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The Friends of E-Discovery group for electronic discovery is the equivalent of open source code to software development!! The goal is to share ideas and problems among people you are comfortable around, (peers and neighbors), who all are interested in learning more about electronic discovery. I first became aware of this approach before an ESIBytes podcast I was hosting with Judge Grimm and Tom Allman on Rule 502. Before Judge Grimm logged onto the show, Tom and I had a few minutes to speak. Tom told me about a group he and Pete Pepiton were running in Cincinnati where a local group of electronic discovery lawyers, judges and technologists were meeting and talking about issues they were encountering. Tom couldn't stop talking about how effective this group had been in helping this local community become acquainted with electronic discovery by mixing a handful of national experts with others who wanted or needed to learn more about the field. He invited me to an event and I found his description to be accurate. In addition, the discussions I witnessed covered very sophisticated topics.
Soon after that I started the Pittsburgh chapter of this group. Over the past several years, we have had 8 breakfast meetings attended by over 140 different judges, lawyers, technologists and law clerks. Our meetings average between 20 – 30 attendees with 12 and 40 being the range of attendees. I have also attended as a guest meetings in Columbus, Ohio's version of the group and witnessed the same cooperation and shared insights from different participants who have different issues in the e-discovery EDRM schematic. These meetings are free and extremely educational. They also help to unite local communities around this challenging topic which are still trying to figure out best practices around.
Over the past year, I have had several inquiries from interested lawyers in other cities who have heard some of the ESIBytes podcasts I have done about Friends of E-Discovery. They want to know how to start a similar chapter in other cities. To assist in e-discovery education, I wanted to open up the playbook and teach others what seems to work in Pittsburgh. I also wanted to provided some motivation to others to start similar chapters and network together on what works and maybe what doesn't. If you are interested, feel free to contact me at firstname.lastname@example.com and we will offer whatever guidance we can to help you get started. While solving e-discovery is an elusive challenge, starting a Friends of E-Discovery group is really not that difficult if you follow some of the tips laid out on the frequently asked questions page.


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This month sees the fifth anniversary of my blog, fancy that five years! So to celebrate I made some cookies. I did something that I don't do very often and that is to bake something that would please me. You know how it is we all make things for our families and friends that we think they will like, but I very rarely do things just for me. You'll never guess though, everyone else loved them too!
I've fancied decorating cookies for a long time now, and my (mostly unused) cookie cutter collection is testament to that. Having recently been inspired by some of the very talented cookie decorating bloggers across the pond this want-to-do has been accelerated up my list of must-dos, until it has reached No1# status.
For now though, I had a roll of white fondant icing in my baking box, and I was wondering what to do with it, indeed I was wondering why I had actually bought it! Inspiration struck however and these cutie pie goose cookies were made. I'm in the process of trying a number of roll out cookie recipes and the one I tried here is from Sweet Sugar Belle's blog. Her recipe which I used is here (I halved the quantity). They are good and have a great flavour, I used vanilla as the flavouring for my cookies.
For the decorating I used one roll of white ready rolled fondant icing and the black and yellow icing tubes from the little boxes that I managed to buy in my local supermarket, and I reckon if I can buy them they must be readily available! Once you have baked and cooled your cookies, use the same cookie cutter to cut out the white fondant geese and attach them to the cookies with a little apricot jam (no lumpy bits!). To decorate use the black tube to do a little eye and the yellow tube for a little beak and feet. Two of my geese have no feet, you have to take care popping out the cookie dough from the cutter or you lose the feet, however I still liked them so left them as on the water geese.
My little flock :)
This is a really easy project to do for little people, or with them if you like. Mind you adults seem to like them too, because they are cute and taste good.
It is royal icing iced cookies that I really fancy doing now and to that end I have ordered some icing bottles to make that easier, more on this soon. I *might* have ordered some new cookie cutters too, you can't have too many right?! I've got cookies on the brain I tell you!
As a thank you from me to you I'm buying one copy of The Hairy Bikers' Big Book of Baking by Si King and Dave Myers (out this week!) to give to one reader who leaves a comment on this post saying why you'd like to win it. The winner will be drawn at random. Closing date Midnight 4th March 2012, winner to be announced on 5th March 2012. Good luck and thanks to readers new and old for keeping on reading le blog! NOW CLOSED!
Next Review Up: Cake Magic

