text:
Questions and Exercises for Classical Scholarships, Second Division ...
J. Thornton, 1879 - 132 pages
What people are saying - Write a review
We haven't found any reviews in the usual places.
Selected pages
Other editions - View all
Questions and Exercises for Classical Scholarships, Second Division
University of Oxford
No preview available - 2016
Questions and Exercises for Classical Scholarships, Second Division (Classic ...
University of Oxford
No preview available - 2015
Questions and Exercises for Classical Scholarships, Second Division ..
University of Oxford
No preview available - 2015
Common terms and phrases
41 HIGH STREET advantages and disadvantages ancient and modern Athenian Athens battles Books briefly Caesar causes character and policy characteristics Charlemagne chief Cicero civilisation Cleisthenes cloth College Compare Constitutional History Contrast Corpus Christi College Criticise Crown 8vo Crusades Demosthenes Describe Discuss Distinguish Edition effects Emperor England English history Epaminondas epochs Essays Estimate Europe EXERCISES FOR CLASSICAL Exeter College Explain the following following terms France French Revolution geographical Give a short Give an account Give some account Gracchus Greece Greek Greek history history of Rome Homer Illustrate importance influence Italy JAMES THORNTON Jeyes Julius Caesar kings late Scholar literary literature Lord meant national character nature Notes ORATIONS origin Oxford Paraphrase passages Peloponnesian Peloponnesian War Pericles poet poetry political position principal QUESTIONS and EXERCISES Reformation republic Revolution of 1688 Richelieu Roman empire Rome School Second Punic War Shakespeare short account social student Thomas Hobbes Tiberius Tiberius Gracchus Trace Translation Tutor
Popular passages
Page 79 - Then Paul stood in the midst of Mars' hill, and said, Ye men of Athens, I perceive that in all things ye are too superstitious. For as I passed by, and beheld your devotions, I found an altar with this inscription, TO THE UNKNOWN GOD. Whom therefore ye ignorantly worship, him declare I unto you.
Page 52 - Could trammel up' the consequence, and catch, With his surcease,* success ; that but this blow Might be the be-all and the end-all here, . But here, upon this bank and shoal of time, — We'd jump the life to come. — But, in these cases, We still have judgment here ; that we but teach Bloody instructions, which, being taught, return To plague the inventor : This even-handed justice Commends11 the ingredients of our poison'd chalice To our own lips.
Page 75 - Surely every medicine is an innovation, and he that will not apply new remedies must expect new evils; for time is the greatest innovator; and if time of course alter things to the worse, and wisdom and counsel shall not alter them to the better, what shall be the end?
Page 2 - For as water will not ascend higher than the level of the first springhead from whence it descendeth, so knowledge derived from Aristotle, and exempted from liberty of examination, will not rise again higher than the knowledge of Aristotle.
Page 33 - In which methodical course, it is so supposed they must proceed by the steady pace of learning onward, as at convenient times for memory's sake to retire back into the middle ward, and sometimes into the rear of what they have been taught, until they have confirmed and solidly united the whole body of their perfected knowledge, like the last embattling of a Roman legion.
Page 130 - When a Mammonite mother kills her babe for a burial fee, And Timour-Mammon grins on a pile of children's bones, Is it peace or war ? better, war! loud war by land and by sea, War with a thousand battles, and shaking a hundred thrones.
Page 63 - The Clouds that gather round the setting sun Do take a sober colouring from an eye That hath kept watch o'er man's mortality ; Another race hath been, and other palms are won.
Page 63 - Fame is the spur that the clear spirit doth raise (That last infirmity of noble mind) To scorn delights and live laborious days; But the fair guerdon when we hope to find, And think to burst out into sudden blaze, Comes the blind Fury with the abhorred shears, And slits the thin-spun life. 'But not the praise...
Page 74 - As the births of living creatures at first are illshapen, so are all innovations, which are the births of time.
Page 16 - The battle of Marathon, even as an event in English history, is more important than the battle of Hastings. If the issue of that day had been different, the Britons and the Saxons might still have been wandering in the woods.


text:
The free download file Depreciation Calculation Utility Automatic is in the form of xlsx and is very useful for students who are going through CS Executive exams and would like to cover the area of Industrial, Labour and General Laws in a detailed manner. Depreciation Calculation Utility Automatic has been uploaded by cakart for the benefit of CS Executive students. The file has been uploaded about 2 years ago and till date has been downloaded by 1030 visitors.
If you download and use Depreciation Calculation Utility Automatic file please do not forget to review and share your comments in the relevant sections below. It will be very helpful for other CS Executive students.
Please note that along with the file CS Executive we have provided other very useful download files that have been uploaded by cakart . We hope you will find them very useful for your CS Executive exam. We have also shared other useful files that are downloaded by students when they download Depreciation Calculation Utility Automatic file. Also, if you have useful files for CS Executive exam or any other exams, please upload them here and share with all.
Have you used
Depreciation Calculation Utility Automatic?

subset: commoncrawl


text:
Kinect Portraits by Mike Pelletier:
Kinect Portraits
I've been experimenting with alternative ways of using the Kinect since Microsoft released the hardware a few years ago. One of the more exciting possibilities was trying to use the Kinect as a 3d scanner.
By moving the Kinect camera around the subject the software constantly updates to create a detailed 3d model. Within a couple minutes you can get a fairly detailed model from a sitting subject, as long as they sit still…
See more photos and details at Mark Pelletier's site.
Check out all the Circuit Playground Episodes! Our new kid's show and subscribe!
Have an amazing project to share? Join the SHOW-AND-TELL every Wednesday night at 7:30pm ET on Google+ Hangouts.
Join us every Wednesday night at 8pm ET for Ask an Engineer!
Learn resistor values with Mho's Resistance or get the best electronics calculator for engineers "Circuit Playground" – Adafruit's Apps!
Maker Business — How Authority and Decision-Making Differ Across Cultures
Wearables — Skin adherence
Electronics — LED Basics!
Biohacking — Stretchable EEG Temporary Tattoos
No Comments
No comments yet.
Sorry, the comment form is closed at this time.


text:
The effect of changes in Social Security on bequests
The net effect on intergenerational transfers of an increase in Social Security benefits will depend on how much of the increase is consumed and how much bequeathed. I show analytically that the marginal propensity to consume an increase in Social Security benefits is indeterminate: it could range from zero to 1.0 or even larger. At one extreme bequests would fully offset the increase in benefits; at the other bequests would fall. According to simulations based on an estimated model of life-cycle behavior, consumption increases by slightly more than the increase in Social Security benefits, causing bequests to fall. That is, bequests do no offset at all an increase in transfers from the younger generation to the older. Copyright Springer-Verlag 1993
If you experience problems downloading a file, check if you have the proper application to view it first. In case of further problems read the IDEAS help page. Note that these files are not on the IDEAS site. Please be patient as the files may be large.
As the access to this document is restricted, you may want to look for a different version under "Related research" (further below) or search for a different version of it.
Volume (Year): 58 (1993)
Issue (Month): 1 (December)
Pages: 157-176
|Contact details of provider:
| Web page: http://www.springer.com
References listed on IDEAS
Please report citation or reference errors to , or , if you are the registered author of the cited work, log in to your RePEc Author Service profile, click on "citations" and make appropriate adjustments.:
- Menchik, Paul L & David, Martin, 1983. "Income Distribution, Lifetime Savings, and Bequests," American Economic Review, American Economic Association, vol. 73(4), pages 672-690, September.
- Michael D. Hurd, 1987. "The Marginal Value of Social Security," NBER Working Papers 2411, National Bureau of Economic Research, Inc.


text:
Privacy Inquiry
Our goal is to respect your privacy. If you have any questions, comments or concerns about our Privacy Policy, you may contact us by email by filling out this form or by postal mail to:
Meg's Makeup, Inc.
269 South Beverly Drive #606
Beverly Hills, CA 90212
Attn: Privacy Officer
Meg's Makeup welcomes your comments and questions.
Always remember, true beauty comes from within...
From within bottles, jars, compacts and tubes.*
From within bottles, jars, compacts and tubes.*


text:
I recently switched my driver's license from PA to NY. Having lived in Japan for 18 years I'm not actually a resident of any state, but upstate New York is now my homebase when I go back for a visit. It's really just a matter of convenience, but I look forward to my exalted status as a New Yorker. Imagine – a place that people actually write songs about! Not that I'm particularly in love with any of those songs. If I were to choose a state simply based on a song it would probably have to be "Kentucky". But I guess true statriotism has to be based on actual residency, and I've only ever lived in three states: PA, DE and NJ.
Recently a workmate introduced me to a band called Zebra Hunt who have a nice power poppy sound. I especially love the first song on their first album, which just so happens to be called "Delaware". New York has been lauded in songs by music industry titans from Frank Sinatra to Billy Joel … the rest of the mid-Atlantic region not so much, especially the tiniest member of all. So I was quite pleased to hear a tune about the Diamond State that I actually liked.
Then just yesterday I checked out Apple Music's suggestions "just for me" and found a Woodsist greatest hits playlist – had to give that a spin. It contained the song "Pennsylvania" by John Andrews & The Yawns, which reminds me somewhat of the great Southern and Appalachian songs about places. This experience made me feel like I should check out Apple's recommended section a bit more often, and sent me on a quest to find a song about New Jersey …
Beyond Bon Jovi and Bruce the options are few, but my search yielded an absolute gem by Red House Painters. I've never really been able to get into Mark Kozelek's stuff, but like the Garden State Parkway shuttling summer vacationgoers "down the shore," this song may just serve as my route in. Glad I stumbled upon this "second version" first – the earlier take isn't nearly as good.
Sufjan Stevens only got two albums into his "50 States" recording project before calling it quits. It's hard enough to find one decent song about a state that someone else wrote, let along write 10-12 good new songs by yourself all about one state. But I'm surprised how well these 3 songs work as a playlist. Might have to try and expand it to the whole country, or at least the Eastern seaboard.


