
I've just come across another editor LoremIpsum, this also has a realtime markdown preview and has been enhanced for Mountain Lion. It includes,, Bookmarks, Markdown smart editing, Cool light and dark themes, Comprehensive keyboard shortcuts, Word and character counters with live update, Autosave and document recovery, In-app themed HTML previews for Markdown documents with in-page anchors, Export your Markdown document to HTML, Well-designed Rich Text editor for .RTF documents.
As they say choice is good.
CWM Global Search
CWM Global Search is an Internet search tool for scientists that want to search for chemical data on the Internet - it makes a federated search over many scientific databases on the Internet.
- Search the Internet by structure
- Find structures for synonyms, CAS Numbers, names
- Submit several compound in one search - use SDFiles.
- Find biological effects of a compound
CWM Global Search presently searches more than 60 free chemical and pharma relevant databases -- containing more than 100 million pages which associate chemical structures with data.
License fee per year: 5 copies for 1000 Euro, single copy for 240 Euro The limitation of the free version is that only a subset of result links can be opened. You will always get the information how many hits a query finds in a given data source, which helps you to decide to re-execute the query using the native user interface. Supports Internet Explorer, Chrome and Firefox on Windows and Safari on MAC computers.
XQuartz Updated
A version of the X.Org X Window System that runs on OS X.
The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.
For OS X 10.6 or later (including Mountain Lion)
LabVIEW on MacOSX
This request appeared on the SciTech mailing list and I thought I'd spread the word.
Dear scitechies who are interested in programming DAQ with LabVIEW on MacOSX,
I recently successfully staged a presentation at this year's NIWeek 2012. Talking to NI representatives during the conference it became clear that NI can no longer neglect Apple's market share specially among university students. In fact NI wants to reinforce their engagement for the Mac platform and they are thinking about how to best go about. Therefore if you have projects in mind that require things which are not presently supported by LabVIEW for MacOSX you could let me know. I shall compile and communicate your ideas and opinions to the people in charge. That way you will at least be sure that your message will arrive. Please post to me directly and I will eventually reply to you and NI with a summary of the received responses. Thank you for your engagement for the cause
Urs Lauterburg email@example.com
Physics demonstrator
Physikalisches Institut
University of Bern
For more information on LabView read http://www.ni.com/mac/
VMWare Fusion 5 released
For those who have the need to use different operating systems then the release of VMWare Fusion 5 is a notable milestone. Not only does it support various flavours of Linux and Windows but now you can run OS X Mountain Lion, OS X Mountain Lion Server, OS X Lion and OS X Lion Server in virtual machines.
Avogadro: An advanced semantic chemical editor
From the latest issue of Journal of Cheminformatics
Avogadro: An advanced semantic chemical editor, visualization, and analysis platform
The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here.
Mac OSX Automation archive
The Mugginsoft application automation archive provides access to a browsable repository of automation documentation for a wide range of OS X applications. Documentation is provided for automation via AppleScript and the ScriptingBridge.
Added to the Applescript Resources page
PyMOL now on iPad
Schrodinger have just announced the release of PyMOL on the iPad. It is a free download from the App Store. With the app you can:-
- View 3D molecular structures, images, and PDFs
- Search and download data from the PDB, PubChem, Dropbox, or your own custom server.
- Intuitively interactive: rotate, pan, twist, zoom, center, and adjust clipping planes, with simple gestures
- Select atoms, residues, molecules, chains, objects, etc. – just by tapping the screen
- Easy-to-use visualization presets cover the majority of visualization needs such as bond representations and surfaces.
- Distance calculations, structure alignments, anaglyph 3D, and much more
Mountain Lion and Chemistry
I spent the weekend updating my MacBook Pro to Mountain Lion, this took much longer than I expected due to the fact that apparently my BT business hub is prevented from downloading any files greater than 2 GB. After several discussions with the BT online help they reconfigured things to allow the 4.2GB download. It seems they have had many thousands of complaints so I added my name to the list.
The download and update went very smoothly, I then installed X11. As I mentioned previously, X11 is no longer included as part of the standard distribution of the operating system. In the future this will be downloaded when needed from the XQuartz server. This happens even if you have previously installed XQuartz.
The XQuartz project is an open-source effort to develop a version of the X.org X Window System that runs on Mac OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5. It may in fact be better if users download the latest version of XQuartz when needed since they provide regular updates which are unfortunately overwritten when you install a Mac OS update.
I also needed to install the latest version of Java, you will be prompted to install the first time it is required or you can use the command line. First open a Terminal window, then type
java -version
you should get a message stating "No Java runtime present, requesting install" followed by a window prompting you to install Java SE in order to open "java", click "Install" to get the latest version.
So far I've done preliminary tests on the following applications without obvious issues.
Aabel Avogadro BBEdit ChemBioDraw 13 ChemDoodle DevonThink Pro Elemental MarvinSketch MarvinView MarvinSpace MOE (X11 enviroment) PYMOL Swiss-PdbViewer Vortex
I've just come across another site providing applescripts, Macscripz.
MacScripz are just really simple scripts. They basically function as tweaks to your system. A script can range from simply deleting a file in your OS to altering a previous setting. What most scripts on this site will do is change a setting set by Apple initially to change a core behavior on your system. For example, the tweak Cloak&Dagger forces Finder (on OS X 10.7 and up) to display files Apple hides from its users. Every script on Scripz.com is pre-screened, so don't ever worry about harming your system with any of our tweaks, we only upload quality content.
I've added it to the Applescript Resources Page.
Mjograph Updated
MjoGraph is an X-Y graph editor that runs on Mac OSX or on other platforms with Java. It is well customized for researchers, especially in the field of science, whose research work includes computer simulations and visualization of their numerical results.
There are many more data analysis tools listed here
Script Debugger 5.0.3 Released
Script Debugger 5.0.3 is a free maintenance release addressing a series of issues that came to light following the release of Script Debugger 5.0. This maintenance release makes Script Debugger fully compatible with Mountain Lion (Mac OS X 10.8) and addresses a number of stability and performance issues.
RCSB Protein Data Bank app
The RCSB Protein Data Bank (PDB) mobile app is a new application that provides fast, on-the-go access to the RCSB PDB resources. The app enables the general public, researchers and scholars to search the Protein Data Bank and visualize protein structures using either a WiFi or cellular data connection. Search the entire PDB database, view the latest protein structure entries to be released, access your MyPDB account, view the entire catalog of Molecule of the Month, airplay support for high resolution screens and more.
Now added to the mobile science page
DEVONthink updated
DEVONthink has been updated to version 2.4.
Update for Mountain Lion plus support for Notification Center and the new sharing services. Share documents with one click via iMessage, Mail, Twitter, Facebook, or Airdrop or add them to Safari's Reading List. The update also brings a completely rewritten scan feature that's available for DEVONthink Personal and Pro
There is a list of reference management apps here.
Four more mobile science apps
I've added four more apps to the mobile science page.
The Aldrich Handbook of Fine Chemicals for your iPad, Convenient alphabetical browsing of chemical substances in list or grid view Substance pages with key technical properties, chemical structures, and links to corresponding products on Sigma-Aldrich.com for additional information,Ability to search by product name, synonym, CAS number, and product number with alphabetically returned results.
Molarity a chemistry calculator tool that generates lab-ready directions describing how to prepare an acid or base solution of a specified molarity or normality from a concentrated acid or base solution. A second tab includes a general molarity function that calculates the mass of any reagent needed to prepare a given volume of solution of desired molarity. A third tab features a stock dilution function that calculates how to dilute a stock solution of any known molarity to your desired volume and molarity.
HPLC Calc Calculates conditions for transfer of an isocratic or gradient method from one HPLC column to another. Recommends flow rates for analytical columns. Allows method scaling from microbore through preparative column range based on the 2 sets of column variables (column length, column I.D., particle size) and current method conditions (flow rate, injection volume, pressure, run time, equilibration time).
CloningBench Restriction Enzyme Finder - Search by cut-site, name or buffer type, obtain technical data that you can share easily with others and order directly from your mobile device. Double Digest Finder - Find the correct buffer and concentration when digesting DNA with two restriction enzymes. Competent Cell Selection Guide - Quickly find the right competent cell for your cloning application and order easily. Search for chemically competent or electrocompetent cells, desired transformation efficiency, specialized application or packaging format that suits your needs.
MOPAC12 released
MOPAC12 A practical quantum chemistry tool for modeling biological systems and co-crystals. MOPAC2012™ brings major improvements in the prediction of intermolecular interactions and hydrogen-bonding. This significantly improves geometries and energies of proteins, crystals, co-crystals, metal clusters, inorganics and other condensed phase systems. New PM7 method significantly improves intermolecular energies, providing increased accuracy for condensed phase chemistry. PM7 can be applied to modeling enzyme reactions and predicting co-crystals.
SZMAP updated
SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding. The newly released tool GAMEPLAN, suggests ways to modify ligand chemistry based on this understanding of water structure in the immediate environment of the ligand.
- The Water Orientation VIDA Extension has been completely rewritten to be easier to use and more feature-rich, making it simple to find key waters and understand their interactions. Each water site can be labeled by its energy, van der Waals energy, and degree of order. The 3D representation shows whether a site is disordered, an acceptor, a donor, or both. Individual waters can be exported for use elsewhere. The other extensions have also been improved.
- A new command-line program called GAMEPLAN has been released. GAMEPLAN runs several quick SZMAP calculations and analyzes the results to examine how the existing ligand chemistry aligns with the pocket environment. It also produces hypotheses of ligand modifications to improve its affinity, based on the energetics of the water environment directly adjacent to the ligand.
- SZMAP output has been simplified: sections are clearly identified, the water orientation data is less obtrusive, and an updated set of grids is produced (neutral difference free energy, van der Waals, order, and mask). The Watercolor VIDA Extension now sets contour levels to emphasize significant results.
- The speed of SZMAP stabilization calculations for both grids and arbitrary coordinates has been increased. Results from an existing apo protein calculation can be re-used, speeding up calculations for a series of compounds and/or poses in a single binding site. The speed of stabilization calculations is improved by avoiding extra calculations on the isolated ligand.
- It is now easy to produce SZMAP results for just the region in the apo pocket where water has been displaced by the bound ligand, clarifying the analysis of water in the apo protein.
- The programs SZMAP and GAMEPLAN will check to make sure input files contain partial charges and explicit hydrogens to avoid wasting time on meaningless calculations when the input is incorrect.
- Protein preparation is easier because PCH (which adds partial charges to molecules and separates protein from ligand) now provides more control over the process and can work around structures that contain unsupported elements. PCH can now split out waters into a separate file.
Added Quantum Expressoto alphabetical listings
Quantum Expresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
Details of the packages is available in the documentation
New tools from COSMOLOGIC
Two brand new tools from COSMOlogic which might be of greater interest for all those working in drug design:
1) COSMOsim3D Based on an idea of Michael Thormann (Origenis) we have implemented COSMOsim3D as a very efficient method for alignment and 3D similarity using local sigma profiles, i.e. local histograms of the COSMO sigma surface on a 3D grid. By that molecules get aligned in a way that maximum similarity of the sigma surfaces is achieved. In a paper which has just got online in JCIM (see http://pubs.acs.org/doi/abs/10.1021/ci300205p) we demonstrate the extraordinary performance of this method for bioisoster search and drug activity class enrichment.
2) COSMOsar3D According to COSMO-RS theory, which is widely validated in fluid phase thermodynamics, the final grid of local sigma profiles produced at the end of a COSMOsim3D alignment of ligands should represent a complete set of descriptors for molecular interactions. Furthermore it can be shown that with these descriptors the free energy of binding of a ligand in a receptor should be a linear function of the descriptors, and thus be optimally suited for the PLS analysis usally applied in molecular field analysis. Therefore we implemented the COSMOsar3D method a new variant of the traditional comparative field analysis, know as CoMFA. And indeed, testing this idea on the Sutherland data set we could show that it outperforms the seven reported 3D-QSAR methods tested therein not only with respect to prediction accuracy, but also with respect to robustness with respect to grid position, grid size, and small misalignments of the ligands. (see http://pubs.acs.org/doi/abs/10.1021/ci30 0231t)
Everybody who likes to test these two methods on his datasets is invited to do this based on a free evaluation license. You can use the tools either stand alone, or integrated in the Open3DQSAR software (http://open3dqsar.sourceforge.net/)
Mac marketshare
The latest data from Net Applications is out and the Mac marketshare continues to rise to almost 7%, the highest figure recorded by Net Applications. Mac OS X 10.8 (Mountain Lion) contributes 0.28% and it will be interesting to see the adoption rate next month.
In the Tablet/Mobile area iOS (65.74%) and Android (20.16%) continue to dominate with JavaME (9.11%) falling below 10% for the first time, all other mobile OS are below 2%. The iPad (37.32%) is now the dominant device for web browsing with iPhone (26.66%) second.
X11 in Mountain Lion
As I mentioned previously, X11 is no longer included as part of the standard distribution of the operating system. In the future this will be downloaded when needed from the XQuartz server. This happens even if you have previously installed XQuartz.
The XQuartz project is an open-source effort to develop a version of the X.org X Window System that runs on Mac OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5. It may in fact be better if users download the latest version of XQuartz when needed since they provide regular updates which are unfortunately overwritten when you install a Mac OS update.
Absoft Pro Fortran 2012 compatibility with Mountain Lion
I known there are a number of Fortran users so I thought I'd highlight this message
The Absoft Pro Fortran 2012 for Mac OS currently shipping is compatible with Mountain Lion. Absoft Pro Fortran 2012 Mac OS customers who purchased earlier than June 2012 who want to run on Mountain Lion will need to download the Service Pack v11.5.2 which can be done at no charge from the Absoft site: http://www.absoft.com/download/downloads.html
Pro Fortran versions prior to 2012 are not compatible with Mountain Lion and will require an upgrade.
CORINA 3D structure generation
I've added CORINA to the alphabetical listing. CORINA is a fast and powerful 3D structure generator for small and medium sized, typically drug-like molecules. Its robustness, comprehensiveness, speed and performance makes CORINA a perfect application to convert large chemical datasets or databases.
YASARA Updates
YASARA has seen several updates since I last mentioned it, most recently the ability to display pi-pi and cation-pi interactions.
YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software . PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard computers. You can push and pull molecules around and work with dynamic models instead of static pictures.
iSpartan and iSpartan server
I was wondering when someone would use an iPad as the front-end to a fully featured modelling package running on a remote server, looks like Wavefunction have done a pretty impressive job with taking their sophisticated Spartan computational chemistry package from the desktop to mobile devices.
iSpartan creates molecules as familiar 2D sketches, directly converts these into 3D structures, and calculates low energy conformations. Atomic and molecular properties, NMR and infrared spectra, molecular orbitals and electrostatic potential maps are available from a 5,000 molecule subset of the Spartan Spectra and Properties Database (SSPD). The database may also be searched by substructure. Properties, spectra and graphical models of molecules in the SSPD subset are available for examination.
iSpartan Server is an available add-on to the iSpartan app. iSpartan Server installs on a Windows or Macintosh computer and converts iSpartan from an application whose primary utility is sketching molecules in 2D and visualizing them in 3D, into an open-ended molecular modeling research tool providing access to the full Spartan Spectra and Properties Database (SSPD), currently ~170,000 molecules) and to the computational engines used to produce the data in the SSPD. For molecules not included in the database, connection to iSpartan Server supports calculation of structures, properties, and spectra for all user generated molecules from iSpartan running on the iPad, iPhone, and iPodTouch.
There is a listing of science apps for iOS here
Script Debugger 5 updated
Script Debugger is an indispensable tool for anyone writing applescripts. If you are not familiar with this application it is worth watching the tutorials
Download Script Debugger 5.0.2
Bugs closed in the 5.0.2 release:
- 17584 Resolved a crash that can occur when closing a paused document with leaked resources (e.g. unclosed files opened with the 'open for access' command).
- 17570 The Recompile command is once again operational.
- 17565 Corrected a problem where Script Debugger would not quit if the top window is an Event Log window.
- 17489 Resolved a problem where Script Debugger would crash opening multiple document tabs on 10.6.4 systems.
- 17548 Resolved a crash that happens when the event log window is opened, closed, reopened and then closed while the document remains open.
- 17528 Script Debugger reopens scripts in their tabs rather than in separate windows following a crash.
- 17521 Corrected a problem where text selections may not be drawn properly following a Replace All operation.
- 17512 Resolved a problem where Script Debugger may report a parameter error (-50) when a script stops on 10.6.4 systems.
- 17517 Improve the presentation when confirming document saving while closing a window with multiple dirty tabs.
- 17487 Libraries added from the Application Support folder now default to 'Relative To Application Support'.
- 17480 Resolved a problem where Script Debugger crashes when launched on 10.6.4 systems.
- 17505, 17543, 15974 Resolved a series of memory related bugs that may improve overall stability.
- 17494 Improved performance when opening and compiling longer scripts.
There is a page of applescript resources here.
Vida updated
Friday the 13th turned out to be a nightmare for OpenEye it turns out that a mathematical operation in the licensing software failed meaning users were unable to use certain versions of their software. To their great credit they delivered an update last night that resolved the problem.
VIDA v4.1.2 has been released. This is a very important bug fix release that enables continued use of VIDA after the licensing problem that was discovered on July 13, 2012.
Elemental for iPad 1.0
Elemental is the Dotmatics chemistry sketch utility provided at no charge
What's New in Version 1.0
- Copy image to Camera Roll
- Copy Image to Clipboard
- File association (tap and hold to load in Elemental)
There is a listing of science apps for iOS here and a comparison of drawing packages here.
Chemicalize now supports iPad
To benefit from the display clarity of devices such as the New iPad, chemicalize.org's chemical structure image generator (built using Marvin) now handles high DPI displays (Retina displays), that also includes iPhone 4 and most new Android devices. Orientation change and touch events like drag, tap and swipe are enabled now.
Mobile Science Publication
A new paper has just been published Redefining Cheminformatics with Intuitive Collaborative Mobile App
The proliferation of mobile devices such as smartphones and tablet computers has recently been extended to include a growing ecosystem of increasingly sophisticated chemistry software packages, commonly known as apps. The capabilities that these apps can offer to the practicing chemist are approaching those of conventional desktop-based software, but apps tend to be focused on a relatively small range of tasks. To overcome this, chemistry apps must be able to seamlessly transfer data to other apps, and through the network to other devices, as well as to other platforms, such as desktops and servers, using documented file formats and protocols whenever possible. This article describes the development and state of the art with regard to chemistry-aware apps that make use of facile data interchange, and some of the scenarios in which these apps can be inserted into a chemical information workflow to increase productivity. A selection of contemporary apps is used to demonstrate their relevance to pharmaceutical research. Mobile apps represent a novel approach for delivery of cheminformatics tools to chemists and other scientists, and indications suggest that mobile devices represent a disruptive technology for drug discovery, as they have been to many other industries.
There is a listing of science apps for iOS here.
ChemFormula added to mobile science page
ChemFormula is a molecular formula and weight calculator ideal for students and anyone else who needs to quickly translate arbitrarily complex formulas into empirical formulas with molecular weights. Written by chemists, it includes support for a large number of common chemical abbreviations, functional groups, and protecting groups.
There is a listing of science apps for iOS here.
Chocolat Mac text editor
Posit Updated to v1.0.2
POSIT - Ligand guided pose prediction POSIT is designed to use bound ligand information to improve pose prediction. Using a combination of OpenEye approaches, including structure generation, shape alignment and flexible fitting, it produces a predicted pose whose accuracy depends on similarity measures to known ligand poses. As such, it produces a reliability estimate for each predicted pose.
The optimizer has been enhanced to produce better aligned structures in certain cases.
A memory leak in the optimizer was fixed, POSIT should now properly handle large streams of molecules. The -mcs flag is now turned off by default. In some cases, the mcs was taking far too long for no real benefit in pose prediction.
Suggestions required
I just got this request,
Hi there, I was wondering if you knew of a program that offers similar functionality as Applied Maths BioNumerics software, but runs on Mac OS X (pref 10.7).
Not really my area, anyone have suggestions?
ChemDoodle web components updated
I just noticed ChemDoodle web components have been updated
This significant update improves performance and graphics for both 2D and 3D components. PDB file reading has been optimized on the Javascript side, and you can now control the resolution of protein and nucleic meshes, leading to significantly faster loading. Two new spectrum components have been added, OverlayCanvas which draws several spectra in the same domain, and SeekerCanvas which shows plot coordinate information.
You might want to have a look at this review and this tutorial
AppleScriptHTML updated
AppleScriptHTML coverts AppleScript source code to HTML representing styles and formatting.
AppleScriptHTML's features. * Clean HTML * Styles are applied by Cascading Style Sheets. It is easy to customise styles after HTML generation.
- Script Link
- Can adding a link to open the AppleScript code in AppleScript Editor. This function is useful for displaying sample codes
In version 2.4, the support of inline css is added.
Try out GPU-accelerated code
NVIDIA invites you to take a free and exclusive test drive to experience running your computational chemistry applications 5x faster with GPUs. The test drive is hosted on a remote cluster loaded with the latest GPU-accelerated applications so you don't need setup any hardware or software. Simply log on and run your application as usual, no GPU programming expertise required. Try it now and see how you can reduce simulation time from days to hours.
Try any of the following GPU accelerated applications:
TeraChem Quantum Espresso Coming Soon GROMACS Coming Soon Or try your self-developed code.
Sign up today:
MacVector 12.6 released
MacVector 12.6 is now available for download
MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions.
The release notes gives full details of the update
Mac and iOS Market Share Trends
Net Applications provide a monthly snapshot of the usage market share for various operating systems and platforms and while it is difficult to draw any conclusions from month to month changes it is interesting to go back and look at the change over longer time periods occasionally.
The June 2012 Mac desktop share stands at 6.72%, in June 2011 it was 5.67%, in June 2010 5.28%, in June 2009 4.74%, and in June 2008 3.70% so in the 4 years of records the Mac desktop share has nearly doubled.
In 2009 with the first analysis of the mobile usage market distribution iOS accounted for nearly 40%, JavaME 36%, Symbian 15% with Android on 2% since then we have seen dramatic changes in the market share with iOS now accounting for over 65%, Android up to 20%, JavaME down to 10% and Symbian almost eliminated with less than 2%. Mobile devices now account for more than 8% of the browsing usage up from around 2% two years ago.
The iPad accounts for nearly 37% of the mobile browsing usage and the iPhone 27%.
I've just added Maltcms to the spectroscopy page.
Maltcms, short for "Modular Application Toolkit for Chromatography Mass-Spectrometry" is an application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics. Its aim is to provide reusable, efficient datastructures, abstracting from the various low-level data-formats like netcdf (ANDIMS), mzXML, mzData and mzML and providing consistent access to data features like mass spectra, chromatograms and metadata. Furthermore, Maltcms provides a platform for the implementation and execution of processing pipelines. New and existing algorithms can be easily implemented or included and executed together with existing processing elements
Maui - Maltcms User Interface is also in beta testing.
Maui is an application for visualization, exploration and processing of raw data from GC/LC-MS and GCxGC-MS experiments. Release 1.0 beta2 Available Features
- chromatogram view (1D and 2D) with interactive selection of mass spectra and database query
- integration of custom scripts for raw data and csv type data via Groovy
- charting of csv and raw data
- import and visualization of Maltcms processing results
- interactive peak exploration
- manual refinement of peak lists
- statistical evaluation of peak tables
- 3D viewer with interactive peak exploration for 2D chromatograms based on jzy3D
- GNU-R integration
- 3D PCA viewer
- pipeline runner for Maltcms
ODDT Publication
There is a paper describing ODDT Open Drug Discovery Teams app.
Investigators of rare and neglected diseases can access some of the latest research in the field, plus data about the disorders themselves, through a recently launched free app for Apple devices.
Papers 2.2
Papers is now at version 2.2, this update includes:-
- Recent papers search for Authors and Periodicals
- Auto-complete of authors and sources in the inspector
- Editing of multiple papers at once and duplicate merging of papers
- Merge and split any duplicate or incorrectly merged sources
- Displaying and navigation of notes and highlights in the inspector
- Addition of tools to allow page rotation and hiding a PDF coverpage
- Creating of collection hierarchies upon import of folders
- Return of column mode for search results in the search section
- Support for inserting footnotes in Microsoft Word
- Improved Papers for iOS syncing
There is a list of reference management applications here.
Bookends Updated
The reference manager application Bookends has been updated.
Direct PubMed searches and using PubMed for autocomplete paper restored. These functions were broken by changes at PubMed.
There is a list of reference management applications here.
Cresset Product Update
I was at the Cresset Science Meeting last week and heard about the plans to update their comprehensive suit of drug discovery and design computational tools.
Together with an interesting updates to the tools the suite has undergone something of a makeover, all of the software tools have be renamed using a "Fire" theme and refocussed to specific users needs rather than the software capabilities. The renaming will not be complete until September so in the interim the links on some of the download pages still point to the originally named application.
TorchV10lite is a free 3D molecule viewing, editing and drawing application that shows your molecules in 3D overlaid with field patterns generated using their proprietary field technology together with 2D structure and physicochemical properties. It is the replacement of FieldView.
TorchV10 is a powerful design and 3D SAR tool for medicinal chemists. It is used to take leaps in structural design by identifying compounds with similar fields but different 2D chemical structures while maintaining or improving biological activity. It is the replacement for FieldAlign and due for release very soon.
SparkV10 is a powerful way of generating novel and diverse structures for your project. sparkV10 uses Cresset's field technology to find biologically equivalent replacements for key moieties in your molecule, enabling you to find new structures in new chemical space. You can then use calculated physiochemical properties to filter and select the best designs. sparkV10 is the exciting replacement for FieldStere and due for release very soon.
The three applications above look to be intended for use by Medicinal Chemists whilst the remaining two applications are perhaps better suited to those more experienced in computational chemistry.
ForgeV10 takes advantage of Cresset's patented ligand comparison method to align, score and compare molecules from a biological viewpoint, using the shape and electrostatic character of your molecules to create qualitative and quantitative 3D models of activity. forgeV10 combines FieldAlign and FieldTemplater in a single application,
BlazeV10 uses the shape and electrostatic character of known ligands to rapidly search large chemical collections for molecules with similar shape and electrostatic properties. It is installed and runs on a Linux cluster but is operated through a web-browser, enabling access from any platform and multiple locations.
Many molecular visualisation/modelling tools seem to assume the charge associated with an atom sits as a point at the centre of the nucleus, whilst this makes the computation easy it does not really reflect what the electrostatic surface really "looks like". Cresset has pioneered the use of field point descriptors to give a more accurate description of the charge around an atom and to enable better comparisons and visualisation. This has been shown to be particularly important when trying to understand some molecular interactions such as Aryl-Aryl interactions or creating bioisosteric replacements.
Cresset now have an impressive suite of tools for drug discovery and I hope to review them in due course.
Automatic numbering of compounds in documents
I was recently asked this question.
"I'm about to hit the tedious part of writing my chemistry PhD thesis in Microsoft Word: having all mentioned compounds numbered in text and in the chemdraw imported files. My question: is there any automated option for this task or do I have to insert every number manually? In particular renumbering after adding a new compound in the middle of the text"
After a little discussion here is an example of what might be required
The photophores used today are generally phenylazides (##), phenyldiazirines (##), or benzophenones (##), which produce nitrenes, carbenes, or diradicals, respectively.
I guess what it requires is the use of some sort of Word-internal "field codes" (?, or other functional unit from Word architecture) to assign a unique name first. e.g.
The photophores used today are generally phenylazides ({chemID="phenyla"/#}), phenyldiazirines ({chemID="phenyld"/#}), or benzophenones ({chemID="benzoph"/#}), which produce nitrenes, carbenes, or diradicals, respectively.
So if I was to use e.g. phenylazides later on again, I could just insert the same field code as before (here: {chemID="phenyla"/#}). At the end, when Word updates all the field codes, each compound is assigned a number (starting with 1 for first compound ever mentioned, replacing the # sign in the field code). At least then if you shuffle some paragraphs (or one's supervisor considers it extremely important to insert this one more structure in your introduction), then the in-text numbering is sorted automatically.
There are a couple of ways to do this in LaTex (http://www.jkwchui.com/2010/03/writing-chemistry-with-latex-33/) and (http://piti.exroot.org/konwerter/) but in my experience LaTex is not particularly popular among chemists. Anyone know of a tool for doing this in Word, Pages or other word processors?
Approved Drugs App
The Approved Drugs app, which came out on the iTunes AppStore just a few days ago, is about to get its first update, whenever v1.0.1 gets approved. The update deals with the loading performance that currently incurs a bit of a hit when the app first loads, and can overload older devices that have less memory (i.e. crash). The reason the loading time does/did take awhile is that the data for 1300 drugs with 2D & 3D structures, enumerated tautomers, and various other adjunct data uses up quite a bit of memory, and it needs to be randomly accessible. The XML datasheet format used to store the data is suitable for streaming, but not at all for accessing arbitrary data entries without loading the whole thing into memory. The solution is a little bit inconvenient: invent a custom format for the read-only data that is indexed, so the app can rapidly scan the contents, in any order, without having to parse it all first.
Registered Apple Developers can now access over 100 session videos to get an in-depth look at the latest in iOS and OS X.
Beilstein Journals App
Beilstein Journals App is available free of charge for iOS. Use this app to read all articles of the two Open Access journals Beilstein Journal of Organic Chemistry and Beilstein Journal of Nanotechnology.