subset: commoncrawl


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Find a list of our hotels here. If you click on the hotel name it will bring you directly to the hotel website.
Click here to manage your booking online or call our central reservations offices on either 1850 885 885 (Republic of Ireland) or +353 57 869 5946 (UK & worldwide).
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Within the Republic of Ireland call 1850 885 885
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Central Reservations can assist you with all your queries and recommend the best hotel to suit your needs.
Enjoy a Nights accommodation at Maldron Hotel Kevin Street.
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I finally got to see the updated visitor center exhibit at Sycamore Shoals State Historic Park. The exhibit narrative offers a pretty good crash course in the history of Tennessee's Revolutionary frontier, using some lovely murals, audio, artifacts, and a few tableaux with life-sized figures.
You can stand eye to eye with Dragging Canoe while listening to an audio dramatization of his speech denouncing the Transylvania Purchase. He delivered these remarks in March 1775, just a short distance from where the exhibit gallery now stands.
When Cherokee warriors launched an assault on the settlements in July 1776, one prong of the assault struck Fort Watauga. Here's Ann Robertson employing a little frontier ingenuity, using scalding water against a warrior intent on setting fire to the fort's wall.
Of course, another important moment in the history of Sycamore Shoals came in late September 1780, when the Overmountain Men mustered there for the march that took them to King's Mountain.
In terms of original artifacts, the highlight is this pair of kettles from Mary Patton's gunpowder mill. Born in England, Patton lived in Pennsylvania before migrating to the Watauga region with her husband. The Pattons' mill supplied five hundred pounds of gunpowder for the King's Mountain expedition. I think these material links to East Tennessee's Rev War years are pretty darn special.
If you wanted to identify one site as ground zero for Tennessee's frontier era, Sycamore Shoals would be as good a spot as any. It's nice to see the place get the sort of modern exhibit it deserves.


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Bacterial Blight
Xanthomonas axonopodis pv. phaseoli
Bacterial blight affects green, snap, field, lima, scarlet runner, mung and tepary beans and is most problematic in hot, humid conditions. The first symptoms to appear are small, angular, pale green, water-soaked spots on the leaves. These gradually enlarge and merge to form large brown blotches with dry centers (commonly surrounded by a narrow yellow zone). In extreme cases the leaves may become scorched and withered and drop off. The stems may also develop brown blotches, as well as cracks or water-soaked cankers that ooze a yellowish liquid (this is very infectious). Spots also appear on the pods, starting small, but enlarging to form dry, brown sunken patches. Depending upon the health of the plants and the severity of the infection, the pods may shrivel and not produce any seeds at all, or they may develop normally. Some bean varieties are resistant to bacterial blight.
Bacterial blight is usually caused by infected seed (a single infected seed can result in a widespread infection). Minimize the spread of this disease by removing infected plants as symptoms show themselves (and don't touch other plants before washing your hands thoroughly). The bacteria can also survive in crop debris, so this should be removed, or incorporated into the soil, where it can break down quickly. This disease needs moisture for transmission and reproduction, so avoid getting the leaves wet (use drip irrigation) and avoid touching the wet leaves. It can also be spread via soil or sap on tools.
To minimize the effects of this disease, give the plants plenty of water and nutrients, good air circulation and well drained soil. Rotate bean crops every 4 years.
Image: Howard F. Schwartz, Colorado State University, Bugwood.org


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Happy Halloween!
Ella is Black Widow
Josiah is Iron Man
Micah is Captain America
"Avengers Assemble!"
I love that the boys told me
"You have to say 'Avengers Assemble' if you want us to get our costumes on"
Seeing as she has no hair…a bright red feather will do…right?
She hated her costume at first….
Thankfully she got over it.
I do love a theme Halloween after all, and they couldn't be the Avengers without Black Widow.
Batman and Robin
Buzz and Woody
Peter Pan