text:
Increase Communication by Having Fewer Meetings
From Project Manager 97Things
Increase Communication – Hold Frequent, Instant Meetings
Richard Sheridan Ann Arbor, Michigan, USA
Software project managers often fall into the deadly trap of regularly scheduling their teams for painful meetings that have the unfortunate, unintended effect of actually decreasing communications. One of the all-time dreaded meetings is the classic Monday morning status meeting. As if Mondays weren't bad enough already!
If you aren't convinced that most meetings should be killed, try this experiment. As the software project manager, don't show up. Ask one of your trusted colleagues about the meeting you skipped. Did they hold it without you?
If the meeting only happens when the boss or project manager shows up, kill it. Your team is telling you they don't get value out of it. Never hold meetings where only one person gets value.
At my organization, we do everything we can to eliminate unproductive meetings and replace them with simpler communication paths between team members. For example, we have the team work all day, every day, in one big open room with no walls, offices, cubes, or doors. Thus, when I need an answer from someone, I can simply say, "Hey, James." In less than 30 seconds, James and I have exchanged the necessary information and get back to work without actually moving (or sending e-mails back and forth).
Imagine an all-company meeting with 60 people, that is as easy to set up as shouting out "Hey, everybody!" Everyone stops what they are doing and responds, "Hey, Rich!". The meeting can take a few, short minutes and then everyone turns back to work without moving from his/her seat.
Our rituals and ceremonies include weekly "Show & Tells" to demonstrate progress on projects to sponsors, weekly "Planning Games" to authorize project scope, daily stand-up meetings, and weekly kickoff meetings to brainstorm how we will work together towards common goals on client projects in the upcoming week. The meeting has a structure that makes participation easy and fun.
Try a daily standup meeting for one week and see if it catches on. Here are some lessons we've learned to make this meeting more effective.
1. Invite everyone involved in the project. We often have 50 to 60 people in this meeting.
2. Call the meeting with an alarm clock loud enough for everyone to hear. An impartial device calling the meeting is more likely to get participation. We use a dartboard that has an alarm clock in it.
3. Use a speaking token. We use a plastic Viking helmet to control the meeting. Just hand it around the circle of people STANDING (no sitting allowed). The person who has the token has the floor.
4. Have people report what they recently completed, what they are working on, and where they need help. Help doesn't come during the meeting, but afterwards.
Our typical standup meeting takes 13 minutes! Call it, assemble it, hold it, give everyone a chance to talk, finish it, and get back to work in 13 minutes. I defy most organizations to complete a useful meeting of 60 people in 13 minutes.


text:
We have been busy planning and preparing for our first ever Fall Boutique for a church fundraiser. We normally have this type of sale at our annual Winter Services, held in February. But, this year we had the idea to throw together some fun items for a November sale.
In the meantime, I wanted to share a few of the bubblegum necklaces we made.
Bubblegum just refers to the approximate size of the acrylic beads. They are cute and chunky. These are all sized perfectly for a 4-7 year old. We sell them for $21 including shipping (so if anyone online is interested, just leave me a comment).
And here is a photo of my oldest and youngest! Eloise loves her peas and carrots necklace.
Thanks for taking a peek! Have a colorful weekend!


text:
«2017» - Free Software Engineering Classics: Software Project Survival Guide/ Debugging the Development Process/ Dynamics of... Ebook Download Full
Gratuit Sage 50 (Peachtree) Accounting Software Reviews Pricing Sage 50 (formerly Peachtree) is core accounting software for small business. It provides billing and invoicing, inventory management, security and analytics reporting. AMD Radeon Software Crimson Relive Drivers ... Wccftech AMD's biggest driver update for 2016, the Radeon Software Crimson Relive edition has leaked out and covered in full details. Receiving Weather Fax and Weather Satellite Images With ... Receiving Weather Fax and Weather Satellite Images With Your Macintosh. Introduction How Weather Fax is transmitted over HF radio How to receive weather fax images HTML.it HTML.it: corsi, guide, articoli e script per webmaster e webdesigner, gli approfondimenti necessari sui trend del design e della programmazione. The Free Software Directory Free Software Foundation Welcome to the Free Software Directory, a catalog of free software that anyone can edit. Free software is a matter of liberty, not price. Think of free as in ... MSC Software Corporation Simulating Reality, Delivering ... MSC Software is a global leader in helping product manufacturers to advance their engineering methods with simulation software and services. id Software Developer of the Quake and Doom series. Trellian Direct Search Network Direct Navigation Traffic Trellian A leader Direct Navigation and Zero Click traffic. Since 1997 Trellian has been developing website marketing and search engine promotion tools to ... Simulation Driven Product Development ANSYS ANSYS is pioneering the development and application of simulation methods to solve challenging product engineering problems. IBM DevOps IBM's DevOps one stop shop: discover what it is, how to get started, best practices, products and solutions. Let IBM help you with your DevOps journey. Open Source Software World Wide Web Consortium (W3C) Browse W3C's Open Source Software Amaya a Web browser editor First released Feb '97, Amaya is not just a browser, but a hypertext editor. libiconv GNU Project Free Software Foundation (FSF) Introduction to libiconv International text is mostly encoded in Unicode. For historical reasons, however, it is sometimes still encoded using a language or country ... MajorGeeks.Com MajorGeeks ...Software Download freeware and shareware software utilities and apps. Download files for your computer that tweak, repair, enhance, protect ... Marc Andreessen on Why Software Is Eating the World WSJ Far from a bubble, we're watching a new generation of tech start ups realize the Web's original potential, says Marc Andreessen. Area by Autodesk Guest point of view from Gaspard Giroud, co founder of New York based marketing and experience design agency, Piranha. Guest point of view from Gaspard Giroud, co ... E book Software for Windows Free downloads and reviews ... The Best Free E book Software app downloads for Windows: Kindle for PC ePub Reader for Windows Google Books Downloader Mobi File Reader ePub to PDF Co Kvisoft FlipBook Maker Pro Powerful HTML5 Page Flip Software Kvisoft Flipbook Maker Pro is a powerful HTML5 page flip software and digital magazine software that converts PDF documents to digital magazines or publications with ... Software for Raymarine Multifunction Displays Raymarine Software Update Information. This software download contains the a, c, e, eS and gS Series software and the latest version of software for the following peripherals: eWEEK.com Technology News, Tech Product Reviews ... eWEEK delivers breaking tech news, the latest IT trends, and in depth analysis daily. For more than 30 years, eWEEK has kept tech professionals ahead of the IT curve. Weather Stations, Emergency Radios and Time by Ambient Weather Provides sales, service, and support of weather stations, weather equipment, weather radios, weather instruments and software. How to Become a Software Engineer: 12 Steps (with Pictures) How to Become a Software Engineer. As technology evolves and becomes a bigger part of everyday life, so too does the need for technology professionals. CD and DVD Burning Software Alcohol Soft copy and ... CD and DVD Burning Software. Alcohol 120%, is a powerful Windows CD and DVD burning software that makes it easy to create backups of DVDs* and CDs. Ecommerce Software Solutions: Online Store ... Vendio Vendio offers a complete ecommerce software solution that includes an online store and simplifies selling on sites like eBay, Amazon and more. Online survey software tool QuestionPro online surveys ... Create professional online surveys fast, easy, and free. Online survey software, customer satisfaction, market research, employee satisfaction surveys Gizmo's Freeware Wiki style searchable collection of freeware programs, organized by function and popularity. Includes guides and tutorials, and user contributed articles. 9 Cleanest Safest Websites to Download Free Software for ... Downloading software can be dangerous. Visit the wrong site and you might accidentally download malware. We have compiled free software download sites you can trust. Windows PC Software Free Downloads and Reviews CNET Download.com is your best guide to find free downloads of safe, trusted, and secure Windows software, utilities, and games. Software GNU Project Free Software Foundation GNU software is available by several different methods: Download a wholly free GNU Linux distribution. Get a copy from a friend. Buy a computer with a wholly free GNU ... HTTrack Website Copier Free Software Offline Browser ... Welcome. HTTrack is a free (GPL, libre free software) and easy to use offline browser utility. It allows you to download a World Wide Web site from the Internet to a ... BMC Bring IT to Life with Digital Enterprise Management Transform your digital enterprise with BMC IT solutions. From mainframe to cloud to mobile, well help you drive innovation and industrial efficiency. Read/download Software Engineering Classics: Software Project Survival Guide/ Debugging the Development Process/ Dynamics of... ebook full free online.