Have a look at the mobile science page for more science apps for the iPhone and iPad.
iMolview 1.5 released
Molsoft has just released a new version of iMolview an app that lets you browse protein, DNA, and small molecules in 3D on the iPhone and iPad.
The key new features include:
- support for high resolution retina display in iPad3
- simultaneous display of multiple proteins and superposition
- side-by-side stereo
- new tools for measuring and displaying distances and angles
- export fully interactive chemical spreadsheets from ICM-Chemist to the iPad
There is also a video of iMolview in action
Have a look at the mobile science page for more science apps for the iPhone and iPad.
Approved Drugs app added to mobile science page
The Approved Drugs app contains over a thousand chemical structures and names of small molecule drugs approved by the US Food & Drug Administration (FDA). Structures and names can be browsed in a list, searched by name, filtered by structural features, and ranked by similarity to a user-drawn structure. The detail view allows viewing of a 3D conformation as well as tautomers. Structures can be exported in a variety of ways, e.g. email, twitter, clipboard
There is a listing of science apps for iOS here.
ChemSpider mobile updated
ChemSpider Mobile v1.1.1 released
There is a listing of science apps for iOS here.
Computational Chemistry Competition
As part of an initiative to provide computational chemistry tutorials there is a competition now on.
Details for the competition Requirements Use freely available software tools and develop tutorials & models for workflows as requested in the challenges. Criteria to Judge
- Quality of predictive models
- Statistical measures, held-out test sets
- Quality of workflows
- Are these state-of-the-art?
- Clarity of the tutorials
- Suitable for undergraduate courses
- Include principles of underlying science
- Include description of "common pitfalls"
- Include description of all preparative steps & required resource
- Ease of use of the tools
- Can they be tailored/amended if new insights emerge (project specific or general insights)?
- Innovation of the computational methods
- Challenge 1: Workflow to analyze HTS data & build models for further hit finding
- Challenge 2: Structure-based design workflow, new chemotypes
- Challenge 3: Structure-based design workflow, medicinal chemistry strategy
- Challenge 4: Call for innovative drug discovery workflows
iKinasePro Universal
iKinasePro is now a universal app running on all iOS devices. iKinasePro for iOS4 provides access into Eidogen-Sertanty's Kinase Knowledgebase (KKB) with fast and powerful substructure-, similarity-, and super-similarity searching capability. In addition, you can search the kinome by target name, by finger-drawn chemical structures, and/or tap through a vast array of ring structures to circumnavigate the Kinome from several different perspectives
There is a listing of science apps for iOS here.
SPRESImobile added to mobile science page
SPRESImobile is an app for Apple iPod, iPhone and iPad mobile devices, developed in collaboration with Eidogen-Sertanty. It provides direct access to ChemReact, a subset of the SPRESI structure and reaction database, which contains more than 400,000 unique reaction types and the related references.
There is a listing of science apps for iOS here.
OpenEye Toolkits updated
OpenEye is pleased to announce that the OpenEye Toolkits v2012.Jun.1 have been released. This release features numerous important bug fixes as well as support for a new platform: Ubuntu 12.04 LTS. Please note that this will be the last release to support Visual Studio 2003, Python 2.5 on Windows, and OS X 10.5. More specific details are provided in the release notes below. The OpenEye Toolkits are available for download now. Existing licenses will continue to work. If a new license is needed, please contact your account manager or email firstname.lastname@example.com to request one.
RELEASE NOTES This is a new release of the OpenEye Toolkits with versions of the following libraries: OEChem TK: 1.8.0 OEDepict TK: 2.0.3 OEDocking TK: 1.1.2 Grapheme TK: 1.0.3 GraphSim TK: 2.0.2 Grid TK: 1.4.0 Lexichem TK: 2.1.2 MolProp TK: 2.1.3 Omega TK: 2.4.6 Quacpac TK: 1.5.2 Shape TK: 1.8.2 Spicoli TK: 1.1.2 Szybki TK: 1.7.1 Zap TK: 2.1.3 Changes in platform support: * Added support for 64-bit Ubuntu 12.04 LTS. A reminder that 32-bit will not be supported on future linux distributions. * Last release to support Visual Studio 2003. Please upgrade to Visual Studio 2008 or 2010. * Last release to support Python 2.5 on Windows. Please upgrade to Python 2.6 or 2.7. * Last release to support OSX 10.5. Please upgrade to OSX 10.6 or 10.7.
MacPro Updated
Whilst it was not mentioned in the WWDC 2012 keynote it seems the MacPro has also been upgraded, a browse of the AppleStore shows a pretty modest upgrade. Whilst the addition of a 12-Core machine is great, there is no USB3 or Thunderbolt. Not surprising it was not highlighted in the Keynote.
XQuartz 2.7.2 released
The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.
The latest version is available from here together with a list of the changes.
StarDrop update released
A new version of StarDrop is now available. The new features include
- FieldAlign – this new module, using Cresset's molecular Field technology, provides a unique, 3-dimensional (3D) insight into the biological activity, properties and interactions of your compounds, helping to guide the design of novel, potent compounds with a high chance of success, there is a review of the FieldView and FieldAlign here.
- R-Group analysis – analyse a chemical series to interactively visualise the impact of variations to R-groups, linkers, atoms or fragments on compound properties. Explore the SAR of your chemistry, identify new optimisation strategies and automatically enumerate the missing combinations
- ADME QSAR – new models for predicting 2C9 pKi, BBB category and P-gp category (the old models remain available for consistency with previously calculated results)
- Nova – now available with the ability to select compounds using a combination of properties and chemical diversity
Added Scaffold Hunter to alphabetical listing
Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It enables generation of and navigation in a scaffold tree hierarchy annotated with various data.
Script Debugger has been updated
Script Debugger an advanced script editor has been updated.
Improved Inline Find & Replace
Inspector Window and Result Drawer Unification
Script Debugger 5.0 combines Script Debugger 4.5′s various floating inspector panels and its Result drawer into three 'tabs' displayed along the right-hand side of each document.
New Bundle Editor Script Debugger 5.0 offers a new bundle editor where you can manipulate the resources contained within a bundled script or a script application.
Floating Mini Debugger This new window floats above all your applications.
New Value Explorer A central feature of Script Debugger is its value Explorers which let you inspect values. For Script Debugger 5.0, value Explorers have been completely re-implemented and simplified. The result is a much more powerful and efficient tool for examining values and exploring the objects and properties offered by the scriptable applications that you control in your scripts.
Element Filtering Script Debugger 5.0's new Scope Bar lets you remove unwanted information from Explorers. For example, unselecting the 'Empty Elements' filter removes empty elements from the Explorer's display.
Improved Handling of Large Element Collections Script Debugger 4.5 could slow down when displaying large element collections, such as the rows in a database. Script Debugger 5.0 avoids this problem by initially displaying only the first 30 rows. Data is then retrieved from the application for only those rows visible in the Explorer. Other rows are read only when they are scrolled into view. Press the new show more button to view additional rows.
New Apple Event Log Script Debugger 5.0 introduces an entirely new Apple Event Log which is integrated directly into the script window.Apple Events are now retained even when the log is not visible, allowing you to look at the event log without having to plan ahead. Additionally, you can change formats (source, raw, AEPrint) on the fly without having to re-run your script.
Explorable Local Variables When stepping through handlers, local variables containing object references can be explored in Script Debugger 5.0. Additionally, object references passed into handlers can show the target application.
Conditional Breakpoints Script Debugger 5.0 lets you assign conditions and actions to breakpoints.
Separate Running & Debugging Toolbars Script Debugger 5.0 offers two toolbar configurations: one for when debugging is disabled; and another for when debugging is enabled. You can customize the toolbar based on how you are using Script Debugger 5.0.
Script Debugger 5.0 improves its object model diagrams by showing element (one-to-many) relationships, and property (one-to-one) relationships.
Improved Spotlight Indexing
Fully 64-Bit Native
StarDrop 5.2 coming soon
Optibrium have just announced the imminent release of the next version of StarDrop
The highlight of this new release is the addition of a new plug-in module that provides access to Cresset's FieldAlign™ technology, which offers a unique, 3-dimensional insight into the biological activity of your compounds. This new development is the first result of the technology exchange, between Optibrium and Cresset, and adds another powerful tool to StarDrop that will enable you to understand the three-dimensional (3D) structure activity relationship (SAR) of your chemistry Version 5.2 also introduces new enhancements of StarDrop's core capabilities, in particular a flexible tool for performing automatic R-group analysis. This new feature analyses a chemical series to interactively visualise the impact of variations to R-groups, linkers, atoms or fragments on compound properties to help chemists to further understand the SAR of their chemistry and identify new optimisation strategies
There are reviews of StarDrop and FieldAlign on the software reviews page and a listing of data analysis packages here.
I've added OpenChrom to the Spectroscopy Page. OpenChrom is an open source software for chromatography and mass spectrometry based on the Eclipse Rich Client Platform (RCP). Its focus is to handle mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files natively. OpenChrom is able to import binary and textual chromatographic data files, such as *.D chromatograms from Agilent Technologies or NetCDF.
FMCS 1.0 - Find Maximum Common Substructure
Andrew Dalke has just released fmcs-1.0. It finds a maximum common substructure of two or more structures. Some of the features are:
- handles 1,000s of structures
- several different atom and bond comparison schemes
- modifiers to require ring bonds only match ring bonds, or that incomplete rings are not allowed in the MCS
- user-defined atom class typing through isotope labels (SMILES) or through an SD tag field
- uses an exact solution to find a maximum common substructure
- eports the current best solution if the timeout is reached
The software is distributed under the 2-clause BSD license and available for no charge from https://bitbucket.org/dalke/fmcs/downloads/fmcs-1.0.tar.gz
You must have the Python bindings to RDKit in order to run fmcs.
Usage details are in the README, shown also in the project page at: https://bitbucket.org/dalke/fmcs/
Science Code Manifesto
Computing is now a critical component of many areas of science and access to the code used is an important component of the review process. The Science Code Manifesto attempts to formalise this.
Code. All source code written specifically to process data for a published paper must be available to the reviewers and readers of the paper.
Copyright. The copyright ownership and license of any released source code must be clearly stated.
Citation. Researchers who use or adapt science source code in their research must credit the code's creators in resulting publications.
Credit. Software contributions must be included in systems of scientific assessment, credit, and recognition.
Curation. Source code must remain available, linked to related materials, for the useful lifetime of the publication.
There is a more detailed discussion here.
FITTED Suite 3.6 released
FITTED is a suite of programs to dock flexible ligands into flexible proteins. This software relies on a genetic algorithm to account for flexibility of the two molecules and location of water molecules, and on a novel application of a switching function to retain or displace water molecules and to form potential covalent bonds (covalent docking) with the protein side-chains.
The Suite includes many new features and implementations:
FITTED is a suite of programs (FITTED, PREPARE, ProCESS and SMART), JAVA GUI for easy keyword file editing and docking, Fully automated and flexible protein docking program, Automated covalent docking, Automatic protein preparation from pdb to mol2, Multi-mol2 support for docking and ligand processing, Uses an evolutionary algorithm, Semi-flexible protein docking with flexible waters, Has the ability to consider water molecules displaceable, Keyword files are simpler than ever, Support for Windows, Linux 32 and 64 bits, Mac OSX.
JSDraw 1.3.6 Release
JSDraw™ is a chemical structure editor/viewer built in 100% Javascript, running on all platforms, including Windows, Mac, Linux, iPad/iPhone, Android tablets/phones and Chromebooks. JSDraw 1.3.6 release includes following improvements and changes: 1. Supporting superatoms: Boc, Me, Et, Bu, Ph, COOH, CHO. And developers are able to use custom superatom table. To download JSDraw: http://www.scilligence.com/web/download.aspx?prod=JSDraw
FastROCS updated
FastROCS is an extremely fast shape comparison application, based on the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity running on the latest high performance graphics cards it can process 2 million conformations per second on a Quad Fermi box.
If you want to find out more about the use of GPUs in scientific computing take a look at this podcast.
SMARTCyp Updated
SMARTCyp 2.2 has been released including the following updates: One new energy rule for sulfur atoms double bonded to sp2 carbon atoms. Update protonated amine SMARTS matching due to analysis of larger 2D6 data set. Faster predictions by rewriting the SMARTS matching code for the pharmacophores in the 2D6 and 2C9 models. Web site update with links to the 2C9 model paper, and prediction accuracy results on nine different isoforms. http://www.farma.ku.dk/smartcyp/
DevonThink updated
DevonThink has been updated.
The maintenance update to version 2.3.5 increases the visibility of the built-in tutorials, adds two new options for archiving email attachments from Apple Mail, and improves a number of other user interface details. Available from the support assistant, the one place for all support and learning resources in DEVONtechnologies apps, the tutorials explain everyday tasks step-by-step from creating databases to, e.g., importing files, searching effectively, and protecting data from prying eyes. The Internet-based content will also be extended in the coming months with even more tutorials and videos.
There is a list of reference management applications here
XQuartz release candidate 3
The XQuartz project is an open-source effort to develop a version of the X.org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.
This development release are now signed with an Apple DeveloperID for increased security.
Download XQuartz-2.7.2_rc3.dmg, and open it with OS X's Installer.
Crystal09 updated in alphabetical listing
Just noticed the website is open and available for registration.
CRYSTAL is a general-purpose program for the study of crystalline solids
New features
- Static polarizability and dielectric tensor through a Coupled Perturbed HF/KS scheme
- Phonon dispersion using a direct approach and infrared intensities through a Berry phase approach
- Transition state search
- Constant pressure geometry optimization of cell constants and atomic positions
- Automated calculation of the elastic tensor of crystalline systems
- Automated E vs V calculation for equation of state
- New GGA functionals for solids
- London-type empirical correction for dispersion interactions (Grimme scheme)
- Automatic generation of nanotubes from single-layer systems
- Helical symmetry for polymers
- New tools for initial guess of SCF for d- and f-partly occupied atoms
- New tools for the treatment of solid solutions
- Revised implementation of Electron Momentum Density analysis and Compton profiles
- Enhanced Massive-parallel version (MPPcrystal - distributed memory)
Adding drop shadows to chemical structures
As part of my day job I maintain Drug Discovery Resources a website intended to act as a resource for scientists undertaking drug discovery. One part of the site has a section on bioisosteres including many examples http://www.cambridgemedchemconsulting.com/resources/bioisoteres/ in which the chemical structures are shown with dropped shadows.
I use ChemBioDraw to draw the structures and then save as PNG files with a transparent background. The structures are then dropped onto webpages created using RapidWeaver, within RapidWeaver there is an option to add dropped shadows to images. I was recently asked whether there was any other way to create the same effect and Matt at macosxtips suggested using ImageMagick. This applescript droplet allows you to do so by simply dropping the file.
forgeV10 takes advantage of Cresset's patented ligand comparison method to align, score and compare molecules from a biological viewpoint
It is designed to
- Decipher complex SAR and communicate the results
- Design better molecules based on predictions you can trust
- Prepare detailed pharmacophores
- Virtually screen 10 000 compounds on your desktop
- Generate ADME and off target activity profiles.
Wolfram SystemModeler released
Stephen Wolfram has announced Wolfram SystemModeler on his blog.
SystemModeler is a very general environment that handles modeling of systems with mechanical, electrical, thermal, chemical, biological, and other components, as well as combinations of different types of components. It's based—like Mathematica—on the very general idea of representing everything in symbolic form.
SMILES MOL and stereochem
An interesting blog entry on Noel O'Blog regarding capturing stereochemistry from 2D representations.
Anyone involved with capturing this sort of information will be familiar with the interpretation of stereochemical information faithfully. I have to say I always store a SMILES string in a database, and not just because it capturers stereochemistry. It is a very compact way of storing chemical information, as a simple text string it is always possible to export to text editor, and after a little practise it becomes a very handy way to create SMARTS queries.
New Additions to alphabetical listings
Added to alphabetical listing
ARP/wARP is a software project for automated protein model building and structure refinement. It is based on a unified approach to the structure solution process. It combines electron density interpretation using the concept of the hybrid model, pattern recognition in an electron density map and maximum likelihood model parameter refinement with REFMAC.
The REFMAC program can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where "missing data" have been restored.
Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Toxtree could be applied to datasets from various compatible file types. User-defined molecular structures are also supported - they could be entered by SMILES, or by using the built-in 2D structure diagram editor.
Markdown Pro
I use markdown extensively on my websites, "Markdown" is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I tend to use BBEdit a lot but I keep an eye out for markdown editors.
Markdown Pro has been recently updated, this two pane editor allows you to write your document in one pane whilst giving you an instant preview of how the document will look. Markdown Pro now lets you add custom templates to the in built selection of templates. The application was built for Mac OS X so takes advantage of many Mac OS features.
Copy file to Dropbox and email link
A while back I posted a script that copied a file to a users MobilMe Public folder and created an email link to that file. With the imminent demise of MobileMe a couple of people have asked me for a script that does the same but uses Dropbox.
This script shows how to copy a file to your Dropbox Public folder and then email a link to it.
SMARTcyp Updated
SMARTCyp has been updated to version 2.1.1. SMARTCyp is a method for prediction of which sites in a molecule that are most liable to metabolism by Cytochrome P450 a major contributor to oxidative metabolism.
The latest update now includes models for prediction of CYP2D6 and CYP2C9 specific metabolism
Script to email Chemical Structures
A reader commented that they often emailed ChemBioDraw .cdx structures to colleagues who it turned out did not have a copy of ChemBioDraw to view them, whilst it is possible to convert the cdx file to other formats using OpenBabel they usually just ended up exchanging an image. They asked if there was a better solution and this is an ideal task for Applescript. This script assumes the structure you want to email is open in ChemBioDraw, it will create an email using Apple Mail containing the structure as a SMILES string, and embed the .cdx file together with an image in PNG format.
KosmicTask is an integrated scripting environment for Mac OS X. Whilst Mac OS X supports a number of scripting technologies either via it's UNIX roots (Shell scripting , Perl etc.) or via Cocoa Framework Scripting using Apple's scripting bridge (Applescript, Ruby, Python etc.) you can end up using a different script editor for each scripting language. KosmicTask allows you to script in a wide variety of languages from within a single editor. KosmicTask uses a plugin architecture that allows it to support a range of scripting languages, details of the languages supported by KosmicTask are shown below:-
- AppleScript
- AppleScript Cocoa - AppleScriptObjC
- Bash Shell
- C Shell
- C and C++
- F-Script Cocoa
- Java
- JavaScript
- JavaScript Cocoa - JSCocoa
- Korn Shell
- Lua
- Lua Cocoa
- Perl
- Python
- Python Cocoa - PyObjC
- Ruby
- Ruby Cocoa
- Tcl
- Tenex C Shell
- Z Shell
KosmicTask also supports another very capable means of achieving automation - appscript. Appscript is supported by both Ruby and Python an alternative to the ScriptingBridge.
It also allows sharing of scripts with other KosmicTask users via the local shared network.
I've also added it to the list of Applescript Resources.
XQuartz release candiate 2
The XQuartz project is an open-source effort to develop a version of the X.org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.
This development release are now signed with an Apple DeveloperID for increased security.
Download XQuartz-2.7.2_rc2.dmg, and open it with OS X's Installer.
Xemistry Web Sketcher Update
Version 3.0 of the javascript chemical drawing package Xemistry Web Sketcher has been released.
This joins a list of javascript powered chemical drawing tools. It seems pretty fully featured but I have to confess I prefer a rather more minimalist interface with templates, elements available from menus. However drawing packages are very much a personal preference.
A Review of CheS-Mapper
I've just completed a review of CheS-Mapper.
CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets of small molecules, a recent publication in the Journal of Chemiformatics describes the application DOI: 10.1186/1758-2946-4-7, In addition more information is available on the wiki page. Whilst there are many applications for the visual analysis of data, very few provide the tools needed to handle chemical structures, CheS-Mapper is a java application that runs under Mac OSX (I only tested Lion) based on the Java libraries Jmol, CDK, WEKA, and utilizes OpenBabel and R, that provides an interesting means to explore chemical data sets.
There a complete list of software reviews here.
IQmol molecular editor and viewer
MMDS UI updated
One of the challenges of creating apps for mobile devices is making functionality available via the user interface and the limited real estate. The UI of the mobile molecular data sheet (MMDS) has been updated to addresses a minor but persistent inconvenience: previously, the main command bank had to be open in order to exit from any of the editor panels.
There is a listing of mobile science apps here.
Chemistry Reference Resolver Safari Extension
I've added Chemistry Reference Resolver to the page of Safari Extensions. This adds a toolbar to your browser as well as adds a right-click menu option for reference resolving
Applescript to report installed and enabled extensions
When Apple released Safari version 5 one of the most important new features was the support for extensions. Extensions are a great way to add features to Safari to personalise web browsing, they enable the addition of features that you find useful. There is a listing of Extensions that might be useful for chemists and judging by the weblogs these are of significant interest. If you are working with them however it is a bit of a pain to check which are installed and which are enabled. This applescript is a very neat way of getting a report, it also serves as a demonstration of how to link to shell scripts, in particular using the unix command
cat, a standard Unix utility that concatenates and lists files, to generate the report.
MyGenome app for iPad
It has now been a couple of years since the human genome was first sequenced and we are now seeing companies offering personal genome sequencing. Illumina are now offering MyGenome an iPad app that allows you to explore a real human genome. In due course they hope to allow you to explore your own genome.
There is more information about the app here.
Now added to the mobile science page.
OEDocking v3 released
OpenEye has to announced the release of OEDocking v3.0.0. OEDocking is a suite of well-validated molecular docking applications (FRED, HYBRID, POSIT) and their associated workflows. This release features the official introduction of HYBRID, as well as a major upgrade to FRED.
POSIT - Ligand guided pose prediction FRED - Fast exhaustive docking HYBRID - Ligand guided docking
Reagents added to mobile science apps
KNIME Newsletter
The 1Q KNIME newsletter is out. Discussion of text mining, the Feb UGM and Tips and Tricks.
KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform.
There is a KNIME tutorial here.
Tools for Mac Fortran Programmers
I'm not a Fortran user myself but I know a lot of scientists swear by it for high performance code, so I thought I'd mention Nocturnal Aviation Software the creators of FTranProjectBuilder the only Mac-native Fortran development environment (IDE) it works with the gfortran, g95, ifort, Absoft Pro Fortran, NAG nagfor and PGI pgfortran compilers.
FTranProjectBuilder is for scientists, engineers and students. It's useful for large, complex projects, but makes even simple programs easy to manage. To speed up program development it has:
- Single window interface
- Editor, console and notes views
- Project wide search
- Execution input from console or file
- Execution timer
- Errors and search results organized by file in outline view
- Add files by drag and drop, or import an existing makefile
FTranProjectBuilder manages the dependencies, object and module files, program executable and a standard makefile for you. You spend your time working on your code. FTranprojectBuilder does the rest.
Chem+ is a chemical reference for your iPad
Elemental for iPad
Elemental from Dotmatics a Chemistry Sketch Utility
Elemental is the Dotmatics chemistry sketch utility provided at no charge within many Dotmatics products. Now provided as a FREE app on the iTunes store.
There is a list of mobile science apps here.
Continued rise of mobile browsing
The latests marketshare data from NetApplications is available, and while there has been a small increase in the Mac desktop share over the year up to 6.53%, perhaps the more interesting feature is the steady rise of mobile browsing. Over the year there has been a 50% increase in the use of mobile devices (smartphones+tablets) from less than 5% to 7.3%. Much of this is driven by iOS which now accounts for 63% of the mobile market share.
Looking at the weblog for the Macinchem website the results are similar with iOS accounting for over 7% of the visitors, software vendors need to think about support for mobile platforms if they have not already.
Siri voice control of cloud computing
In this screencast BioTeam shows how it can orchestrate an Accelrys Pipeline Pilot experiment running on a remote cloud (BT Compute) via Apple iOS Siri voice control.
ByoDyn a python tool for biological simulations
In systems biology it is becoming a routine task to build models of increasing complexity on a given biochemical network or pathway of interest. One of the main problems in building such models is the determination of the parameters underlying each modelled process. ByoDyn has been designed to provide an easily extendable computational framework to estimate and analyse parameters in highly uncharacterised models
Graphite - LifeExplorer
Just added to the alphabetical listing
Graphite - LifeExplorer is a tool for modelling DNA, the tool generates DNA along a Bézier curve, open or closed, allows fine-tuning of atoms' position and, most importantly, exports to PDB. This software allows to model in 3D assemblies of proteins and DNA. Its main feature is the capability to create 3D models of DNA in a highly intuitive manner. To date, the modeling and visualization tool allows to: - import PDB files - create isosurface of molecular object - highlight residues of interest - calculate distance between residues pairs - import and export in 3D formats - model DNA and export the result in PDB - visualize a 3D scene with Level of Detail - explore a scene with real-time ambient occlusion - import a file with x,y,z coordinates and convert it into a DNA representation.
You can see a it in action here
Papers 2 updated
The award winning reference management application Papers has just been updated to version 2.2
- Recent papers search for Authors and Periodicals
- Auto-complete of authors and sources in the inspector
- Editing of multiple papers at once and duplicate merging of papers
- Merge and split any duplicate or incorrectly merged sources
- Displaying and navigation of notes and highlights in the inspector
- Addition of tools to allow page rotation and hiding a PDF coverpage
- Creating of collection hierarchies upon import of folders
- Return of column mode for search results in the search section
- Support for inserting footnotes in Microsoft Word
- Improved Papers for iOS syncing
The full list of new features are described here.
There is a list of reference management applications here.
Chemkit added to alphabetical listing
DEVONthink has been updated
DEVONthink has been updated, this maintenance release prepares DEVONthink Pro Office for the upcoming sync technology, introduces the new Activity panel, brings interface and usability enhancements, and fixes some minor bugs and glitches. It is recommended for all users of DEVONthink Pro Office.
DEVONthink Pro Office only:
- Improved: Compatibility to eastern European languages.
- Improved: Support for all versions of ExactScan.
- Improved: Threading of imported email messages.
- Fixed: Installation of Apple Mail plugin with ~/Library/Mail replaced with an alias or symbolic link.
- Fixed: Creator and producer attributes of OCRed PDF documents.
- Fixed: Size of date field of metadata entry window.
DEVONthink Pro and up:
- NEW: Script Add message(s) & attachments to DEVONthink for easily importing both messages and attachments.
- NEW: Support for categories of Atom feeds.
- Improved: Opening multiple databases uses now one progress indicator.
- Improved: Support for sheets, e.g. imported .csv files, with varying number of columns.
- Improved: Scripts > Import > Del.icio.us no longer uses the discontinued keychain scripting. In addition it is able to download and set a thumbnail for the group again.
- Improved: Encoding support for Add mailbox(es) to DEVONthink and Add message(s) to DEVONthink scripts.
- Improved: Automator action Set Current Group.
- Improved: Smart groups in the sidebar using the Date Opened condition are immediately updated.
- Improved: Handling of feeds not containing dates.
- Fixed: Issue preventing Sente 6 smart template from linking back to the original reference in Sente.
- Removed: Obsolete script Scripts > Feeds > Apple - Latest Mac OS X downloads.
DEVONthink Personal and up:
- NEW: Activity panel. Replaces the OCR Activity panel.
- NEW: Copy Frame Link contextual menu command for movies.
- Improved: Handling of Quick Look panel on OS X 10.6 Snow Leopard and later.
- Fixed: Two issues with tabbed document windows.
- Fixed: Crashes caused by Quick Look on OS X 10.8 Mountain Lion (workaround).
- Fixed: Dragging linked images from Safari stored them as bookmarks since the latest Safari updates.
- Fixed: Bookmarks to pages of PDF documents didn't always work on OS X 10.7 Lion.
- Fixed: Duplicate shortcuts in Format popup menu of Clip to DEVONthink panel.
- Fixed: Empty folders were not always deleted e.g. after deleting indexed items.
All editions:
- NEW: View option View > Columns > Aliases and sorting option View > Sorting > By Aliases.
- NEW: Number of items in groups , smart groups, and feeds is now displayed right aligned and gray.
- NEW: Creating new documents in Tags view adds them either to the currently selected group tag or to the inbox of the database and tags them with the currently selected (ordinary) tag(s).
- NEW: Double-clicking on entries in the Log panel reveals them or shows them in the Finder if possible.
- Improved: Data > See Also > Classify can now also be used when the drawer is already visible, e.g. to close it using the keyboard shortcut.
- Improved: Reliability when inserting links and attachments into rich text documents.
- Improved: Memory management.
- Improved: Overall reliability and performance.
- Fixed: Some minor user interface issues on OS X 10.7 Lion.
- Fixed: Smart groups using Item contains aliases were not always automatically updated.
- Fixed: Mouse cursor did not show as arrow over popup and clear buttons of search fields.
- Fixed: Reordering items in ordinary tags (inside the Tags group) wasn't possible in unsorted views.
- Fixed: Send by Email commands were not disabled if no documents were selected.
- Fixed: Using services or Clip to DEVONthink could cause issues while synchronizing with DEVONthink To Go.
- Fixed: Spotlight metadata cache didn't always contain all files.
- Fixed: Minor bugs and glitches.
There is a list of reference management applications here.
XQuartz 2.7.2 beta 5 released
The latest beta test version of XQuartz has been released. Mac OS X 10.6.3 or later is required to install this package.
The XQuartz project is an open-source effort to develop a version of the X.org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.
ASObjC Runner released.