text:
By Ellen Nakashima
Washington Post Foreign Service
Sunday, January 16, 2005; Page A24
BANDA ACEH, Indonesia -- "Go left! Left!" shouted Andi Basrul. Rachmat the elephant heaved forward, pulling a chain tight around his massive shoulders and hauling up a log from the ruins of a shattered house.
The twisted body of a woman appeared in the wreckage, a red shirt over her head, legs folded back at a cruel angle. Her mottled hand clutched a metal post, which she must have grasped when the black waves crashed into the house less than a mile from the sea.
"Go on! Go on!" called Basrul, 46, the director of Aceh province's conservation office. The beast twisted away jagged wedges of tile-topped brick, further uncovering the body.
Basrul has been involved in the recovery effort every day since the Dec. 26 earthquake and tsunami, which killed more than 115,000 people in Indonesia. He said the work is a form of therapy, because he lost his wife, Martini, and daughter, Gabby, 11, in the disaster.
"Yes, it's difficult," he said. "But if my own family can't be found, perhaps by finding other people's bodies, that will help me through."
Basrul has brought in six elephants from wildlife reserves he oversees because, he says, they are more practical than earthmovers and bulldozers in searching for remains. "Elephants are smart," he said, and their dexterous trunks can lift debris without unduly disturbing a corpse.
Officials say about 75,500 bodies have been recovered in Aceh, on northern Sumatra island. Some people might never be found, and the odds of finding all the dead decrease each day as the bodies decompose in the punishing tropical sun and torrential rains.
"What can I say?" asked Basrul, a rotund man missing some of his front teeth, pausing Thursday as he directed the men handling the elephants.
At first, Basrul searched for his wife among the ruins, but he stopped after a few days.
"I just had a feeling at that time that my wife still somehow had survived, that I'd find her alive," he said. "But then after three days, somehow, I'm not sure if I was dreaming or awake, I had a feeling that she came to me. She wore clean clothes, and she looked at me, and then she looked away, and then she left me."
It was a sign, he said, that she was dead. He kicked through rubble as he spoke. "I was feeling sad and very touched, but I thanked God that He had given me that sign."
But Basrul's son, Kiki, 21, is still looking for his mother and sister. He goes to every hospital morgue, every relief camp. It has been three weeks, and "there are still plenty of places" to search, Kiki said. He wants to look now in smaller refugee camps, "even those with four families."
His father does not try to stop him.
Basrul wanders in a vast wasteland of mud, water and detritus. This was his neighborhood, now strewn with memories: a mangled child's bicycle, an overturned Butterfly sewing machine, a canvas backpack with a waterlogged Koran.
As he walked, occasionally taking a puff from a cigarette, he motioned to the sea, toward the direction of his demolished house. He stopped several times, at one point spotting a pair of corduroy pants in the muck -- his own, he said, swept hundreds of yards from his home. He shook the pants out and tossed them onto a log and a cement slab. In flip-flops, he traversed fallen coconut tree trunks and slabs of corrugated metal.
Not far from the woman's corpse, another team of elephants was trying to excavate a body from a heap of rubble in what had been a house. Basrul watched as an elephant named Marni arced her trunk and plucked a section of wooden house frame from a pile of bricks that had collapsed on the corpse, a shirtless man lying on his stomach.
"Move to the right!" Basrul ordered. The man atop the elephant guided the pachyderm to the right.
For four hours, Basrul was mostly on the move, directing the elephants, picking up and tossing away debris, patting one elephant's trunk, feeding a piece of coconut to another, inspecting corpses.
"That's the main point for me," he said. "If I have something to do, I will forget the pain temporarily. Because the grief is there."
It comes in waves, "when I'm alone, when everyone is sleeping, in the middle of the night." He finally sleeps at 3 a.m., holding tight to Gabby's orange drum majorette costume and baton, which he found in some wreckage.
He said he is happiest when he is awake, "when I can surrender myself to God." Then, he said, he feels that he can move on.
"But sometimes, when things are not right, and Satan possesses my mind, I cannot help but think, why did God take my daughter? She deserves to live more than me. She's still young. I still want to be close to her. Why did this happen?"
When the wave hit, Basrul was out of town for work. Kiki was with his mother and sister and carrying his own 2-year-old son. When he tried to reach out for Gabby's hand, his mother shouted, "No, run! Save yourself and your son."
"Kiki's feeling regret because he didn't save his sister," Basrul said.
For two days after the tragedy, he said, Kiki avoided him, afraid he would be angry. "He asked for my forgiveness for not saving Gabby and his mother," Basrul said. "I said, 'No, you're not to blame.' "
He was interrupted by the excavation crew retrieving the body of the shirtless man.
"Plastic!" Basrul called, ordering up more sheeting.
Unlike his men, he wears no surgical mask, no plastic gloves, no boots. "I cannot smell anything, frankly," he said. "I'm numb."
Rescuers deposit the bodies directly into a mass grave, without identifying them or taking snapshots, a practice that is sure to add to the already considerable confusion surrounding the numbers of dead and missing in Indonesia. But Basrul said he believes that burying the dead as soon as possible is better than letting them rot in the sun.
When he had finished his work for the day, he rested under a shade tree near an office he had set up while his own, which was damaged, was being cleaned. Kiki sat near him.
Basrul said there was enough work clearing bodies to keep him busy for two more months. Tomorrow, father and son both will search again.


text: Eric Horner Ministries :: Geek Stuff Eric Horner MinistriesEric Horner Ministries - a music ministry of God and Country. FAQ Search Memberlist Usergroups Join! (free) Profile Log in to check your private messages Log in Geek StuffModerators: NoneUsers browsing this forum: None Eric Horner Ministries Forum Index -> Geek Stuff Mark all topics read Topics Replies Author Views Last Post S10 WebAlbums!! 0 Billy's Dad 2895 Wed Apr 01, 2009 8:14 pmBilly's Dad BUG!! 0 Billy's Dad 2772 Fri May 09, 2008 4:13 pmBilly's Dad Orphan Remover! 0 Billy's Dad 3333 Tue Oct 23, 2007 1:33 pmBilly's Dad Shrink Pic 1.4.1 is here! FREE!! 2 Billy's Dad 3141 Fri Oct 05, 2007 12:40 pmBilly's Dad Easy Thumbnails!! 0 Billy's Dad 2500 Thu Oct 04, 2007 11:46 pmBilly's Dad Photo ToolKit v1.6 is here! 0 Billy's Dad 2354 Tue Oct 02, 2007 6:55 pmBilly's Dad Excited! 0 Debby Horner 2505 Tue Oct 02, 2007 3:30 pmDebby Horner MWSnap is here!! 0 Billy's Dad 2327 Mon Oct 01, 2007 1:27 pmBilly's Dad PIXresizer....it's still FREE!! 0 Billy's Dad 2304 Mon Oct 01, 2007 1:22 pmBilly's Dad Display topics from previous: All Topics1 Day7 Days2 Weeks1 Month3 Months6 Months1 Year Eric Horner Ministries Forum Index -> Geek Stuff All times are GMT Page 1 of 1 Jump to: Select a forum Eric Horner Ministries----------------WelcomeNews & UpdatesChurch RecommendationsHow can you help? Spiritual----------------Prayer RoomBible StudyPraisesTestimoniesRevival in AmericaHow To Be Saved Military----------------Military SupportPrayers for US TroopsWays to Support Music----------------Favorite SongThe Studio Misc. Stuff----------------Geek StuffWebsitesWords Of Wisdom New posts No new posts Announcement New posts [ Popular ] No new posts [ Popular ] Sticky New posts [ Locked ] No new posts [ Locked ] You cannot post new topics in this forumYou cannot reply to topics in this forumYou cannot edit your posts in this forumYou cannot delete your posts in this forumYou cannot vote in polls in this forum Card File Gallery Forum Archive Powered by phpBB © 2001 phpBB Group Chronicles phpBB2 theme by Jakob Persson (http://www.eddingschronicles.com). Stone textures by Patty Herford.


text:
FRAMED Gameplay 1 iOS / Android
By: Loveshack
Genre: Puzzle
Video Tips
Let's play FRAMED! This is part 1 of my walkthrough guide for the iOS game, FRAMED by Loveshack Entertainment Pty Ltd.
I will update this post with more tips and tricks, so please bookmark this page and keep on checking in!
If you have any questions, feel free to ask for extra help in the comments section.
Hit like if this helped you!
Visit FRAMED walkthrough page for level videos, tutorials, cheats and more.
Gameplay Questions
Questions related to gameplay of FRAMED iPhone game.


text:
We haven't had a whole lot of snow here yet…but all my girls need is just a little bit. They have such creative imaginations, and always come up with something fun to do outside! Just wanted to share a few pics! On this day, it wasn't absolutely freezing out. In the 30's! The snow was… Read More »
What rainy days are for…
Dressed in our gear, going for walks, splashing in puddles…. We love days like this! (L)
Wednesday Morning
I woke up again today at 6:30 a.m. wide awake! I get my coffee and a little computer time–so I'm not complaining. :) Today it is supposed to hit 80 degrees, the warmest yet this year. The girls and I will have to go out and take advantage and maybe play in the sprinklers or… Read More »
Flooding and bad weather…
The last thing we needed was a winter storm on top of everything else. While we in West Fargo seem to be safe (due to a diversion that was put in place years ago) ,there are lots of people that will lose so much due to the flooding that is predicted to happen. The red… Read More »
This weather is a tease!
Ok, so a high of 45 today is not bad. The other day we got up past 55…and now this afternoon and tomorrow we are expecting light snow…and then a high of 34 tomorrow! All not bad, and way better than negatives..LOL–but I am SO READY for warm weather. That high of 55 the other… Read More »
Yet another blizzard…
Seriously–winter needs to take a hike now! lol This was taken Tuesday! Click to view larger!
random stuff
So my blog needs a new and super cute look! Hopefully I can find the time to change it up! Today I'm gonna be super cleaning lady…my house needs it! What I really need to do is stop procrastinating…not with cleaning, but with other little projects I need to do. New Years resolution!? I think… Read More »


text: SPIDER-MAN: Marvel Boss Says Spidey Belongs in the MCU September 30, 2015 Get link Facebook Twitter Pinterest Google+ Email Marvel Studios can do "great things" with Spider-Man, says Kevin Feige in a recent interview. THR has the full story below. Kevin Feige: Spider-Man "Belongs" in the Marvel Cinematic Universe Spider-Man Get link Facebook Twitter Pinterest Google+ Email Comments Post a Comment


text:
Videology is an online video advertising platform that enables advertisers, agencies and publishers to eliminate waste and improve performance by connecting brands with specific audiences, while concentrating on the advertiser's objective.
TRACKINGSOFT, LLC is comprised of a team of dedicated, attentive and passionate professionals who have numerous years of experience in advanced ...
TidalTV is leading in Top 10K Sites, Top 100K Sites and Top 1M Sites.
TidalTV has better usage coverage in more websites categories. Including News & Media, Arts & Entertainment, Computer & Electronics, Shopping and 67 other categories.
TrackingSoft is leading in People & Society, Business & Industry, Games, Video Games and 47 other categories.
TidalTV is leading in most countries, including United States, United Kingdom, Russia, Canada and 87 other countries.
TrackingSoft is leading in Italy, Liechtenstein, Malawi, Nigeria and one other country.


text:
You're invited to experience an evening of Dance, Healing, and Divine Feminine Fun!
Every woman needs some Diva Time! A Divas Night out is your time to do something nice for yourself. Grab a few girlfriends and join us for a feminine fiesta like no other.
Tag Archive: lap dance
Divas Night Out ATL – Vixen Edition 10/22
You're invited to experience an evening of Dance, Healing, and Divine Feminine Fun!
ATL Spring Party Specials
January 2014 Special w/ Sweet Satisfaction
I'm your DIVA ON DEMAND
Monthly Girl's Night Social
Drop your inhibitions…Bring a comfortable pair of heels, man's oversized shirt and bottle of wine (or beverage of choice) and have a great time with us!! Beginning in June, Room to Move Studio and Soultry Fuzion will host a Girl's Night on the 3rd Friday of every month. Hang with the girls, learn a sexy routine …
Sweet Satisfaction
Exoticise Special Workshop
Spring 2012 – Chicago
Spring is here and its time to get Sandal and Sundress ready! Let's shed the winter insulation and SPRING into fabulousness! We have Pole Dancing & Tease-n-Tone on the Schedule so register today. Classes Begin the Week of April 2nd! Wednesday's 8p – 9p Fun Dance Fitness 1654 E 87th St Included in any membership …
Ms Fabulous
December Sun
Jaguar Rain
Live the Fabulous Life
Being Fabulous astounding, amazing, extraordinary, remarkable, incredible, astonishing, legendary, immense, unbelievable, breathtaking, phenomenal! A woman who gets it all done with grace, style, and ease! Part 1: Dancing STYLE: Seduction in Motion:The Art of Lap Dancing Lap Dancing is my absolute favorite form of Exotic Dance! It allows you to get up close and personal …


text:
International Garden Festival reveals designs for 2017
The international call for proposals invited designers to create "Playsages" in order to inspire today's young that outdoor play is | Read More
The international call for proposals invited designers to create "Playsages" in order to inspire today's young that outdoor play is | Read More
Last November we were proud to attend the opening ceremony of the Muslim Burial Ground Peace Garden at Horsell | Read More
What was once an abandoned, neglected lot full of towering un-finished concrete structures that served as an eye sore as | Read More
Appletons were appointed as part of a design team to prepare a package of work to construct an orangery, additional | Read More
Building on the community vision and strength held the keys to the successful revitalization of Regent Park, a historically marginalized | Read More
What makes a garden what it is? How effectively design a garden so that it can become a space with | Read More
The project was created to celebrate the 50th anniversary of the Constitution of Kuwait. Al Amiri Diwan, the government agency, | Read More
The Getty Salad Garden, an installation of organic heirloom vegetables and salad greens growing in graphically rendered raised beds, emerged | Read More
Philadelphia's hottest open air restaurant, the Independence Beer Garden (IBG) is located in the heart of historic Philadelphia. Spearheaded by | Read More
"Las Violetas" Garden was designed in 2013 in the Costa de la Luz region of Huelva, Spain. The garden is | Read More


text:
Refinery Equipment Surface Coating System for Tanks Pipeworks Pumping Equipment & Hydrocarbon Processing Machines
|FOB Price:
|US $1,000-10,000 / Piece
|Min. Order:
|1 Piece
|Min. Order
|FOB Price
|1 Piece
|US $1,000-10,000/ Piece
|Huangpu, China
|Transport Package:
|Wooden Case
|Payment Terms:
Request a custom order and have something just for you!Send Customized Request
- Model NO.: sx
- Certification: ISO9001
- Service Scope: Worldwide
- Specification: pending
- Method: Spray
- Substrate: All Kind of Basic Material
- Trademark: Sanxin
- Origin: Guangzhou, China
Thermal Spray Coating Solutions we provide are widely used in different industries for enhancing surface properties. It can be applied to automotive, aviation, chemical processing, health care, agriculture, construction, electronics, heavy machinery, marine & shipping, metal, mining, printing, rail / underground, textile, hydrocarbon processing, oil & gas, power generation, pulp & paper, water, additive manufacturing industries and so on.
What products we supply:
Electric arc spray coating machine seriesHVOF spraying coating equipment seriesPlasma spray coating system seriesSpaying torch / spraying gun seriesCoating material - pure metal / alloy wire-pure metal / alloy powderSpraying auxiliary devices such as spray robot arm, rotatorPeripheral equipment such as sand blasting box, air compressor, dust collector, spraying booth, dryer, high / medium frequency heating machine, quenching machine, chiller, etc.Coating performance testing devices such as metallurgical microscope, tensile testing machine, soft spray tester, hardness meter, roughness tester, thickness gaugeWorldwide coating processing services
We are happy to provide free guidance of coating processing and choosing equipment. If you are interested, please send us the info form and we will send you a thermal spray coating ppt and other free solution suggestion service.
Who are we:
20-year experience in thermal spray surface treatment field, specializing in manufacturing thermal spray equipment and providing cost-effective spray coating processing services.
We are qualified supplier with ISO recognition, providing professional, efficient, stable services to our customers. We never stop improving ourselves to be a reliable partner to the clients who are doing long-term, win-win business with us.
We supply large profit margin products for your market.
We do OEM.
Sample available.
We offer instant and free technical support.
We are looking for long-term overseas partnership We welcome import-export agencies / trading companies / distributors / to visit our factory.


text:
AUGUSTA, Ga. - Mr. Henry "Bostick" Chavous, II, 74, husband of Rachel Clark Chavous, entered into rest Sunday, August 12, 2007 at the residence after a battle with Bladder Cancer. Funeral services will be held Wednesday, August 15, 2007 at 11:00 a.m. in the Chapel of Chance & Hydrick Funeral Directors with Reverend Tracy Pressley officiating. Interment will follow in the Old Union Church Cemetery. Mr. Chavous was born in Augusta to the late Milton and Mary Broome Chavous. He was a Tractor Dealer for 49 years in the Augusta area and a U.S. Army veteran of the Korean conflict. He was a member of Pine Hill Baptist Church, VFW Post 205 and the Augusta Bowling Association Hall of Fame and bowled in the American Bowling Congress National Tournament for 39 consecutive years. Additional survivors include his son, Henry Bostick "Hank" Chavous, III and wife Kay; and his daughter, Mary Sarver and husband Ken all of Evans; brothers, Sonny Chavous and his wife Jewel and B.B. Chavous and his wife Peggy all of Augusta; four grandchildren, Henry Bostick "HB" Chavous, IV, Brooke Sarver, Kaylyn Chavous, and Blake Sarver. Active Pallbearers will be Alan Birchfield, Morgan Jones, Pope Turner, Mike Graham, Scott Davis, and Bill Bonnette. Honorary Pallbearers will be the Augusta Bowling Association Hall of Fame members. Memorials may be made to the Fleming Baptist Church Building Fund, 3027 Peach Orchard Road, Augusta, Ga. 30906. The family will receive friends Tuesday evening from 6:00 until 8:00 p.m. at the funeral home. Chance & Hydrick Funeral Directors, 2502 Richmond Hill Road, Augusta, Georgia 30906. Sign the guestbook at AugustaChronicle.com
The Augusta Chronicle-August 14, 2007


text:
Visit us @OTC Houston
From 1-4 May we will be present at the OTC Exchibiton&Conference in Houston. You can find us in the Holland Pavilion, booth 1629-2
From 1-4 May we will be present at the OTC Exchibiton&Conference in Houston. You can find us in the Holland Pavilion, booth 1629-2
Kenz Cranes recently unveiled a new design for an advanced and multifunctional offshore gangway construction with an X-wing foundation. The design of the fully motion compensated gangway will be used for personnel transfer to wind turbines. The X-wing allows to keep maximum deck space on a vessel and brings an advantage for existing vessels in case of replacement, the company said. Because of this appliance a 360⁰ reach can be realized.The DNV GL-certified gangway can also be used for full motion compensated offshore lifts with crane hook attachment.
Kenz Figee has a new owner/shareholder: MeeMaken BV. MeeMaken BV is an active participation company with a large worldwide network and a strong portfolio comprising service companies to the offshore energy business. The former senior management at Mammoet, Roderik van Seumeren and Natasja Sesink will be the new owners of Kenz Figee as partners of MeeMaken BV. Kenz Figee stated that they are very happy with this takeover not only because of the long term vision of MeeMaken BV but also because they believe in the synergy with the other companies within the group. Robert de Rijcke, Commercial Director of Kenz Figee Group: "We believe that MeeMaken BV can lift us to the next professional level.
Kenz Cranes have been awarded with a contract for the design and production of two knuckle boom cranes for Heerema Marine Contractors. These will be replacing the current knuckle boom cranes on the deepwater construction vessel Aegir. Kenz Cranes will design a 200t active heave compensated knuckle boom crane with a deep water winch suitable for 3300 mtr water depth and an outreach of 50 mtr! The other knuckle boom is a 50t crane with an outreach of 42 mtr.
Following its successful installation and commissioning at the Jurong Shipyard in Singapore, two EHC 100/4000 boom hoist cranes are handed over to Seadrill for the West Rigel semi-submersible.
Specializing in custom made and fit-for-purpose hoisting and lifting equipment, Kenz Cranes designed and built the two cranes in the Netherlands according to the highest Norwegian standards DNV 2.22/Norsok R002 and EN13852-1. As Kenz Cranes is one of the few suppliers able to deliver according to these standards, the company is chosen as manufacturer of the cranes which will be operational on the Norwegian continental shelf.
The two West Rigel Kenz cranes have been assembled at Jurong Shipyard where they have been successfully installed and load tested under supervision of DNV on the West Rigel drilling rig. The Petroleum Safety Authority (PSA) subsequently released the cranes for use.


text:
All of a sudden Delhi has become the most loved and visited travel destination in India. Well a lot has to do with the films, serials and travel magazines which have been capturing and covering the beautiful city .
And why would not be. After all, it is the Capital of our country. It is also the historical city of our country. Delhi looks very green, very clean and very planned or rather organised.
There are few problems definitely. But why look at the negative side.
Being an ardent fan of Historical Places, I found Delhi an archeological wonder. I am happy that many of the monuments are being restored and sad that some have been devastated before something could be done about it.
Never the less, Qutb Minar which was originally constructed by Qutb-Ud-Din-Aibak who was the first Muslim ruler to mark his presence in the North Of India , and stands tall right in the center of the city surrounded by lush green garden. The place is always crowded by tourists both local and foreign.
Mostly constructed in sandstone, the rest of information about the UNESCO World Heritage site can be found here :
When I visit any historical place or monument, I like to take the picture of monument as it is without any human presence. But is that really possible ? No,Its absolutely impossible.
Taking one for Qutb Minar was almost impossible as people pass through every 5 seconds and that disturbed my focus, I found it really hard to take a nice shot which I would be satisfied with. At the same time, its difficult to capture the entire Minar in one frame.
The intricate work on the zharokha (window) and the light passing through it is breathtaking. Every window has a differnt pattern and we cannot find any goemetrical error.
Here is a picture of the Mosque
And now a picture of the perfect round top of the Tomb. Wonder how could craftsmen with minimal facilities build a perfect tomb when craftsmen in the current times can't even build a perfect two bedroom hall kitchen.
Some more pictures. Love that little door on the top.
Oh finally I did a good shot of the entire Minar in one frame without anybody's presence. Love it.