ASObjC Runner is an invaluable scriptable faceless background helper application. It has a dictionary with a range of commands focused on the areas where vanilla AppleScript comes up short. It adds the ability to use the power of Cocoa frameworks within Applescript.
You use it like a scripting addition, except you address the commands to the application. It provides better string handling (e.g. change case, encoding URL's, regular expression, formatting dates), list sorting and filtering, improved file handling and progress dialog boxes.
I've added to the page of Applescript Resources
CFOUR added to the alphabetical listing
CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Møller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. Studies of excited electronic states and other "multireference" problems are possible using the equation-of-motion (EOM) coupled-cluster techniques. These techniques which are closely related to (and in some cases identical to) so-called Fock space multireference coupled-cluster theory, offer a powerful means to study open-shell systems and decided advantages when configuration mixing is important. At present, these include the EOMEE approach for singlet and triplet excited states, and the EOMIP and EOMEA methods that are best applied to low-spin doublet states. Analytic derivatives are available for these methods. A number of methodological developments have been added to the program in the last two decades. These include: analytic second derivatives for all coupled-cluster approaches up to full CCSDT; the calculation of NMR chemical shifts at MP and CC levels of theory; the calculation of anharmonic force fields (via numerical differentation of analytic derivatives); relativistic corrections; corrections to the Born-Oppenheimer approximation at the CC level; nonadiabatic coupling within the EOM framework, and several others.
Schrödinger Suite 2012 supports Mac OS X
It was recently announced that the Schrödinger Suite 2012 now supports Mac OS X, I don't have many details other than those on the website. There is now a Mac OS X native version of Maestro 9.3, and PyMOL 1.5 supports Mac OSX 10.7, there is encrypted file transfer channel to clusters, including the Cloud (Linux and Mac only). There is also a Mac OS X native version of Canvas 1.5.
If anyone has more information please let me know.
ODDT Released
Open Drug Discovery Teams (ODDT) is now available on the iTunes Store.
The idea behind ODDT is that there are many rare of neglected diseases that might benefit from collaborative efforts from scientists from multiple disciplines, ODDT is an application that supports informal interactions, provides a means to explore relevant information in a flipboard like interface in particular information tagged by other scientists with similar interests. The image below gives you an idea of the topics currently discussed.
This slideshow explains the genesis of the project, and how it has evolved.
So why not fire up iTunes and download the free app and get involved?
iNMR offers
Just got this message I thought I'd pass on.
The iNMR reader will remain at €39 for another 5 days only. Staring from Tuesday, it will return to its old (historical) price of € 50. The same applies for the student promo and the laptop extensions, everything that now costs €39 will cost €50 starting from next Tuesday.
iNMR is the only NMR software expressly written for Mac OS X, it uses Mac technologies and is tightly integrated with Mac OS X.
There is a listing of spectroscopy applications here.
Lab Notebook
I just got sent this.
As part of BioMed Central's commitment to reproducible research and transparency in scientific communication, authors submitting manuscripts to some BioMed Central journals can obtain a complimentary subscription to LabArchives with an allotment of 100MB of storage. This account has all of the features of the Pro Version of LabArchives ELN with the exception of the storage allotment.
LabArchives apparently runs on all platforms including Mac there is also a free version with limited storage which I guess would be useful for trying it out.
Safari Extensions
Just updated the chemistry Safari extensions so they are compatible with the upcoming Safari 5.2.
FierceBiotechIT on Apple in Life Sciences
It looks like the iPad is opening doors for Apple in the Biosciences.
There's mounting evidence that drug companies are changing the way they consume new tech, and one prime example of this shift is the industry's well-documented affection for Apple's iPad. Pharma companies are buying the tablets by the thousands, doling them out to sales reps and executives, some of whom probably already own the popular devices.
Read more: Pharma's iPad attraction marks tech adoption shift - FierceBiotechIT http://www.fiercebiotechit.com/story/pharmas-ipad-attraction-marks-tech-adoption-shift/2012-04-05#ixzz1rZGxpPVh
When the research firm asked more than 100 top life sciences companies about their plans for buying tech hardware in 2012, more than 30% of respondents expected to purchase Apple products, up 220% since 2009.
Read more: Apple emerges as 'dominant' life sciences IT player - FierceBiotechIT http://www.fiercebiotechit.com/story/apple-emerges-dominant-life-sciences-it-player/2012-04-03#ixzz1rZIGrYS1
JSDraw2 interface updated for touchscreens
JSDraw2 interface is changed a lot to fit the touch user experience: 1. The default button sizes are much bigger for fingers to touch 2. For smaller screen size, the toolbar buttons are smartly grouped and shrinked. So even for phone screens, the JSDraw toobar is much easier to use 3. Zooming, moving, rotating and undo/redo gestures are fully implemented
Sdfchecker is a free inspection and manipulation program for SDFiles (.sdf). Summary of functions: - Indicate number of structure records - Indicate number of blank structure records - Display list of Data Field names - Remove blank structure records - Split large files into smaller multiple files, a single random sized file, or containing a specified range of records - Convert into individual MOL files - Inspect for duplicate Data Field names within each record
Mobile Molecular Datasheet has been updated
The Mobile Molecular DataSheet (MMDS) has been updated. Two major usability enhancements:
(1) Additional tool banks on the left and right side of the sketcher provide simplified drawing tools that are more familiar to users of desktop chemical drawing software.
(2) A tooltip system provides tips, live demonstrations and links to documentation.
Utopia Documents
Utopia Documents is an interesting PDF reader that has a number of useful features. It allows you browse through a publications images using a screen flow like display. It also provides links to online resources to enhance the document.
There is a listing of reference management applications here.
AMBER 12 released
A new version of AMBER 12 and AMBER Tools 12 has been released, the main changes are:-
- Force fields: Amber has a new fixed-charge protein force field, ff12SB, enchanced support for polarizable potentials and a new modular lipid force field Lipid11 designed to be compatible with the other pairwise additive AMBER force fields.
- Expanded options for numerical Poisson-Boltzmann solvation calculations, including models for membrane systems and support for periodic systems.
- An enchanced 3D-RISM integral equation model, using the Kovalenko-Hirata (and other) closure approximations, with a better treatement of aqueous electrolytes.
- Improved ideas for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
- Simplified installation and automatic update support.
- Semi-empirical quantum calculations can use d-orbitals, allowing the use of Hamiltonian models such as AM1/d and PM6.
- QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available.
- More features from sander have been added to the pmemd code for both CPU and GPU, including Temperature Replica Exchange, Isotropic Periodic Sum, Accelerated Molecular Dynamics and support for various harmonic restraints based on the use of NMRopt on GPUs.
- Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations.
- New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.
There are detailed instructions for installing AMBER 12 under MacOSX and building CUDA enabled AMBER 12.
Using Flot and Chemical Identifier Resolver
I recently wrote a couple of Applescripts that use the Chemical Identifier Resolver (CIR) a web service that performs various chemical name to structure conversions and it occurred to me that is should be possible to use this service to generate images for use as popups on a graph in the same way that I've previously described using Flot and ChemSpider. This works well but relies on the structure already being in the ChemSpider database, for novel structures we need a service for generating the image from a chemical identifier. CIR provides a simple web service for doing exactly this, for example submit a SMILES string and it can return a 2D image.
This tutorial shows how to create an interactive plot using Flot and CIR
KNIME Desktop updated
From the KNIME newsletter
"…good news for our Mac Users! We have just released KNIME 2.5.4 which fixes issues caused by the latest Apple update of the Java environment. We are grateful to the very active KNIME community which has helped to identify and fix this problem."
KNIME Desktop 2.5.4 can be downloaded from the download page (http://www.knime.org/download) or you can upgrade your existing KNIME installation by using the built-in update functionality available in the "File" menu
There is also a KNIME tutorial here
Biscu-it™ a Python wrapper for RDKit
VEGA Updated
Virtual models for property Evaluation of chemicals within a Global Architecture (VEGA), Using the VEGA platform, you can access a series of QSAR (quantitative structure-activity relationship) models for regulatory purposes, or develop your own model for research purposes. QSAR models can be used to predict the property of a chemical compound, using information obtained from its structure. This version comes with some minor error fixes and with a new model (BCF Read-Across).
Data Extractor
Data Extractor allows to extract data from files and collect them ready to be exported for later use Data is collected in records with custom specified fields inside an internal table. Data can be exported at any time. Data extractor can parse thousands and thousands of file in few seconds and collect all the data inside these files using simple instructions on how to recognise data, how to extract them and where to put these data inside Data Extractor tables, ready to be exported and transferred to a database.
There is a comprehensive list of data analysis applications for the Mac here.
SYBYL-X 2.0 release now available
SYBYL-X 2.0 release now available - with new Molecular Data Explorer, QSAR enhancements, and updates for Surflex-Sim and Surflex-Dock to make performing your CADD modeling studies more intuitive and efficient.
The Molecular Data Explorer is a multi-component tool for molecular data analysis and visualization, and early testers tell us they obtain insights into their dataset in minutes that previously would have taken days.
Scripting the Chemical Identifier Resolver Updated
I was reminded that whilst scripting menu items was the traditional way of controlling ChemDraw the more recent releases allow control by scripting commands. This is a major advance since menus can change or be translated into other languages. I've thus updated the script.
I was asked if it would be possible to do the same thing for other drawing packages such as MarvinSketch?
The answer is yes but because MarvinSketch does not have applescript support we have to do it slightly differently. Rather than using scripting commands we script system events to evoke the "Paste" command.
Full details of the script are here
SPRESImobile added
SPRESImobile provides direct access to ChemReact, a subset of the SPRESI structure and reaction database, which contains more than 400,000 unique reaction types and the related references. SPRESImobile allows searching by name and structure queries, exact, substructure and All-in-one (Flex) search. There is a list of iOS applications on the mobile science page.
Scripting the Chemical Identifier Resolver
The name to structure feature in ChemBioDraw is very useful but is pretty much limited to systematic names and certainly does not support other chemical identifiers like CAS Numbers. There are a number of online services that do support these sort of functions but you end up having to cut and paste from different web sites. This is where the Chemical Identifier Resolver script comes into play.
POSIT Updated
Equalizer 1.2 Released
Equalizer is the standard middleware to create and deploy parallel OpenGL-based applications. It enables applications to benefit from multiple graphics cards, processors and computers to scale the rendering performance, visual quality and display size. An Equalizer application runs unmodified on any visualization system, from a simple workstation to large scale graphics clusters, multi-GPU workstations and Virtual Reality installations. Equalizer 1.2 is a feature release extending the 1.0 API, distilling seven years of development and decades of experience into a feature-rich, high-performance and mature parallel rendering framework and an object-oriented high-level network library. It is intended for all application developers creating parallel, interactive OpenGL applications. Equalizer 1.2 can be retrieved by downloading the source code or one of the precompiled packages.
There is an interesting publication in Journal of Cheminformatics 2012, 4:7 doi:10.1186/1758-2946-4-7 describing CheS-Mapper .
CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets with small compounds.
It can be used to analyze the relationship between the structure of chemical compounds, their physicochemical properties, and biological or toxic effects. CheS-Mapper divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity.
iBabel update
I've been doing a little work to update iBabel, I've updated all the tools developed by Silicos-it to use the new names and options.
The SVG support in Openbabel has undergone significant improvements due to the brilliant efforts of Noel O'Boyle and Chris Morley in particular the ability to colour a substructure within a molecule. This requires installation of the development version of OpenBabel at present.
I've added a movie to show it in action.
Stardrop Review
I've just posted a review of Stardrop an application from Optibrium that is designed to aid decision making for scientists involved in drug discovery.
Scripting Vortex 8 molecular shape matching
One of the critical activities of most drug discovery programs is the identification of novel leads, these hits can come from high throughput screening or fragment-based screening There is however great interest in virtual screening which allows the evaluation in silico of a vast number of compounds and the selection of a subset that have a greater chance of desired activity. The virtual screening can be achieved by searching using sub-structures or molecular descriptors, by docking potential ligands into the target protein and scoring the resulting docked pose, or by comparing with the shape and/or electrostatic map of a known ligand.
Shape-it is a tool developed by Silicos-it that aligns a reference molecule against a set of database molecules using the shape of the molecules as the align criterion. It is based on the use of Gaussian volumes as descriptor for molecular shape as it was introduced by Grant, J.A.; Gallardo, M.A.; Pickup, B.T. (1996) 'A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape',J. Comp. Chem. 17, 1653-1666.
This script shows how to run shape-it from within Vortex, bringing in the shape matching scores for filtering and analysis.
New applications added to alphabetical listing
Open3DALIGN is a command-line molecular alignment tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is installed on the system while Open3DALIGN is being operated interactively, the setup of alignments can be followed in real time on PyMOL's viewport.
Open3DGRID is an open-source software aimed at high-throughput generation of molecular interaction fields (MIFs). Open3DGRID can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL script).
Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields.
ICM Update
MolSoft have announced the release of ICM version 3.7-2c.
New features include Atomic Property Fields APF is a 3D pharmacophoric potential implemented on a grid. APF can be generated from one or multiple ligands and seven properties are assigned from empiric physico-chemical components (hydrogen bond donors, acceptors, Sp2 hybridization, lipophilicity, size, electropositive/negative and charge).
The 3D ligand Editor is a powerful new tool for the interactive design of new lead compounds in 3D. It allows you to make modifications to the ligand and see the affect of the modification on the ligand binding energy and interaction with the receptor.
Use AQUASITES to design chemicals based on their ability to displace or keep water molecules inside the ligand binding site of proteins. The first step is to identify water binding sites and then the second step is to estimate the free energy of water displacement for a particular ligand(s).
Protein Modelling Inside ICM there are many features for homology modelling and loop modelling. This new option can be used if you have a gap in your protein and you want to find loops in the PDB which fit the gap.
"Pipe-able" Scripting in ICM. New options to pipe icm commands and scripts. Easy way to write pipe-able scripts (see $ICMHOME/molpipe/*.icm). Easy way to add parallelism to unix/mac ICM scripts: fork with pipe option ($ICMHOME\molpipe*.icm)
Absoft Pro Fortran 2012 -- Xcode 4.3 Compatibility Pack for Mac OS X
Absoft Corporation, today announced general availability of a new Xcode 4.3 Compatibility Pack for Absoft Pro Fortran 2012 customers running Mac OS X. The Compatibility Pack is available (only) as part of Absoft's new Service Pack v11.5.1 for Pro Fortran 2012 Mac OS customers.
The Compatibility Pack allows installation of Pro Fortran 2012 with Xcode 4.3 and is compatible with Apple's reorganized directory structure.
The Service Pack v11.5.1 which includes the Compatibility Pack for Mac OS X can be downloaded at NO CHARGE by current Absoft Pro Fortran 2012 Mac OS X customers from:http://www.absoft.com/download/downloads.html
For additional details contact: firstname.lastname@example.com or www.absoft.com
Vortex script for MayaChemTools
I've just added a new Vortex script, this one uses a PERL script that is part of the excellent MayaChemTools.
Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using filter-it
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE
Scripting Vortex 5 Calculating similarities using OpenBabel
Scripting Vortex 6 Filtering compounds
Scripting Vortex 7 Using MayaChemTools
Added JTreeView to data analysis tools
Dotmatics LinkedIn Group
Thos who use LinkedIn might be interested to see that Dotmatics now have a dedicated group.
I wrote a review of the Dotmatics tools a while back and have written a series of scripts for Vortex.
I've just added MagicPlot to the list of data analysis tools.
MagicPlot looks like a useful plotting/fitting tool that is free for students.
- Publication-quality customizable X-Y plots with multiple axes
- Handy nonlinear fitting
- Visual multi-peak fitting
- Powerful text table import dialog with plot preview
- Data manipulation
- FFT, integration, differentiation, histograms, descriptive statistics (Pro)
- Auto recalculation on data change (Pro)
- Batch Processing without programming (Pro)
- Plot scale navigation with mouse
- Plot style templates (Pro)
- Multi-level undo/redo with history
Brain Lab
I've just added Brain Lab to the list of mobile science applications Brain Lab is a brain cell simulator, currently it offers
- A passive integrate and fire model
- A full Hodgkin-Huxley model with sodium and potassium channels
- A Library to learn more about brain science
Brain Lab offers real scientific brain cell models that can be used by anyone, no matter if you are a student, a scientist, or someone who is just interested in brain science. To carry out your experiments, they have set up a Lab for you with all the necessary equipment. If you need to brush up your brain science knowledge or look up a specific technical term, you can go to your Library and read it up.
UCSF Chimera Updated to version 1.6
UCSF Chimera is a highly extensible, interactive molecular graphics program is available for MacOSX, both X-windows and native versions are available. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics
This is a major update and whilst some of the new features and tools are described below full details can be found at http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.6.html#1.6. Note this will be the last release supporting Mac PowerPC platforms.
New Tools:
- Animation (Utilities) under development, not fully functional, may change significantly — save/restore Chimera scenes
- Cage Builder (Higher-Order Structure) — create polyhedral cages composed of hexagons, pentagons, and other polygons
- Change Chain IDs (Structure Editing)
- MultiFit (Volume Data) — simultaneous rigid fitting of multiple structures into density (uses RBVI web server running the program MultiFit from the Sali lab)
- Palette Editor (Utilities) — create and choose palettes (series of colors and interpolation method; currently used for background color gradients)
Renumber Residues (Structure Editing)
New Commands:
background — set background color(s) or image
- changechains — reassign chain IDs
- fitmap — command implementation of Fit in Map, plus features not available in that tool:
- global search with random initial placement
- sequential fitting of multiple different structures
- symmetric fitting of copies of the same structure
- invert — swap substituents
- resrenumber — renumber residues
- ibclass — set ribbon residue class: which atoms control ribbon path and which are hidden by ribbon
- ribspline — set ribbon path method: B-spline or cardinal spline; control additional smoothing and "stiffness" of cardinal spline ribbon
- scene — save and restore scenes, which include positions, display status and styles, labels, etc. (see also new tool: Animation)
- zonesel — select atoms and/or surfaces within a cutoff distance of specified atoms and/or surfaces (this command allows defining zones by surfaces, whereas the standard command-line zone operators < and > refer to atoms only)
Net Applications Mac global market share
The latest data from Net Applications is in, Mac OS X is up to around 7% whilst Windows is now down to just below 92%.
iOS continues to dominate the mobile/tablet market (60%), with Android (19%) and Java ME (14%) being the only others in to double figures.
Open Drug Discovery Teams iOS app alpha test
The Open Drug Discovery Teams (ODDT) project is a mobile app primarily intended as a research topic aggregator of open science data integrated from various sources on the internet. It exists to facilitate interdisciplinary teamwork and to relieve the user from data overload. Initial research topics include areas of chemistry and adjacent molecule-oriented biomedical sciences, with an emphasis on those which are most amenable to open research at present. The ODDT project uses a free mobile app for iOS-based devices (iPhone, iPod and iPad) as the hub. The app has a Flipboard-inspired interface, and serverside infrastructure for hosting data and value added services. The project is open to participation from anyone, and much of the content is derived from public sources but is amenable to commercial data input and they are now looking for alpha testers. One of the key components is a back-end server that is in charge of monitoring the appearance of tweets with certain hash tags (#tuberculosis, #malaria, #hivaids, #huntingtons, #sanfilipposyndrome and #greenchemistry).
There is a screencast here to give you an idea of the functionality.
Scripting Vortex 6
I've just added another Vortex script. In this script we will make use of the ability of filter-it to categorise input molecules into 1) a set of molecules that fulfil all criteria as defined in the filter definition file (passed molecules), and 2) a set of molecules that do not fulfil at least one of the defined filter criteria (failed molecules). The filter file defines the criteria for acceptable calculated phisicochemical properties and also any substructures that should be included or excluded during the filtering. The filter file is a simple text file that users can define for themselves, there is a detailed explanation on the silicos-it website. They also provide several example filters "Leadlike", "Druglike", "CMCLike" and "Clean" which cleans up a file without imposing a "drug like" filter. It should be relatively straight-forward for users to create their own filters, one could imagine a rule-of-3 filter that might be used in fragment-based screening approaches, or a toxicphore filter based on SMARTS shown to be implicated in a specific toxicity. It might also be possible to define project specific filters if a project requires a specific profile. If you need help it might be worth contacting Silicos-it.
RESP ESP charge Derive version III.5
I just got this message.
I am pleased to announce the release of the program RESP ESP charge Derive version III.5 (or R.E.D. III.5) and its related tools (Ante_R.E.D.-1.5 and X R.E.D. III.5) available @ http://q4md-forcefieldtools.org/RED/. New features available: - Bug corrections and code cleaning, - Update of the Mini-HowTo & Tutorials, - Better handling of Gaussian, GAMESS and Firefly error messages, - Charge value rounding off errors automatically corrected at 10-6 up to 10-2 depending on the user choice, - Handling geometrical constraints in the P2N file format (geometry optimization using the Gaussian program), - Two new scripts for data submission in R.E.DD.B., - New version for the RESP program: version 2.2 with updated documentation. The R.E.D. III.5 tools are distributed under the GNU General Public License after a simple Register & Download procedure. The article describing the R.E.D. tools is available @ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/. News about the latest developments of R.E.D. IV can be found @ http://q4md-forcefieldtools.org/RED/popup/news.php. Best regards, The q4md force field tools team
R.E.D. allows computational biologists involved in AMBER/GAFF, CHARMM, GLYCAM & OPLS force field based biological studies to automatically derive highly effective and reproducible charge values, and to build force field libraries for new molecules and molecular fragments.
X11 in Mountain Lion
A couple of people have contacted me about the news that X11will not part of the standard distribution of the next version of the Mac operating system. X11 is a key UNIX windowing system for a number scientific applications and I can understand the concern. However whilst X11 has been included in the past it should be noted that the distributed version is simply a snapshot of XQuartz, in the future this will be automatically downloaded.
The XQuartz project is an open-source effort to develop a version of the X.org X Window System that runs on Mac OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5. It may in fact be better if users download the latest version of XQuartz when needed since they provide regular updates which are unfortunately overwritten when you install a Mac OS update.
Indeed the team have already provided a latest development version that is compatible with Mountain Lion (XQuartz 2.7.1 rc4 - 2012.02.11), if you find any bugs or issues I urge you to report them to the XQuartz team !
Silicos-it tools
I've mentioned Silicos-it in the past and I thought I'd highlight them again since they have had a major makeover, the website has moved and the tools have been updated and renamed.
Silicos-it has contributed it's expertise to the chemoinformatics community by porting its source code into the open source domain. Examples include the spectrophore descriptors, the filtering program filter-it and the pharmacophore tool align-it.
Command-line tools
Filter-it™ is a command-line program for filtering molecules with unwanted properties out of a set of molecules. The program comes with a number of pre-programmed molecular properties that can be used for filtering.
I used the filter-it (previously called Sieve) in a Vortex script, I've rewritten the script and the tutorial to account for the name change.
Strip-it™ is a tool to extract molecular scaffolds according predefined rules. These rules are based on the definitions of scaffolds as described by Bemis & Murcko (J. Med. Chem. 1996, 39, 2887), Pollock (J. Chem. Inf. Model. 2008, 48, 1304) and Schuffenhauer (J. Chem. Inf. Model. 2007, 47, 47).
Align-it™ is a pharmacophore-based tool to align small molecules. The tool is based on the concept of modeling pharmacophoric features by Gaussian 3D volumes instead of the more common point or sphere representations. The smooth nature of these continuous functions has a beneficent effect on the optimisation problem introduced during alignment.
Shape-it™ is a shape-based alignment tool by representing molecules as a set of atomic Gaussians. The software is based on the method described by Grant and Pickup (J. Phys. Chem. 1995, 99, 3503).
Spectrophores are one-dimensional descriptors generated from the property fields surrounding the molecules. This technology allows the accurate description of molecules in terms of their surface properties or fields. Comparison of molecules' property fields provides a robust structure-independent method of aligning actives from different chemical classes. When applied to molecules such as ligands and drugs, Spectrophores can be used as powerful molecular descriptors in the fields of chemoinformatics, virtual screening, and QSAR modeling. The Spectrophore code was developed by Silicos, and donated to the OpenBabel project in July 2010.
Perspectives on the state and future of Computer aided molecular design
I just thought I'd mention that Journal of Computer-Aided Molecular Design commissioned some Perspectives on the state and future of the field to commemorate the journal's 25th anniversary and have made this content open access for a limited period.
Special Issue: The next 25 years: Commemorating the 25th anniversary of the Journal of Computer-Aided Molecular Design
There are some very interesting insights, well worth reading.
Have a read of Alpha shock by Mark A. Murcko • W. Patrick Walters
Sanjay toggled the telepresence feature on his iPhone (standard since IOS 27.2) and he and Paolo were instantly ''together'' examining a set of images from the virtual pharmacology study.
OMEGA updated
OMEGA v2.4.6 has been released. This is a major release with new features including an extension to the MMFF94 force field for three coordinated boron compounds. Designed for use with the large libraries required for computer-aided drug design, OMEGA rapidly generates multi-conformer structure databases.
VVI Graph SDK
VVI® today announced the availability of Vvidget Code, its Graph SDK for iPhone, iPad and Mac, version 10.7.6, bringing the following improvements:
The features are extensive and shown by the Graph app on the iTunes and Mac App Store. All the graphs in those applications are now available in the new version. See the links: Graph for iPhone, iPad and iPod touch and Graph for Mac to install those applications and test the Vvidget Code Graph SDK.
ChemVector and ChemCore
I've added two new applications from Metamolecular to the alphabetical listing.
ChemVector™ offers a modern solution to the chemical structure imaging problem. Features
- Runs with all commonly-used browsers on Windows, Linux, Mac, and iPad. This includes Internet Explorer 6-9 in addition to Firefox, Google Chrome, and Safari.
- Renders structures directly from individual molfiles on a server, or as inline content.
- Renders chemical structure content directly from ChemDraw™ binary files (.cdx).
- Declarative syntax replaces <img> tags with analogous <object> tags, making it easy for both developers and designers to work with the resulting markup.
- Non-blocking implementation makes it possible to render dozens of structures on a single page while maintaining UI responsiveness.
- Structures can be magnified pre- or post-rendering with no pixelation.
ChemCore is the chemiformatics foundation of all of the Metamolecular products and services. Written in Java and cross-compilable to a number of target runtimes and platforms, ChemCore is both fast and flexible.
- Fast subgraph matching
- Powerful graph query capabilities
- Flexible, efficient graph traversals
- Fast file input/output
- A complete system of atomic weights and elemental properties
- Sensible handling of implicit hydrogens
- Molecule validation and correctness-checking
- Molecule transformations, including canonicalization and salt-stripping
- 100% Java cross-compilable to JavaScript and other target runtimes and platforms
- Extensively tested and documented
iOS Simulator
A great tip from Dan at Dotmatics, if you want to know how your website might look on an iPhone/iPad use the iOS Simulator in the developers tools.
OpenEye Applications added to listing
I was reading the announcements of new products from OpenEye and I thought I should update the listings.
AFITT from OpenEye is the only software to offer a fully automatic ligand fitting process that optimizes a real-space fit to density while keeping conformational strain to a minimum. It capitalizes on a combination of core technologies that OpenEye has developed, specifically conformer generation, shape potential, high quality small molecule structure minimization, and visualization. The key step, after finding the appropriate conformers and aligning them to density, is the implementation of a refinement that combines force field and shape potentials, via a series of adiabatic optimizations [1]. The AFITT distribution includes both a GUI and a collection of command-line applications.
BROOD is a software application designed to help project teams in drug discovery explore chemical and property space around their hit or lead molecule. BROOD generates analogs of the lead by replacing selected fragments in the molecule with fragments that have similar shape and electrostatics, yet with selectively modified molecular properties. BROOD fragment searching has multiple applications, including lead-hopping, side-chain enumeration, patent breaking, fragment merging, property manipulation, and patent protection by SAR expansion.
FILTER is a very fast molecular filtering and selection application. It uses a combination of physical property calculations and functional group knowledge to remove undesirable compounds before they enter experimental or virtual screening. Undesirable properties may include: toxic functionalities, a high likelihood of binding covalently with the target protein, interfering with the experimental assay, and/or a low probability of oral bioavailability.
QUACPAC provides pKa and tautomer enumeration in order to get correct protonation states. It also offers multiple partial charge models (including MMFF94 [1], AM1-BCC [2], and AMBER [3]) that cover a range of speed and quality in order to allow appropriate charging for every end use. QUACPAC's approach to tautomeric enumeration is to provide multiple tautomeric states rather than one "correct" tautomer. Subsequent downstream processes are then used to identify the appropriate tautomeric form.
SZYBKI optimizes molecular structures with the Merck Molecular Force Field, either with or without solvent effect, to yield quality 3D molecular structures for use as input to other programs. Since the chemistry of molecular interactions is a matter of shape and electrostatics, it is impossible to consider either without reasonable 3D molecular structures. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.
A chart & graph library for iOS and Mac OS X developers.
- Fully native Objective-C library for direct, easy use in any iOS XCode project.
- Several samples and demo projects to make integration and getting started a snap.
- Over 50 powerful graph types, including bar, line, area, pie, scatter, bubble and waterfall.
- An easy-to-use yet powerful object oriented API gives you full control over your charts with a minimum of effort.
- Real 3D graphs with controls to zoom, pan, rotate and skew!
- Adjust and control every element on every chart. Multiple Y-axis, depth effects, reference lines, scale controls and much more.
- The full power of the PGSDK (charting library of choice for MicroStrategy, IBM/Cognos and many more) now for your mobile application!