text:
About Me
I got started Cosplaying - when i went to my first proper con in Leeds. I am planning to make my 2nd ever cosplay - which is Hinamori Amu, so wish me luck with that.
My proudest moment was when I was at the Anime lineup and we started singing Hare Hare Yukai - it was fun, if you were there in '08 <3
Contact Information
My msn be : firstname.lastname@example.com ( Let me know who you are please >:))Website : http://www.facebook.com/charlotte.cruel


text:
These are the last sets of postcards I designed in 2011. The unobtrusive text on the back is outdated, which is why I'm offering these sets for a discounted price.
A set of 6 colorful postcards featuring pictures taken by yours truly at the beach of an old gas pump, derelict piano and other awesome objects I found. I'm a Lomographer and use analogue photography. The outcome is very surprising at times!
These pictures where shot on a rainy day at the beach in Zandvoort with a Lomo Diana and a Diana Mini. The 2 full shots of the pump are shot with a method so the image also goes onto the 'sprockets' of a roll of film. This is how I achieved the little holes in the top and bottom, the red and yellow stripes are normally used by machines to process the film.
In this set:
2 cards of a old gas pump and a surfboard
2 cards featuring a close up of the inner workings of the pump
1 card featuring a double picture of the lettering on the wall
1 card featuring an old weathered piano
These cards are perfect as postcards for post crossing or a birthday, or just because you want to send your aunt a cool card every now and then. The back of the cards is purposely as blank as possible. This way you could also use it as a little love note to your partner or have the card accompany a great gift for a friend!
The cards are printed on 350gsm, sustainably sourced paper with a glossy laminate finish on the image side. The other side is lightly coated with a satin finish. At the bottom of the back there is a unobtrusive line of text with copyright stuffs.


text:
Responsibilities: The Assistant Director of Athletic Communications will play a key role in publicizing Merrimack's 24-sport athletics program, which competes mainly in the Division II Northeast-10 Conference, as well as well as men's and women's ice hockey competing in Division I Hockey East. The successful candidate will be able to deliver content to a broad base of constituents in a variety of formats. Extensive evening, weekend and holiday work is required.
Key responsibilities include:
Contributing to the Athletics department website (www.MerrimackAthletics.com) and all social media platforms, with content type ranging from written, graphic design and multimedia/video;
Being directly responsible for ALL publicity efforts in select sports (to be assigned), including writing, editing and distributing all press releases; social media management for multiple accounts across a variety of platforms; editing videos (season previews, game highlights, etc.); and designing of game day programs, flyers and similar materials;
Management of student employees and game-day event staff for all home games for assigned sports, as well as home games for other sports as requested (i.e., football & men's ice hockey);
Assigning and supervising student staff to assist with in-game responsibilities (scoreboard, public address, statistics, etc.), in-game updating of social media platforms and score reporting;
Communicating with and soliciting media for event coverage and feature stories on Merrimack College student-athletes, teams, and other department milestones and accomplishments;
Planning and implementing historical archiving, as well as maintenance of photography database;
Completing conference, regional and national award applications to recognize coaches and student-athletes from assigned teams and programs
Compiling, disseminating, and maintaining sports statistics for assigned teams, including serving as official scorekeeper for all home games;
Assisting with the setup, live production and breakdown of webcast equipment;
Travel with teams as necessary, primarily for postseason contests (other travel may be required);
Other duties as assigned and necessary;
Salary Information: $2,000/month for nine months beginning on or around August 15, 2017. Position does not include benefits or housing/meal stipend. Opportunity for one-year renewal is at the discretion of the Assistant Athletic Director for Communications.
To Apply: Please apply online with resume, writing samples, and three references.
Merrimack College is an Equal Opportunity Employer.
Preferred Qualifications:


text:
A beautiful Aquamarine the color of the sea is set into a warm 14k Gold prong setting to let in light all around the stone. Combined with a organic band. This ring was hand carved and created in 100% recycled 14k Gold.
Perfect for an alternative engagement or everyday ring.
> Metal: Solid Eco Friendly 14k Gold
> Band Approx: 1.6 - 1.7mm
> Stone: Aquamarine .25ct {4mm}
> Grade: AA
> Mohs Hardness: 7.5 - 8
> Sizes: 1/4 Sizes Available
Fabrication Time: Custom made per order using reclaimed metals. Please allow 3 - 4 weeks from date of order to fabricate.
Handmade with Love in Las Vegas.
Beautiful pale blue grade AA Aquamarines are set into my wax carved prong settings making perfect everyday...
Inky Black Rose Cut Diamonds are set into my hand carved and cast setting of...
Sold Out
A gorgeous 2.03ct Blue/Purple Spinel is cradled in a 3 prong 14k Gold wax carved ring. The color...
I love clean and simple rings and with a bit of texture so I made...


text:
( 1958 1959 1960 1961 1962 1963 1964 )
2,421 Classics and Exotics For Sale Today - Buy One From Us
For Sale in our 16 locations - St. Louis, Louisville, Chicago, Detroit, Indianapolis, Tampa, Orlando, Houston, Ft. Lauderdale, Nashville, Dallas, Milwaukee, Atlanta, Philadelphia, Denver, Scottsdale.
#507-FTL Ft. Lauderdale
Gateway Classic Cars of Fort Lauderdale is proud to present this modernized classic, 1946 Ford Deluxe. ... More
#446-FTL Ft. Lauderdale
For sale in our Fort Lauderdale showroom is this excellent 1976 Chevrolet Corvette. Why is this Corvette ... More


text:
PAINS Vortex script
One of the great features of the latest version of Vortex (> build 29622) is the ability to script multiple sub-structure searches using SMARTS. There are many occasions when this sort of feature is useful, if you want to flag molecules that contain reactive functional groups, toxicophores, or PAINS functional groups that have been shown to interfere with high-throughput screens. Vortex tutorial 24 described how to do this multi-substructure searching.
There have now been a couple of new publications describing the identification of false positives in high-throughput screening campaigns in which the binding of glutathione S-transferase (GST) to glutathione (GSH) is used for detection of GST-tagged proteins.
- Identification of Small-Molecule Frequent Hitters of Glutathione S-Transferase–Glutathione Interaction DOI
- Identification of Small-Molecule Frequent Hitters from AlphaScreen High-Throughput Screens DOI
There have also been some suggestions as to how some of the motifs might be interfering with the assay, as shown below.
I've now added the additional structural motif definitions taking the total to 550 SMARTS definitions. It is perhaps worth mentioning that some of these motifs may not be an issue when using alternative screening technologies, but it may be very worthwhile to double check any molecules flagged by this script before committing significant resources to follow up.
This comment in Nature is perhaps worth noting
Academic researchers, drawn into drug discovery without appropriate guidance, are doing muddled science. When biologists identify a protein that contributes to disease, they hunt for chemical compounds that bind to the protein and affect its activity. A typical assay screens many thousands of chemicals. 'Hits' become tools for studying the disease, as well as starting points in the hunt for treatments. These molecules — pan-assay interference compounds, or PAINS — have defined structures, covering several classes of compound. But biologists and inexperienced chemists rarely recognize them. Instead, such compounds are reported as having promising activity against a wide variety of proteins. Time and research money are consequently wasted in attempts to optimize the activity of these compounds. Chemists make multiple analogues of apparent hits hoping to improve the 'fit' between protein and compound. Meanwhile, true hits with real potential are neglected.
I've updated the tutorial and the scripts for download.
A workflow for docking/virtual screening part 2
In the previous workflow I described docking a set of ligands with known activity into a target protein, in this workflow we will be using a set of ligands from the ZINC dataset searching for novel ligands. Once docked the workflow moves on to finding vendors and selecting subsets for purchase.
Weekend Reading
A couple of things for your weekend reading ;-)
What makes Python super popular
Machine Learning in Python tutorial
A workflow for docking/virtual screening (updated)
Whilst high-throughput screening (HTS) has been the starting point for many successful drug discovery programs the cost of screening, the lack of access to a large diverse sample collection, or the low throughput of the primary assay may preclude HTS as a starting point and identification of a smaller selection of compounds with a higher probability of being a hit may be desired. Directed or Virtual screening is a computational technique used in drug discovery research designed to identify potential hits for evaluation in primary assays. It involves the rapid in silico assessment of large libraries of chemical structures in order to identify those structures that most likely to be active against a drug target. The in silico screen can be based on known ligand similarity or based on docking ligands into the desired binding site.
In this workflow I'll be looking at using docking to identify potential hits.
I've updated the description to give more information about preparing the target protein.
A Functional Group Count Script
I recently wrote a review of Reaction Workflows, a web-based tool that allow users to build workflows from nodes that provide inputs and outputs or perform actions, including ones to perform reaction-, scaffold-, and transform-based enumeration, and it is all done within a web browser interface using drag and drop. Whilst you can draw input structures one of the real strengths is the ability to import pre-categorised reagent files e.g.Acid Chlorides or secondary amines. This script is intended to help with this within Vortex.
This script is a variation of the high performance sub-structure search scripts described previously, however instead of simply flagging the presence (or absence) of a SMARTS query we provide a count of the number of times a SMARTS query is identified within a molecule. The script uses all available cores and is thus capable of running multiple queries in parallel and can thus handle very large datasets. The script currently contains around 70 different SMARTS queries for both functional groups and atom counts and I'd be happy to add any suggestions.
RDKit and Python3
Greg Landrum posted the following to the RDKit users and since a couple of the Jupyter Notebooks I've published make extensive use of RDKit I thought I'd flag it.
As many of you are no doubt aware, the Python community plans to discontinue support for Python 2 in 2020. A growing number of projects in the Scientific Python stack are making the same transition and have made that explicit here: http://www.python3statement.org/
I will be adding the RDKit to this list. The RDKit will switch to support only Python 3 by 2020. At some point between now and then - likely during the 2018.09 release cycle - we will create a maintenance branch for Python 2 that will continue to get bug fixes but will no longer have new Python features added. This branch will be maintained, and we will keep doing Python 2 builds, until 2020 when official Python 2 support ends.
Additionally, starting during the 2018.03 release cycle we will accept contributions for new features that are not compatible with Python 2 as long as those features are implemented in such a way that they don't break existing Python 2 code (more on this later). This will allow members of the RDKit community who have made the switch to Python 3 to start making use of the new features of the language in their RDKit contributions.
If you have not made the switch yet to Python 3: please read the web page I link to above and take a look at the list of projects that have committed to transition. The switch from Python 2 to Python 3 isn't always easy, but it's not getting any easier with time and you have a few years to complete it. There are a lot of online resources available to help.
Best Regards, -greg
The list of projects that will be making the transition so far includes; IPython, Jupyter notebook, pandas, Matplotlib SymPy, Astropy, Software Carpentry, SunPy xonsh, scikit-bio, PyStan, Axelrod osBrain, PyMeasure, rpy2, PyMC3, FEniCS, An Introduction to Applied Bioinformatics, music21, QIIME, Altair, gala, cual-id, CIS
Getting PDB information
A while back I published two scripts that use UniChem a web resource provided by the EBI, a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between multiple databases.
Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S. and Overington, J.P. UniChem: A Unified Chemical Structure Cross-Referencing and Identifier Tracking System. Journal of Cheminformatics 2013, 5:3 (January 2013). DOI: http://dx.doi.org/10.1186/1758-2946-5-3
The first script uses the ChEMBL ID to search for other identifiers, the second script allows more flexible searching using any of the identifiers available within UnicChem. One of the identifiers returned is from the PDBe (Protein Data Bank Europe) and represents the ID of the ligand in the PDB. Whilst this is interesting it would also be very useful to have the identity of the crystal structures that contain the ligand. Fortunately PBDe provide a series of web services that can be used to interrogate the database, together with a really useful page to help build the calls.
Full details of the script are here..
There is a comprehensive listing of scripts, tips, jupyter notebooks etc here.
Psi4 1.1: An Open-Source Electronic Structure Program
A recent paper describes Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability DOI
Psi4 is an ab initio electronic structure program providing methods such as Hartree–Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools.
Psi4 1.1 can be downloaded from here with versions supporting Python 2.7, 3.5 and 3.6.
Note the installation instructions for Mac: Install XCode via the App Store, Make sure you open XCode and accept the license agreement after you install.
Conformer generation
The generation of multiple conformations is an important step in a number of operations from input to ab initio calculations to providing input files for docking studies. A recent paper compared seven freely available conformer ensemble generators: Balloon (two different algorithms), the RDKit standard conformer ensemble generator, the Experimental-Torsion basic Knowledge Distance Geometry (ETKDG) algorithm, Confab, Frog2 and Multiconf-DOCK DOI, and also provided a dataset of ligand conformations taken from the PDB.
A recent twitter discussion involving Greg Landrum and David Koes prompted Greg to publish a blog post describing conformation generation within RDKit. The post compares using distance geometry to select diverse conformations versus an approach that combines the distance geometry approach with experimental torsion-angle preferences obtained from small-molecule crystallographic data (ETKDG). He also looks at the impact of force-field minimisation.
A really interesting read with code provided.
aRMSD: A Comprehensive Tool for Structural Analysis
aRMSD is an open toolbox for structural comparison between two molecules with various capabilities to explore different aspects of structural similarity and diversity. Crystallographic data provided from cif files is fully supported and the results can be rendered with the help of the vtk package.
A. Wagner, H.-J. Himmel, J. Chem. Inf. Model, 2017, 57, 428-438 DOI
Working with MOL2 Structures in DataFrames
A great tutorial describing how to use 'Biopandas' MOL2 DataFrames to analyze molecules conveniently.
The Tripos MOL2 format is a common format for working with small molecules.
A webinar demonstrating using Jupyter, the free iPython notebook
This is a recording of the March 2017 Global Health Compound Design meeting. A webinar demonstrating using Jupyter, the free iPython notebook.
How to get started
Accessing Open Source Malaria data
Calculating physicochemical properties and plotting
Predicting AMES activity.
Predicting AMES activity Jupyter Notebook
I've been experimenting with the use of Jupyter Notebooks (aka iPython Notebooks) as an electronic lab notebook but also a means to share computational models. The aim would be to see how easy it would be to share a model together with the associated training data together with an explanation of how the model was built and how it can be used for novel molecules.
The Ames test is a widely employed method that uses bacteria to test whether a given chemical can cause mutations in the DNA of the test organism. More formally, it is a biological assay to assess the mutagenic potential of chemical compounds. PNAS. 70 (8): 2281–5. doi
In this first notebook a random forest model to predict AMES activity is described….
Molecular Design Toolkit
The Molecular Design Toolkit is an open source environment that aims to seamlessly integrated molecular simulation, visualization and cloud computing. It offers access to a large and still-growing set of computational modelling methods with a science-focused Python API, that can be easily installed using PIP. It is ideal for building into a Jupyter notebook. The API is designed to handle both small molecules and large bimolecular structures, molecular mechanics and QM calculations.
There are a series of Youtube videos describing some of the functionality in more details, starting with this introduction.
Several ways of scripting Name to Structure
Too often I come across datasets that Chemical names or identifiers but no actual molecular structure, recently Dan at Dotmatics suggested I look at OPSIN. There are also several web services for converting names to structure and I've highlighted a couple of options here and described three scripts that allow them to be used from within Vortex.
There are many more scripts on the Hints and Tutorials Page.
Scripting Vortex 34, analysis of catagorical information
I often need to tag individual molecules within a dataset with a specific property, perhaps the results of clustering algorithms, the results of PAINS filtering, or Liver toxicity filters. Alternatively if you have a drug discovery project with multiple chemotypes you might want to tag particular groups of compounds as belonging to a named series to aid analysis.
A question that might then arise is "How many molecules belong to each category?". Whilst you can see the numbers in the sidebar there is not an easy way to export the results.
Hopefully this script can help.
RDkit and Conda install of postgres cartridge on Mac OS
There has been an interesting discussion about installing rdkit-postgresql95 on Mac OS X on the rdkit mailing list and I thought it might be of wider interest.
Here's the resolution of the difficulties I was having installing rdkit-postgresql95 on Mac OS X. The problem turned out to be that the package originally posted used Py3.5, and I'm still using 2.7. I may change to 3.5 at some point, but Greg was kind enough to add a 2.7 version of the package.
So, the following invocations work to set up rdkit with the cartridge in a new env on Mac OS X. I'm on El Capitan, by the way, and for clarity, I've not tested the installation, but only checked that it completed successfully.
conda create -n rdk1 -c rdkit rdkit
. activate rdk1
conda install -c greglandrum rdkit-postgresql95
(The last command also installs postgresql 9.5.4-0.)
JupyterLab: the next generation of the Jupyter Notebook
An interesting development on the Jupyter Blog
It's been a long time in the making, but today we want to start engaging our community with an early (pre-alpha) release of the next generation of the Jupyter Notebook application, which we are calling JupyterLab.
Full presentation is here
Accessing ZINC supplier information
ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 100 million purchasable compounds in ready-to-dock, 3D formats. Sterling and Irwin, J. Chem. Inf. Model, 2015. This is an invaluable resource for any type of virtual screening or for anyone looking to create a physical screening or fragment collection.
Once you have done the virtual screening you will rapidly realise that the really time-consuming a tedious part now lies ahead. Finding out which vendors stock a particular molecule and then ordering them. Looking up the vendor details for individual compounds is extremely tedious and so this Vortex script may be very useful.
Many more scripts, iPython notebooks and tutorials can be found here.
17th annual KDnuggets Software Data Analysis Poll
The results of the annual data analysis poll are in and show some interesting trends, in particular the dramatic increase in Python use.
R remains the leading tool, with 49% share (up from 46.9% in 2015), but Python usage grew faster and it almost caught up to R with 45.8% share (up from 30.3%).
Actually looking down the list I notice there is also an entry for scikit-learn, which is Python based, and if you add that in Python is now the most commonly used data analysis tool.
There was a 10% drop in the use of KNIME, and a 36% drop in the use of TIBCO Spotfire two products used in cheminformatics.
In terms of programming languages Python is by far the most extensively used.
|45.8% share (was 30.3%)
|51% increase
|16.8% share (was 14.1%)
|19% increase
|Unix shell/awk/gawk
|10.4% share (was 8.0%)
|30% increase
|7.3% share (was 9.4%)
|23% decrease
|Other programming languages
|6.8% share (was 5.1%)
|34.1% increase
In the Big Data area Hadoop (22.1%) and Spark (21.6%) dominate.
There is a listing of data analysis tools for MacOSX here.
I came across the jupyter-docker-pymol recently and thought I'd give it a mention. It is a Container-based installation of PyMol, with interaction through the browser via ipymol and Jupyter notebook (based on jupyter/notebook).
This project uses PyMol 126.96.36.199 and Python 3
RDkit updated
RDkit has been updated .
If you used home-brew to install RDkit as described here updating is very simple
brew update
brew upgrade rdkit
You can check which version you have installed using
MacPro> python
Python 2.7.11 (default, Dec 23 2015, 16:11:50)
[GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import rdBase
>>> print rdBase.rdkitVersion
Dealing with Greek characters in column names
This is just a very quick tip when dealing with Greek characters in Vortex column names when creating a script. It may be obvious to many but I struggled for several hours before finding the problem and a solution
MCPB.py: A Python Based Metal Center Parameter Builder
MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach.
Pengfei Li and Kenneth M. Merz, Jr., "MCPB.py: A Python Based Metal Center Parameter Builder." J. Chem. Inf. Model., 2016, Accepted, DOI.
There is an excellent and very detailed online page describing the use of MCPB.py http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm.
Flexible UniChem Search
UniChem is a web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between multiple databases. Currently the UniChem contains data from 27 different data sources. Currently UniChem provides links to 108,941,995 structures.
Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S. and Overington, J.P. UniChem: A Unified Chemical Structure Cross-Referencing and Identifier Tracking System. Journal of Cheminformatics 2013, 5:3 (January 2013). DOI: http://dx.doi.org/10.1186/1758-2946-5-3
The previous script showed how to search using ChEMBLID, however one of the attractions of UniChem is that you can search with any molecule identifier if you know the corresponding datasource. This script allows the user to use any molecule identifiers and then search a specified datasource using a common web service.
Getting UniChem data from ChEMBL
UniChem is a web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between multiple databases. Currently the UniChem contains data from 27 different data sources. Currently UniChem provides links to 108,941,995 structures.
Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S. and Overington, J.P. UniChem: A Unified Chemical Structure Cross-Referencing and Identifier Tracking System. Journal of Cheminformatics 2013, 5:3 (January 2013). DOI: http://dx.doi.org/10.1186/1758-2946-5-3
ChEMBL also provide a RESTful Web service that users can use to retrieve data from the UniChem database in a programmatic fashion.
Flagging potential aggregators in Vortex
Promiscuous inhibition caused by small molecule aggregation is a major source of false positive results in high-throughput screening. A recent particularly valuable publication, Irwin, Duan, Torosyan, Doak, Ziebart, Sterling, Tumanian and Shoichet, J Med Chem, 2015, 58(1 7), 7076-7087 DOI, has collated over 12,000 organic molecules known to act as aggregators at concentrations used in screening campaigns, and provides a resource Aggregation Advisor that can be used to try and predict possible false positives. However in many instances it would be unwise to submit proprietary information to the public web service. Potential aggregators are flagged based on calculated LogP >3 and/or similarity >0.85 to a known aggregator (using path based fingerprint) this script calculates xLogP using the algorithm provided by Dotmatics and then uses OpenBabel fast search to calculate the closest similarity to a known aggregator.