EBioTools 3
There have been a few comments about an older blog posting concerning EBioTools so I thought I'd bump it to the top of the list.
EBioTools is a compilation of bioinformatics software that has been packaged for easy installation on Mac OS X. It covers many areas, from simple sequence analysis to RNA folding and sequence assembly.
The included software is:
- Name Version
- Boost1.3.41
- Clustal W1.83.UNIX
- PHYLIP3.6b
- EMBOSS.kaptain0.98
- gd2.0.35
- Glimmer3.02
- Jmol11.2.12
- Kalign2
- Kaptain0.72
- MrBayes3.1.2
- MRSr482
- NCBI Tools2.2.16
- NEdit5.5
- Primer31.1.2
- sim42003-09-21
- soap4r1.5.8
- Staden1.7.0
- ViennaRNA1.6.5
As mentioned in the comments added to the older post "EBioTools works under Snow Leopard and Lion but Staden is broken because Apple changed several Libraries to make the MacOSX core "smaller". Most issues are due to Apple changing graphic libraries."
Users might also be interested in eBioX which brings easy-to-use sequence analysis to Mac-using biologists. It features an editor for sequences and multiple alignments, and graphical viewers for trace files and molecule structures. Many popular file formats are supported. Databases can be created locally or queried over the network, both for metadata and homology (BLAST). Analysis functions include searching for patterns, primers, restriction sites and repeats, translation and back translation, calculating DNA melting temperature, dot plots, as well as aligning sequences (multiple, local and global). Multiple alignments can be created by several of the most popular algorithms
Cloud Computing in Science
In December the DOE Office of Advanced Scientific Computing Research (ASCR) published a report on Cloud Computing for Science. The key findings were
- Cloud approaches provide many advantages, including customized environments that enable users to bring their own software stack and try out new computing environments without significant adminis- tration overhead, the ability to quickly surge resources to address larger problems, and the advantages that come from increased economies of scale. Virtualization is the primary strategy of providing these capabilities. Our experience working with application scientists using the cloud demonstrated the power of virtualization to enable fully customized environments and flexible resource management, and their potential value to scientists.
- Cloud computing can require significant initial effort and skills in order to port applications to these new models. This is also true for some of the emerging programming models used in cloud computing. Scientists should consider this upfront investment in any economic analysis when deciding whether to move to the cloud.
- Significant gaps and challenges exist in the areas of managing virtual environments, workflows, data, cyber-security, and others. Further research and development is needed to ensure that scientists can easily and effectively harness the capabilities exposed with these new computing models. This would include tools to simplify using cloud environments, improvements to open-source clouds software stacks, providing base images that help bootstrap users while allowing them flexibility to customize these stacks, investigation of new security techniques and approaches, and enhancements to MapReduce models to better fit scientific data and workflows. In addition, there are opportunities in exploring ways to enable these capabilities in traditional HPC platforms, thus combining the flexibility of cloud models with the performance of HPC systems.
- The key economic benefit of clouds comes from the consolidation of resources across a broad community, which results in higher utilization, economies of scale, and operational efficiency. Existing DOE centers already achieve many of the benefits of cloud computing since these centers consolidate computing across multiple program offices, deploy at large scales, and continuously refine and improve operational efficiency. Cost analysis shows that DOE centers are cost competitive, typically 3–7x less expensive, when compared to commercial cloud providers. Because the commercial sector constantly innovates, DOE labs and centers should continue to benchmark their computing cost against public clouds to ensure they are providing a competitive service.
Eagle Genomics have a nice summary, that addresses many of the highlighted issues.
DivCon Discovery Suite Updated
QuantumBio Inc. have announced the release of Version 5.1.1 of its DivCon Discovery Suite which includes support for the newest version of the Molecular Operating Environment (MOE) platform from Chemical Computing Group, Inc.
MOE/DivCon GUI is an integration interface that joins the QBLib with the powerful Molecular Operating Environment (MOE) from the Chemical Computing Group (CCG), creating a technological innovation for protein/ligand scoring (energetically favorable), featuring QM, PWD, and NMR Scores.
The update also includes:-
- MOE/DivCon: For pairwise energy decomposition heatmap, sequence alignment within the MOE/DivCon interface has been completely overhauled in order to use CCG's sequence alignment tool.
- MOE/DivCon: Multitasking within the MOE/DivCon graphical user interface runs freely while DivCon is running in the background. Improved QM convergence reporting to MOE's svl window.
- File Processing: Included HDFView and QBReporter applications for opening and processing *.h5 output files, and translating them to Excel or OpenOffice spreadsheet files. Reported results include QMScores, partial charges, gradients, and significant events. QBReporter requires that OpenOffice 3.3.0 or greater from OpenOffice.org has been installed and that the resulting soffice executable is available within the command line $PATH.
- Core: Support for Sun Grid Engine (SGE) in addition to the Portable Batch System (PBS). Note: SGE requires that its parallel environment (PE) be activated in order to run multiprocessing jobs.
- Core: Shipment of both 32bit and 64bit native versions of all Linux binaries in order to account for larger memory, disk, etc (and therefore larger target/ligand structures).
- Core: Separation of QuantumBio-specific software from 3rd party binaries (such as mpirun) in order to allow for parallel installations of the same.
- MOE/DivCon: Inclusion of ${QBHOME}/bin/qbmoe and ${QBHOME}/bin/qbmoebatch to run system-installed MOE and MOE/batch with QuantumBio-required options.
- MOE/DivCon: Addition of support for MS Windows7 (64bit) both for preparation and analysis. Prepared structures can then be characterized with qbmoebatch on Linux or Mac OS X.
- Documentation: Completely updated on-line documentation for MOE/DivCon.
- MOE/DivCon: Entirely redesigned and streamlined dialogs, and improved integration with standard MOE structure preparation and analysis tools.
- MOE/DivCon: Patented QMScore integrated as an available score function for MOE tools including Dock, Scaffold Replacement, BREED, etc.
- DivCon: Support for additional input file formats including cif, sdf, and h5.
- DivCon: Command line --help switch improved to provide default settings, simplified
Added 3 apps to Mobile Science Page
iFormulas is a clean, simple, easy to use mathematical formula reference guide. Formulas : Algebra, Calculus, Chemistry, Geometry and Trigonometry. Over 380 formulas, definitions, laws, properties, etc.
MyCalculator is an innovative 2D and 3D graphing calculator featuring One Touch Graphing™ and an innovative memory system to store and recall answers. Just touch the answer bar to store numbers in multiple memory slots.
MathStudio, formerly SpaceTime, is the most comprehensive math app available for iPhone and iPad. Whether you need a simple calculator to do your finances or a replacement for your TI graphing calculator,
Scripting Vortex 5
I've just posted the latest tutorial on scripting the chemically intelligent spreadsheet application Vortex, this tutorial shows how to use OpenBabel to provide similarity searching.
The full list of Vortex scripting tutorials are shown below.
Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using Sieve
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE
Scripting Vortex 5 Calculating similarities using OpenBabel
More hints and tutorials can be found here.
AppleScriptObjC Explored
The 'AppleScriptObjC Explored' Addenda and Errata page has been updated to cover a change made in Xcode since version 4.0 came out. <http://www.macosxautomation.com/applescript/apps/errata.html>
AppleScriptObjC Explorer v2.2 is now available. It's a free update to existing users, and incorporates all the changes in the last beta version, plus built-in updating.
Myriad Helpers 1.0.2 is now available. It's a minor update, offering a new method fordTrig: to give access to trigonometry functions. <http:www.macosxautomation.com/applescript/apps/helpers.html>
Q-Chem Updated
I just got this message:-
We are pleased to announce the official release of Q-Chem 4.0. Q-Chem 4.0 represents the latest development in quantum chemistry methodology and includes:
- Dispersion-corrected and double hybrid DFT functionals;
- Faster algorithms for DFT, HF and coupled-cluster calculations;
- Structures and vibrations of excited states with TD-DFT;
- Methods for mapping complicated potential energy surfaces;
- Efficient valence space models for strong correlation;
- More choices for excited states, solvation and charge-transfer;
- Effective Fragment Potential and QM/MM for large systems;
- Shared-memory for multicores and implementations for GPU's.
A complete list of the new features can be found at the our website: http://www.q-chem.com.
NWChem 6.1 and ADF2012 released
The updates to two of major packages for computational chemistry have been announced
NWChem 6.1 has been released with the latest Global Arrays Toolkit (GA-5.1). Full details of the update can be found here.
SCM has announced the 2012 release of its suite of chemical modelling programs: ADF, BAND, DFTB, MOPAC, ReaxFF, and COSMO-RS. Full details of the update can be found here.
MolPrime added to mobile science page
MolPrime is a chemical structure drawing tool based on the unique sketcher from the Mobile Molecular DataSheet
Added to the Mobile Science Page.
Net Application market share
The January market share data is out from Net Applications.
The desktop share is dominated by Widows (92%) and Mac OSX (6.4%), interestingly nearly 50% of the Windows machines are still operating XP.
The remorseless rise in the use of mobile platforms continues with mobile/tablet browsing now up to 8.8% an increase of over 1% over last month and more than 100% over the year. iOS continues to dominate (53.6%) with Java (19%) and Android (18%) juggling for second place. Blackberry is now down to 2.6% and falling rapidly.
Vortex developer wanted
This might be of interest.
Dotmatics is looking to expand the team working on Vortex, its data analysis platform. The candidate should have several years software development experience with Java and preferably with the Swing graphical user interface toolkit. The ideal candidate will have a degree or PhD in the life sciences, and will have experience with data visualisation and analysis techniques such as clustering. Experience with cheminformatics systems or statistical software, such as R, will be advantageous. Candidates will probably have experience working within the pharmaceutical/biotech sector or the life science software development industry.
The position will be based at the UK headquarters in Bishops Stortford (Herts, UK). We offer a competitive salary, benefits and a pleasant working environment at the Old Monastery site. Further information about the company and our software can be found at http://www.dotmatics.com.
AppleScriptObjC Explored Third edition
Over the years I've migrated from Applescript Studio applications to AppleScriptObjC using Xcode 3 and last week I made the transition to Mac OSX 10.7.x and Xcode 4. With each transition there has been a very steep learning curve and to be honest the documentation provided by Apple has been woefully inadequate. Thankfully Shane Stanley has stepped up to the plate and provided a definitive guide for this people who want to build applications using applescript. AppleScriptObjC Explored is the definitive guide to building AppleScript Objective-C applications. It guides you step-by-step through the process of integrating the power of Cocoa into your AppleScript applets and applications, demonstrating each concept and technique in fully editable and annotated example projects.
The latest edition also includes a detailed navigation of Xcode 4, for those of us who had just learnt our way around Xcode 3 the changes made in the new version are significant and the section explaining where everything is and what they are for is invaluable, in fact it is probably worth reading this section before you start trying to write your first application.
Once you have a basic understanding of Xcode adding an interface to your script becomes largely point and click.
There is also a very useful section on trouble-shooting, and explanation of "gotchas" that will crop up occasionally.
The book comes with a collection of over 20 ready built Xcode tutorials/projects that demonstrate key implementations but that can also act as starting points for your own projects.
Whilst I keep a list of applescript resources, I suspect that AppleScriptObjC Explored is probably the most useful.
ORCA 2.9 version available
ORCA is a modern electronic structure program package has been updated
New Features
1) The parallelization of the program is now completed. All modules, including MRCI, are now parallel. Parallel performance has been improved in numerous cases.
2) A new module for performing efficient spin adpted single excitation configuration interaction calculations for open shell systems (ROCIS). This is particularly powerful for the calculation of transition metal L-edge X-ray absorption spectra. It is parallelized
3) A new module performing molecular dynamics calculations with ORCA. Also available for methods that only feature numerical gradients.
4) MDCI module: • Orbital optimized coupled cluster version for RHF and UHF (also parallelized) • Brückner coupled cluster (including triples) for RHF and UHF • SEIO functional for orbital invariant, stationary coupled pair calculations • Open shell LPNO-CEPA,QCISD and CCSD methods • Parameterized CCSD (pCCSD) in canonical and LPNO versions (RHF and UHF)
5) CASSCF: • Relativistic CASSCF for the variational treatment of spin orbit coupling. Also uses symmetry. • Projection SOC states on spin-free states possible • Kramers restricted RELCAS • Numerous improvements in NEVPT2 (COSMO, Trajectories and scans, Direct-RI modeless storage) • Improved convergence and convergence aids (... but we are still working on this) • Spin-Spin coupling in QDPT CASSCF/NEVPT2 for magnetic properties • Determinant based full CI program added for the CI step
6) MRCI • Fully parallelized including the QDPT procedure for magnetic properties
7) General/Misc. improvements • VDW10. Latest dispersion correction from the group of Grimme • Nonlocal DFT-NL for incorporation of dispersion in DFT • PW6 B95, PWP B95, RI-PWP B95 functionals • Rappoport/Furche optimized basis sets for properties • Basis set extrapolation now works also with def2 basis sets • Densities for interactive orcaplot • Differences and transition densities in orcaplot • Natural orbitals for unrelaxed MP2 density • SOS-MP2, SOS-RI-MP2, SOS-OO-RI-MP2 energies + gradients • DKH picture change for g-tensors • Overlap fitted RIJCOSX procedure leads to further speedups and improvements in accuracy • Libint2 for more efficient integral evaluation (uses contraction) • Parallelization of point charge correction for QM/MM • Interface to the MRCC program by Mihály Kállay
Scripting Vortex
This is the fourth tutorial on scripting Vortex a chemically intelligent data visualisation package. In the previous tutorials we have looked at getting data from OpenBabel, sieve, and cxcalc in this tutorial we will be using MOE as the compute engine. MOE from Chemical Computing Group is probably best known as a graphical user interface to a suite of computational chemistry tools, whilst this is indubitably the means by which many users will interact with the program it is worth finding out about the command-line tools that are available. These tools are often accessed by pipeline tools such as Knime to allow rapid processing of large files. CCG provides four very useful command-line tools in particular sddesc allows the calculation of some or all of the MOE molecular descriptors for each molecular entry.
The Vortex Scripts
Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using Sieve
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE
You might also want to look at Data Wrangler for an online tool for cleaning up data.
There is a comprehensive list of data analysis packages that run under Mac OSX here
Reference Miner
Reference Miner searches the Internet to find and display reference information from PubMed, Amazon (US, UK, Germany, France, Canada, Japan, Italy, and China), Google Scholar, JSTOR (requires access privileges and ip authentication) and the Library of Congress. The Internet search features of Reference Miner, and much more, are built into Bookends. If you own Bookends you do not need Reference Miner.
Chemical Drawing Packages compared
Chemical Drawing Programs – The Comparison of Accelrys (Symyx) Draw, ChemDraw, DrawIt, ACD/ChemSketch, ChemDoodle and Chemistry 4-D Draw
There is also a comparison of six chemical drawing packages here
Graph version 10.7.3 available
VVI® today announced the availability of Graph version 10.7.3 on the Mac App Store, bringing the following improvements:
- Copy paste is now implemented for textual (labels) table cells and columns.