Full details of the Vortex script are here.
LSH-based similarity search in MongoDB is faster than postgres cartridge
There is a great blog article on ChEMBL-og, describing their work evaluating chemical structure based searching in MongoDB. MongoDB is a NoSQL database designed for scalability and performance that is attracting a lot of interest at the moment.
The article does a great job in explaining the logic behind improving the search performance.
They also provide an iPython notebook so you can try it yourself.
Finding Duplicate structures
It is always interesting to note which scripts attract the most attention, often it is scripts that aid with relatively simple tasks. Among the Applescripts it is the script to simply print the clipboard.
Recently I wrote a script to remove duplicate structures from within Vortex
When working with multiple data sets of molecules, particularly if combining them from multiple sources, one of the most common tasks is removal of duplicates. This can be a time-consuming and error prone process if carried out manually and this script should hopefully make this a much easier task.
This seems to have attracted interest but I got a comment that it "works fine but is slow for larger data sets". So I've been looking at improving performance.
In order to test the performance I took around 150,000 random structures from ChEMBL and then duplicated 0.01% to give a test set of 160,146 molecules. The original version of the script took 95 mins, using the same test set, version 2 of the script took less than 3 mins! This increase in performance means that it is now practical to use the script on much larger datasets.
You can read full details and download it here.
There are many more Hints, scripts and tutorials here.
Polyphony is an open source software suite written in python. Its purpose is the superimposition free analysis and comparison of multiple 3D structures of the same or closely related protein molecules.
Absolute Requirements
python 2.6 or later, scipy, numpy, Biopython, especially the Bio.PDB module
Highly recommended
All following documentation assumes that you have these installed.
ipython , for interactive python scripting, matplotlib, for graph plotting, PyMOL, for interactive 3D visualisation. Open source version available on SourceForge
William R Pitt, Rinaldo W Montalvão and Tom L Blundell, BMC Bioinformatics, 2014, 15:324 doi
ChEMBL python update.
Excellent blog post on the ChEMBL python update.
Accessing Open Source Malaria Data using an iPython Notebook
The Open Source Malaria project is trying a different approach to curing malaria. Guided by open source principles, everything is open and anyone can contribute. To date a lot of people around the world have made contributions and the project is at a very exciting stage. Whilst everyone can see the compounds that have been made and the biological data, it is often spread over multiple web pages and can be tricky to link molecule with identifier with data. Over the last couple of months a significant effort has been put into populating a spreadsheet with all the information.
I've recently published a Vortex script to access the information, I've now published an iPython notebook that also shows how to import the data. Why not give it a try and then contribute your findings and suggestions to the Open Source Malaria project.
Script to remove duplicates in Vortex
When working with multiple data sets of molecules, particularly if combining them from multiple sources, one of the most common tasks is removal of duplicates. This can be a time-consuming and error prone process if carried out manually and this script should hopefully make this a much easier task.
There are many more Hints, scripts and tutorials here.
Installing Open Drug Discovery Toolkit (ODDT)
A recent paper in J Cheminformatics described Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field DOI a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. Open Drug Discovery Toolkit is released on a permissive 3-clause BSD license for both academic and industrial use. ODDT's source code, additional examples and documentation are available on GitHub.
To install ODDT on a Mac you first need to install the appropriate toolkits, the easiest way is to use Homebrew, I've written a page detailing how to do this here.
Once installed you can install ODDT using PIP as described here.
Poll on data analysis tools
The results of the 16th annual KDnuggets Software Poll on data analysis tools is in.
The top 10 tools by share of users were
R, 46.9% share ( 38.5% in 2014, 37% in 2013)
RapidMiner, 31.5% ( 44.2% in 2014, 39% in 2013)
SQL, 30.9% ( 25.3% in 2014, NA in 2013)
Python, 30.3% ( 19.5% in 2014, 13% in 2013)
Excel, 22.9% ( 25.8% in 2014, 28% in 2013)
KNIME, 20.0% ( 15.0% in 2014, 6% in 2013)
Hadoop, 18.4% ( 12.7% in 2014, 9% in 2013)
Tableau, 12.4% ( 9.1% in 2014, NA 2013)
SAS, 11.3 (10.9% in 2014, 10.7% in 2013)
Spark, 11.3% ( 2.6% in 2014, NA in 2013)
The results very much reflect my own interactions, whilst R has a significant installed user base and of course a vast repository of open source packages, Python seems to be gaining traction. Certainly in part because Python seems to have become the lingua franca for scientific computing.
I've always thought of KNIME and Tableau as excellent tools for implementing workflows but looking at recent iterations it is clear there is now greater emphasis on interactive analysis.
There is a listing of data analysis tools for Mac OS X here.
Scripting Vortex 25
Whilst most of the Vortex scripts mentioned on this site to date involve chemical structures we should not forget that Vortex is an excellent general data analytics tool and the data set does not have to include any molecular structures. Recently I was asked about the number of publications associated with a particular potential therapeutic target and it struck me that Vortex might actually be an excellent tool to investigate this.
PYMOL under Yosemite
Reading through the discussion on Scientific Applications under Yosemite it seems some people are having problems with PYMOL, I thought I'd mention that installation of PYMOL using Homebrew is included on the page describing how to set up a Mac for Cheminformatics. The page also describes how to install a wide range of other useful tools.
Substructure searching very large compound collections.
I described the use of the ability to script in Vortex multiple sub-structure searches using SMARTS. There are many occasions when this sort of feature is useful, if you want to flag molecules that contain reactive functional groups, toxicophores, or PAINS functional groups that have been shown to interfere with a variety of screens. Whilst the script worked fine it was rather slow for larger datasets, in the latest tutorial you can see how to take advantage of some of the latest features in Vortex to substantially improve search speeds allowing searching of 70 million compound collections on a desktop.
Scripting Vortex 24:- Substructure searching very large compound collections.
There are many more scripts listed on the Hints and Tutorials Page.
I must admit I'm a big fan of BBEdit for all my text editing, Markdown and python programming but I still keep an eye out for interesting alternatives. I was recently sent a link to PyCharm a Python IDE. PyCharm's code editor provides support for Python, JavaScript, CoffeeScript, TypeScript, CSS, and a number of other languages. What caught my eye was the recently added support for iPython notebooks, with PyCharm 4 you can perform all the usual IPython Notebook actions with *.ipynb files. Everything you're used to doing with the ordinary IPython Notebook is now supported inside PyCharm.
Another very useful features for scientific programming is the NumPy array viewer to easily get a graphical view of a NumPy array and support for matplotlib.
There is a really comprehensive support section that includes demos and screencasts .
Vortex scripts to access ChEMBL
ChEMBL is a manually curated chemical database of bioactive molecules . It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory (EMBL), based at the Wellcome Trust Genome Campus, Hinxton, UK. The database currently contains over 1.4 million unique structures with the associated activity at 10,579 different targets. It also acts as a repository for Open Access primary screening and medicinal chemistry data directed at neglected diseases.
Whilst the database can be downloaded, the data can also be accessed via a web interface (shown below) and a series of web services, these Vortex scripts show how it is possible to pull data from ChEMBL into Vortex.
As usual I've written it as a tutorial to try and offer some explanation how the script works, Scripting Vortex 23:- Accessing ChEMBL using Web Services
I think this rather nicely shows the power of web services and json.
There is a list of other Vortex scripts on the Hints and Tutorials page
Scripting Vortex
One of the really neat features of the latest version of Vortex (> build 29622) is the ability to script multiple sub-structure searches using SMARTS. There are many occasions when this sort of feature is useful, if you want to flag molecules that contain reactive functional groups, toxicophores, or PAINS functional groups that have been shown to interfere with a variety of screens. Alternatively if you have a drug discovery project with multiple chemotypes you might want to tag particular groups of compounds as belonging to a named series to aid analysis.
The latest Vortex tutorial/script shows how to do this.
Cheminformatics iPython notebook
George Papadatos, from the ChEMBL group, has produced a superb iPython notebook tutorial demonstrating the use of RDkit.
Sage mathematics software
Sage is a Python based free open-source mathematics software system licensed under the GPL. It builds on top of nearly 100 open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R to provide a common unified interface, either as a notebook in a web browser or the command line.
In addition to a local installation it is also possible to use SageMathCloud a free service with support from the University of Washington.
I've added Sage to the list of data analysis tools for Mac OS X.
I've just added Computable to the mobile science site. Computable brings iPython and SciPy to the iPad allowing to create, edit and run iPython notebooks on your iPad. Computable comes with full-featured SciPy stack, Numpy, SciPy, SymPy, Pandas, Matplotlib. The free download includes a series of 32 example notebooks and lectures that allow you to evaluate the application. To create or edit your own notebooks you will have to make an in app purchase to unlock the full feature set ($9.99).
Learning Python
It seems that Python is becoming the preferred language for scripting in science and I wrote a getting started page for Chemists and several people have pointed out a couple of resources that may be useful in particular Roaslind.
Rosalind is a platform for learning bioinformatics and programming through problem solving.
I looks like an excellent starting point for newcomers and more experienced programmers, whilst focussed on bioinformatics the exercises are useful for all disciplines.
For chemists chempython looks to be a very useful resource.
Vortex script to classify acid, base, neutral
I've written several Vortex scripts that use external tools to calculate physicochemical properties including the use of ChemAxon (e.g. charge, pKa, logP, logD). However I often need to simply classify molecules as acid, base, neutral or zwitterion, so I've updated the script to create another column containing a text annotation.
Scripting Vortex 21, displayling web pages
Well things can change quickly at times, in the last tutorial I wrote..
Vortex has a limited capacity to render HTML, it is however a very limited ability so there is no support for javascript or CSS but you can introduce a number of useful extra features.
If you download the latest daily build of Vortex from the Dotmatics Support site there is a version that comes bundles with Java 8, if you download this version are a host of new options for displaying plots. In particular you can now display web pages, follow links on pages, and there is support for javascript.
In Scripting Vortex 21 there is a demonstration of this feature and an example script that uses SMARTCyp to predict sites of metabolism.
There are many more scripts on the Hints and Tutorials Page.
Scripting Vortex 19 Updated
This is another Vortex script, this one is used to implement a central nervous system penetration (CNS) algorithm described in the literature.
It is clear from many publications that a number of physicochemical properties influence central nervous system (CNS) penetration and it is often possible to play off one property against another in an effort to improve CNS penetration. An interesting paper from Wagner et al Moving beyond Rules: The Development of a Central Nervous System Multiparameter Optimization (CNS MPO) Approach To Enable Alignment of Druglike Properties describes an algorithm to score compounds with respect to CNS penetration.
The CNS MPO score was built based on six fundamental physicochemical properties: ClogP, ClogD, MW, TPSA, HBD, and pKa each weighted from 0 to 1.0
One of the popular features in Vortex is to colour code columns, this is done automatically but sometimes you want to customise the colouring. For example in one set of values smaller values might be better, in another columns (perhaps an off-target activity) larger numbers might be better. Chatting to Sune Askjær, the author of the Unichem Script, it seemed that this might be a nice addition to this script.
Scripting Vortex 19
This is another Vortex script, this one is used to implement a central nervous system penetration (CNS) algorithm described in the literature.
It is clear from many publications that a number of physicochemical properties influence central nervous system (CNS) penetration and it is often possible to play off one property against another in an effort to improve CNS penetration. An interesting paper from Wagner et al Moving beyond Rules: The Development of a Central Nervous System Multiparameter Optimization (CNS MPO) Approach To Enable Alignment of Druglike Properties describes an algorithm to score compounds with respect to CNS penetration.
The CNS MPO score was built based on six fundamental physicochemical properties: ClogP, ClogD, MW, TPSA, HBD, and pKa each weighted from 0 to 1.0 full details of the script are here.
Python, Chemistry and a Mac 1
After I posted the page on setting up a Mac for Cheminformatics I was asked if I could do something similar for writing chemistry (or Science in general) Python scripts on a Mac. So I've written a "How to" page on setting up your Mac to use the iPython notebook and write simple scripts that use Pybel to access OpenBabel.
The page is here Python, Chemistry and a Mac 1, and I'll probably add more pages/scripts in the future.
Cheminformatics on a Mac
I've recently needed to set up a new Mac and I realised that the current installation process for all the applications, tools, chemistry toolboxes, and associated dependencies was unmanageable. I have a mixture of apps that I have compiled myself, others that I have simply used the precompiled binaries, others from Macports etc.
I decided to write a detailed account of the process of installing a number of toolkits and packages using Homebrew and PIP.
You can read the full account here in the hints and tutorials.
I'd be delighted to hear of any comments or suggestions for addition.
Scripting Vortex 17 tutorial
In the tutorial Scripting Vortex 15 I showed how it is possible to create a contextual script for Vortex that downloaded a specific PDB file, then a FlexAlign Vortex script first identifies the structure column and then get the SMILES string of the selected molecule generates a 3D structure and uses Flex Align to do a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.
While this is useful if you have similar structures (perhaps analogues in a series) there will certainly be situations where it may be preferable to dock the new ligand into the binding site. The Scripting Vortex 17 tutorial describes how to achieve this.
Ever had problems with an unusually formatted PDB file? PDBinout is a file conversion tool for PDB files that might interest you. It was created by Tomasz Woźniak at the Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences
PDB format is the most commonly used by various programs to define three-dimensional structure of biomolecules. Those programs however, often use different versions of this format. Therefore, it is often necessary to write own re-formatting scripts or change files manually, which makes PDB files less convenient to use. There are only few tools allowing to change one or two versions of PDB format into another and no comprehensive approach for unifying PDB format was developed. Here we present an open-source, Python-based tool PDBinout for processing and conversion of various versions of PDB file format for biostructural applications. Moreover, PDBinout allows to create one's own PDB versions.
The download also includes a tutorial.
Reference Woźniak T. and Adamiak R.W. (2013) Personalization of structural PDB files, Acta Biochimica Polonica 60, Paper in Press
Scripting Vortex 16
OCHEM is a free open access site of annotated models and chemical data. OCHEM contains 1831772 experimental records for about 477 properties collected from 12457 sources you are free to upload your own data and also build predictive models using existing or your own data.
There are also a number of already built models that the public can access, these include
- Ames test
- CYP1A2 inhibition
- LogP and Solubility
You can run predictions on OCHEM using simple REST-like web services, these vortex scripts submit tasks to the various models and then retrieve the resulting prediction.
Scripting Vortex and MOE
One of the new features in the latest version of MOE from Chemical Computing Group is the Listener. The MOE socket listener provides an alternative to MOE/web for executing functions remotely on a running instance of MOE.
The script will download the associated PDB structures from the rcsb Protein Data Bank, put them into a database then start the browser. It may take a few seconds to download the structure; this does rely on MOE having the right proxy settings to access the internet (use the Java console to set them). You can now transfer this to MOE and amend the display to highlight the ligand.
The MOEflexalign script takes the SMILES string of the selected row generates a 3D structure and does a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.
It is probably easier to see this in action, if it appears rather small click on the YouTube icon in the bottom right corner of the video.
Scripting Vortex 14
In tutorial 4 we looked at using the command line tool sddesc from Chemical Computing Group to calculate a number of molecular descriptors and then import them into Vortex. However there a couple of issues with doing this not the least ensuring all the environment variables are set correctly. An alternative is to use MOE as a web service and access the tools using the SOAP protocol (Simple Object Access Protocol). This protocol provides a specification for exchanging structured information in the implementation of Web Services in computer networks. It relies on XML Information Set for its message format.
Chocolat Mac text editor
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.