- Column paste now accepts many number delimiters such as blank, comma, tab, Return, etc.
- Added Save and Open Panels to export and import data into tables.
- Added a main title to the pie chart.
- Arrow keys now move the table cell editor to the expected adjacent cell instead of move the text cursor.
- When a sheet is present, ESC and Command-. shortcuts dismiss (cancels) the sheet.
- When the cell editor is used to enter an empty value in the last row of a column then that column length is reduced by one except when the data needs to be rectangular (as in the Z-Values table).
- ESC dismiss (cancels) the cell editor without entering the data.
- Made many small adjustments to the user interface to make it look and perform better.
- Implemented elemental table behaviour in the backend.
There is a list of data analysis applications here
Using Pasteboard Pro 4
PTHPasteboard is comprehensive clipboard manager that supports multiple text and image clipboards, these can then be accessed via a customisable icon in the menu bar or from a floating window, clicking on an item in the clipboard history displays the application that the data was copied from and for text items shows the number of lines/words/characters and for images the size. PTHPasteboard also supports filtering of clipboard text allowing you to convert to unformatted text, convert to lower/upper case, change to Mac/Unix/Windows line endings. There is also a custom filter dialog that allows you to build your own filters for example to convert a list from a text document into an html list. It also allows the creation of custom clipboards. PTHPasteboard PRO's Syncing support takes advantage of Mac OS X's Bonjour technology to seamlessly sync your pasteboard items across multiple machines.
I've been using it for a couple of weeks now and I thought I'd share few tips.
Bookends Updated
There is a new update to Bookends (11.2.4 )
- Updated Google Scholar direct search and Autocomplete Paper to deal with changes made by Google
- Import abstracts from Google Scholar Note that the abstracts Google Scholar provides are incomplete, but still may be helpful.
- Type ahead search works in the single column reference list The search is always for the author, regardless of the sort status of the list. It will only jump to an exact match of the typed characters.
There is a comprehensive list of reference management software here.
ViennaRNA Updated
I was just catching up with some reading and I came across an article in Algorithms for molecular biology describing ViennaRNA 2.0 consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. With the new release of version 2.0, they introduce the most recent nearest neighbour energy model for all free energy calculations. Additionally, most of the stand-alone programs included are now able to read FASTA formatted input data. The distribution includes:-
- RNAfold -- predict minimum energy secondary structures and pair probabilities
- RNAeval -- evaluate energy of RNA secondary structures
- RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
- RNAinverse -- inverse fold (design) sequences with predefined structure
- RNAdistance -- compare secondary structures
- RNApdist -- compare base pair probabilities
- RNAsubopt -- complete suboptimal folding
- RNAplot -- RNA structure drawings in PostScript, SVG, or GML
- RNAcofold -- predict hybrid structure of two sequences
- RNAduplex -- predict possible hybridization sites between two sequences
- RNAup -- predict RNA-RNA interaction sites using accessibilities
- RNAalifold -- predict the consensus structure of several aligned sequences
- RNAaliduplex -- comparative (multiple alignment) version of RNAduplex
- RNALfold -- predict locally stable structure of long sequences
- RNAplfold -- compute average pair probabilities for local base pairs in long sequences
- RNApaln -- fast structural alignment of RNA sequences using string alignments
- Several small but helpful Perl Utilities
According to the authors both 1.8.x and 2.0 versions of the Vienna package compile and run on Mac OS X. Currently there's a small compile problem with the included Perl module and the latest gcc versions on Intel based Macs. The defaults for gcc recently changed to compile only Intel code, while the installed Perl is a fat binary containing both PPC and Intel code. The download page contains instruction how to work around this by simply setting an environment variable.
Molecular FORECASTER
I just heard about a platform - FORECASTER - that includes programs for drug discovery and process chemistry, these include
- FITTED, a docking program
- PREPARE, PROCESS and SMART, programs that can prepare protein and ligand files automatically
- CONVERT, a program that converts 2D molecules to energy-minimized 3D molecules (adds hydrogens, generates tautomers and protomers)
- SELECT, a program that computes compound similarity, extracts focused highly diverse libraries or identifies analogues
- REDUCE, a program that filters using descriptors and functionnal groups
- REACT, a program that performs combinatorial chemistry in silico from user-defined chemical schemes
- IMPACTS, a sites of metabolism prediction program (CYP 450)
- ACE, a program that predicts the stereochemical outcome of reactions
All the programs are integrated into a new web-based graphical interface that allows complete automation of the different workflows.
You can read more details here, Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery
A Review of Data Creator
I'm occasionally asked for is a test data set that can be used to evaluate an application. Whilst I keep a couple of data sets that I can use perhaps Data Creator will provide a more comprehensive solution.
Data Creator is an application that has been designed to fill this important niche, Data Creator can be used to build very large data sets using field types defined by the user and then filled with random realistic content. I've just added a review of Data Creator.
There is an increasing collection of software reviews here.
iNMR5 Released
After many months of beta testing the latest version of the popular Mac dedicated NMR spectroscopy application iNMR5 has been released. The key new features are tabulated below.
- 64-bit
- Version 5 requires a 64-bit Intel chip and Snow Leopard. Version 4 is 32-bit Universal Binary and requires Tiger.
- real-time dragging
- When you drag the margins of the plot, or the integrals, or most of the objects, the plot is continuously updated. Overlay manager
- The Overlay Manager becomes non-modal and can be enlarged to show the full path of the individual documents. Sorting the overlays is simpler and more transparent.
- Manual phase correction
- The zero-order correction is controlled by a knob that never reaches the end of the run. The fine-coarse selector has many more stops. The phase panel is more compact.
- Other dialogs
- "Units and Scales" and "Colors and Levels" change the corresponding plots as soon as you click into a control. The Preferences dialog includes a "Preview" button. The color panel is no more modal. When the open dialog is open, the corresponding menu item isn't dimmed anymore. The console is more compact than in the past, but can be enlarged at will.
- Fit to overlay
- Fitting a simulated spin system is visibly faster.
- Cursors
- The new cursors are more specific. The horizontal palette has a single row of buttons.
- Info tool
- The interpolator is faster, more predictable and more reliable.
- Animation
- The visual effect of the command "New Page" is realistic.
- Printing
- The printed area is no more centered and no more clipped.
- Tabulator
- Shows an estimate of the T1.
Depending on your existing license you may be eligible for a free upgrade, for other users there is a small upgrade fee.
There is a list of spectroscopy applications for the Mac here
KNIME User Group Meeting
I just got this message:-
"Following our very successful user meeting and workshops in 2011, we will be holding a similar event in 2012. The 5th KNIME Workshop and Users Meeting will take place between January 30 and February 3, 2012 at Technopark in Zurich, Switzerland. Early bird registration closes on Jan 15th. You can register here .
There is a KNIME tutorial here.
MacVector Updated
I just got a note that MacVector has been updated to version 12.5 MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions. MacVector is widely regarded as the most intuitive, easy to use program available for sequence analysis.
A comparison of Clipboard Managers
For many years I've used the excellent Clipboardsharing to exchange the clipboard contents between my laptop and desktop machines, it also supports multiple clipboards. However it is not supported under Mac OS X 10.7.x (Lion) and the developer website seems to have disappeared. I spent a while looking at various alternatives and I thought I'd summarise my findings.
I should add I had a pretty clear view on my needs.
- Exchange clipboard contents (text and images) between laptop and desktop machines running Lion
- Have multiple clipboards
- Ability modify text e.g. remove formatting
Nice to have
- Keyboard shortcuts
- Option to encrypt clipboard contents before transfer
- Also exchange clipboard contents with iOS devices
Clipboard Evolved
Clipboard Evolved features a clipboard-like window for managing clips, a menu bar icon, and now a cover-flow interface for quickly pasting clips. It supports both text and images, and Clipboard Evolved has eight "complex" animation options to choose from: Ripple, Copy Machine, Star Burst, Irregular Holes, Disintegrate, Swipe, Crystallize, and Dissolve. It does not support clipboard sharing.
ClipMenu is a clipboard manager that supports a number of text and images types including Plain text, Rich Text Format (RTF), Rich Text Format Directory (RTFD), PDF, Filenames, URL, TIFF image, PICT image. The clipboard history can then be accessed via an icon in the menu bar or via a shortcut key. ClipMenu can manage re-usable text as snippet. You can select it from menu and paste it anytime. It does not support clipboard sharing.
Clips automatically generates and arranges copied items into Application-specific clipboards, these can then be accessed via a Finder like interface or via an icon in the menu bar. It also supports live search so you don't have to scroll through them, just start typing in the Clips Board or Organizer and non-matching items will fly off the screen instantly. It does not support clipboard sharing.
Clyppan is a clipboard history application that keeps a list of text you have copied to the clipboard, these can then be accessed via an icon in the menu bar. Clyppan only supports text clippings, but the history is searchable and pressing the spacebar will give you a Quick Look-style preview of the clipping, it also does not support clipboard sharing.
CopyLess supports all data types supported by the Mac OS X clipboard and has inline searching and Quicklook integration to allow you to check what you are pasting, it also keeps track of the application the data was copied from. It does not support clipboard sharing.
CopyPaste Pro
CopyPaste Pro is a popular clipboard history tool that can then be accessed via an icon in the menu bar or a graphical browser, CopyPaste Pro also has a selection of clipboard tools that allow the user to manipulate the data on the clipboard. It also allows the creation of archives to store clips for later use. It does not support clipboard sharing.
CuteClips 3 is a recent update, it supports text and images which can then be selected from a list. It supports shortcuts and has an extensive list of keyboard shortcuts for manipulating the list and pasting options. It does not support clipboard sharing.
iClip supports copying plain-text, rich-text, images, audio, video, or files and all can be accessed in a rather neat iClip dock that sits on the side of the screen, you either drag and drop to and from the iClip history bins or copy and paste. It is possible to preview images in clip bins which might be very useful if you are working a lot of the time with images. It supports keyboard shortcuts, but does not have clipboard sharing.
Jumpcut is an open source application that provides multiple clipboards. Every time you copy some text it is added to the Jumpcut stack, these can then be accessed via a scissors icon in the menu bar. Alternatively you can view the list via a hot-key. It does not however support images and as far as I can tell no plans for clipboard sharing.
PTHPasteboard Pro 4
PTHPasteboard is comprehensive clipboard manager that supports multiple text and image clipboards, these can then be accessed via a customisable icon in the menu bar or from a floating window, clicking on an item in the clipboard history displays the application that the data was copied from and for text items shows the number of lines/words/characters and for images the size. PTHPasteboard also supports filtering of clipboard text allowing you to convert to unformatted text, convert to lower/upper case, change to Mac/Unix/Windows line endings. There is also a custom filter dialog that allows you to build your own filters for example to convert a list from a text document into an html list. It also allows the creation of custom clipboards. PTHPasteboard PRO's Syncing support takes advantage of Mac OS X's Bonjour technology to seamlessly sync your pasteboard items across multiple machines.
Savvy Clipboard
Savvy Clipboard holds a list of items that you copied — text fragments, graphics, URLs, multimedia data, or links to files — and lets you access them using this list from either a floating window or menu bar icon. You just select the needed item from the list, and it is ready to use from the system Clipboard, so you can paste it anywhere you want. While it is possible to export a list and transfer to another computer it does not support clipboard sharing.
ShadowClipboard is another fairly comprehensive application, with unlimited clipboard sets, clipboard sharing, clipboard filtering and clipboard set backups, the clipboard history can then be accessed via an icon in the menu bar or from a window. It supports keyboard shortcuts, and shadowClipboard uses Apple's ZeroConf networking called Rendezvous. shadowClipboard clients will automatically recognise each other on a local network.
Stuf 2
Stuf 2 has a different way to share clipboards in that Stuf stores your clippings and can share them with any other Stuf users, even in a different country, with your permission of course. Stuf can use any network drive to share clippings, but they really recommend you use DropBox. Stuf 2 is available for both Mac and PC. It supports text and images and clipboard history can then be accessed via an icon in the menu bar.
So I bought PTHPasteboard which best meets my needs but obviously your needs may vary. There are also a couple of clipboard sharing tools Syncopy, which is nice because it supports Mac OS X and iOS, CrossClip which works between Mac, Linux and PC.
Website Update
The migration of the site is now complete, and I think all the missing images, incorrect formatting, broken links etc. are now fixed, many thanks to all those who reported problems.
I've been adding Google Analytics to pages so I have a better idea of what is popular and to get a better view of the readership. It is early days yet but it looks like the site is getting 15 - 20, 000 hits a month, with around 70% being new visitors to the site. The average time spent on the site is 4 mins which would suggest most find content that they want to read. As you might expect 70% of the visitors are using Mac OS X, 20% Windows but interestingly 5.5% are now using an iPad. In fact >95% of the visitors using a mobile device are using iOS. Nearly 40% of the visitors from the US and 15% from the UK, the remaining european countries contribute a couple of percent each as do Japan, India, China and Australia there was even one visitor from Trinidad and Tobago who spent 4 minutes browsing the site.
The top search terms are iBabel, emolecules, chemical drawing, atom modelling knime and tutorial.
The most popular pages are the blog, mobile science, the reviews, data analysis tools and applescript.
The RSS feed and Twitter feed seem to be picking up new readers each week.
I'll look again in six months and see how things have progressed
Data Creator
I've compiled a list of data analysis tools and sometimes when I'm just trying a new application out I need a set of random data. Data Creator looks like it might be ideal for those sort of occasions, it can create structured data table (fields) and fill them with random proper content (records) with a single click. These data can be saved on disk and imported into databases and applications for test and demonstration purposes. Data Creator can be used to create very large data sets (thousands and thousands of records) for stress test of structures and scripts.
I've just installed Ubuntu and whilst doing so I came across one tip I thought I'd pass on, during the installation you lose the mouse cursor, however you can still navigate menus/options using the arrow keys. Took me a little time to realise :-)
VMware Fusion (Mac)
Chirys Draw added to mobile science page
Chirys Draw is an innovative, best-in-class application for drawing publication-quality molecular structures and reactions. Designed from the ground up for the iPad, Chirys Draw takes advantage of unique multi-touch capabilities to make drawing molecular structures and reactions easy and accurate. Chirys™ Sketch is an innovative, best-in-class application for drawing publication-quality molecular structures and reactions. Designed and built from Chirys Draw, the iPad version, Chirys Sketch takes advantage of unique multi-touch capabilities to make drawing molecular structures easy and accurate.
There are many more applications on the mobile science page.
Added CMol to mobile science page
CMol is a molecular viewer designed specifically for the iPad, iPhone and iPod touch, offering a more powerful system for displaying and understanding biological molecules than has yet been seen on any iOS device.
There are many more applications on the mobile science page.