text:
I watched 47 Ronin over the weekend. Universal Studios Home Entertainment sent me the movie for review on my film blog. 47 Ronin is about a group of masterless samurai who seek to avenge the death of their master. The movie is based on one of Japan's greatest legends. Don't worry, this is not a foreign film. It's a western film that stars Keanu Reeves. In other words, there are no captions to read. 47 Ronin didn't do well at the box office, but I actually enjoyed watching the movie. So did my wife and kids. It's an excellent addition to my Blu-ray library. 47 Ronin is available now on Blu-ray 3D and Blu-ray Combo Packs, DVD, UltraViolet and Video On Demand.
6 Things About 47 Ronin
The story is based on a Japanese legend
47 Ronin is based on a legend about 47 masterless samurai (ronin) who seek vengeance and want to reclaim their honor after their master dies. In the movie, their master is given the honor of killing himself after he is tricked into attacking a rival master. The ronin are exiled and their princess is given to the rival clan for marriage so that the two groups can be united. The ronin is determined to stop the marriage, but the rival master has hundreds of people under his command.
Beware of the shape-shifting witch
I'm not familiar with the 47 ronin legend, but I'm fairly certain it doesn't involve a shape-shifting witch, demonic monks and a rhino-like beast with six eyes. These are the elements that turned the movie from a traditional samurai story into one about swords and magic. I didn't hate the magical elements in the film, but I can't help but wonder if the story would have been better without the mystical tangents.
The movie is also a love story
47 Ronin isn't just an action story about samurai without a master. It's also a love story between the main character and the princess. At least that's what we are suppose to believe. That's actually one of the problems with the film. We're suppose to believe they are in love, but they didn't actually spend much time together in the movie. In addition, the ending was a little sappy with a line that was repeated twice, "I will search for you through a thousand worlds and ten thousands life times until I find you."
47 Ronin features Keanu Reeves and a bunch of unknowns
The star of the movie is Keanu Reeves. He played the part of Kai, a half-Japanese outcast who serves the samurai of Ako. The other actors might be famous in Asia, but I don't think most people in America will know who they are. These actors include Hiroyuki Sanada (Ôishi), Ko Shibasaki (Mika), Tadanobu Asano (Lord Kira), Rinko Kikuchi (Witch), Min Tanaka (Lord Asano), Jin Akanishi (Chikara), Masayoshi Haneda (Yasuno), Hiroshi Sogabe (Hazama), Takato Yonemoto (Basho), Hiroshi Yamada (Hara), Shû Nakajima (Horibe), Cary-Hiroyuki Tagawa (Shogun Tsunayoshi), Neil Fingleton (Lovecraftian Samurai), and Natsuki Kunimoto (Riku). 47 Ronin was directed by Carl Rinsch.
47 Ronin includes several bonus features
The Blu-ray Combo Pack includes the movie on Blu-ray, DVD and Digital HD with UltraViolet. In addition, it includes the following special features:
- Keanu & Kai
Keanu Reeves, the director and other members of the filmmaking team reveal how this adventure would not be possible without Reeves' mastery of martial arts and total immersion in the role
- Steel Fury: The Fights of 47 Ronin
This featurette explores the intense research, choreography and rehearsals that went into creating the film's unique action sequences, including Kai's epic battle against the silver Samurai and the heart-stopping Kirin hunt sequence
- Myths, Magic & Monsters: The FX of 47 Ronin
47 Ronin's creative team reveals the technological magic it used to bring to life the creatures of ancient Japanese folklore, including The Kirin (a giant hybrid beast with the head of a dragon and the body of a deer), the Kitsune witch, the Oni troll and the demonic Tengu Monks
- Re-forging the Legend
The filmmakers talk about how they brought one of Japan's most time-honored legend to the big screen, from script to costumes, visual design, and culture
- Deleted Scenes
- Keanu & Kai
It's rated PG-13
The 119-minute film is rated PG-13 for intense sequences of violence and action, some disturbing images, and thematic elements. There is violence in the movie, and there's even a couple of scenes that involved heads getting chopped off, but I'm fine with letting my kids watch this film.
More info: 47 Ronin Blu-ray