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Top Six (We Had A Tie) Women's Freestyle Boards
For the sixth season, TWS has organized and executed the most thorough, unbiased, freestyle board test in existence.
Palmer Halo 149
Sometimes things perform best in their most basic and simple state. That's the case for the Halo. It's not one of Palmer's top-of-the-line carbon- , honeycomb- , titanium-accessorized blingers. The Halo depends instead on the subtle effects of the multi-radii Klothoid-shaped sidecut, which provides easy turning and handling without compromising performance, which is exactly what Palmer set out to build for entry-level riders.
The Halo's solid ride comes from the full sidewall construction and a tip-to-tail woodcore-the factors that made our testers want to place this board firmly underfoot.
According to our testers, all this mellow results in a powerful board. Dana summed up the pop of the Halo in one sentence: "I may have to leave my boyfriend at home, because this board makes me go bigger than him." Sara said it was "an all-around solid board," only finding fault when she was riding switch on the directional stance (it's set back twenty millimeters). Emily found that the Halo is a board that's good in the pipe and the trees. Choose this board if you want an easy-riding slope cruiser.
Board length: 149
Effective edge: 116.5 cm
Sidecut radius: 6.8 m (klothoid)
Waist width: 23.9 cm
Maximum stance width: 22 in
Available lengths: 146, 149, 152
Price: $389
Web site: palmersnowboards.com
Rome Vinyl 151
If we were to buy a board just for the graphics, the entire Vinyl line would make the cut. Luckily, we'd be making a good decision-the Vinyl has been loved by board testers for two years running, and for good reasons. Josh Reid, the man behind Rome snowboards, broke it down for us: "In the Vinyl, we merged the more buttery feeling StraightBiax laminate with a mellow core profile, which results in a board that's easy to manipulate, super stable on landings, and generally fun underfoot." The buttery flex does double-duty as a great board for hitting the jumps and rails, and as a less-aggressive board for the weekend warrior who just wants to cruise the mountain without getting bucked off.
Sara liked that the board has "mad pop while still being stable." Emily commented that the Vinyl is a "fun freeriding board with surprising pop in the tail for jumps-a great riding platform." Dana gave the board all tens: "It's perfect for all-around aggressive park riding, and it's a great board for spinning."
Sound like something you'd want to ride?
Board length: 151
Effective edge: 113.5 cm
Sidecut radius: 7.3 m
Waist width: 24 cm
Max stance width: 23 1/8 in
Available sizes: 144, 147, 151, 155
Price: $360
Web site: romesnowboards.com
TechNine True Love/Lipstick 156
This is the third year TechNine has been pumping out boards to go with its popular bindings, and already it's making a debut in the board test. TechNine's slogan for their first women's board ever says it all, "Move over, diamonds, we are now a girl's best friend." TechNine VP Ethan Stone says, "The True Love is designed for every level of riding from pro to beginner. The flex and sidecut are perfect for all conditions, and the snappy pop makes it impossible to not have fun."
TW tester Dana said, "This is the kind of board that makes you late to work 'cause you just had to do another lap." Crazy Sara thought the stance options were the shit: "I could get a 22.5-inch centered stance." She also went off about the great responsiveness and stability on rails: "I actually enjoyed riding it." It figures that a company with the likes of Bozung onboard would figure out the wider stance options.
And how about them graphics? E-Stone says the graphics were so popular with the rest of the team that they almost ended up on the men's boards.
Board length: 156
Effective edge: 123.5 cm
Waist width: 24.1 cm
Max stance width: 22.5 in
Available sizes: 144, 151, 156
Price: $375
Web site: technine.com
Santa Cruz Muse Tribute 151
The Muse is clocking into the top five for round two. Two years running the board has killed it in the test, but this time it's the smaller 151 delivering the KO punch. Our testers loved this board. The Muse features a unique sidewall construction, which involves sandwiching strips of shock-absorbing rubber with ABS plates above the edges, the result is a board that absorbs vibrations and chatter, and delivers a smooth damp ride. As a bonus, the rubber is more durable in absorbing edge hits instead of getting all dinged up like straight metal edges.
The Muse is geared toward intermediate to advanced riders (beginners should check out the Cuna Union). All three girls could agree on one thing, this board performs aggressively. Dana noted that it "likes to go big in the pipe." Emily said the board was straight-up gangsta: "It has awesome pop for jumps-if you don't want to go big, steer clear of this board."
Board length: 151
Effective edge: 113 cm
Sidecut radius: 7.4 m
Waist width: 23.6 cm
Maximum stance width: 23 in
Available sizes: 148, 151, 154, 157
Price: $460
Web site: scskate.com
Burton GTwin 150
This women's twin-tip board was developed over the course of a full year with Natasza Zurek and Anne-Flore Marxer. They built it for a rider who's looking for an easy-riding, fun snowboard that holds an edge well in a turn, yet is playful and forgiving enough to learn new tricks on and progress your riding. Burton Testing Director John Genrdt says, "This is the freshest, newest, most current shape and construction possible." He added, "We took our time and dialed this board in exactly how the girls wanted it. For me, this was one of the most rewarding boards to work on in a long time because of the rider-driven process and the final outcome." The winner of the first U.S. Roxy Chicken Jam, Natasza agreed, "We were allowed to design it totally how we wanted, and what we wanted was a fun freestyle board that was still stable in the turns. Who wouldn't like a board like that?"
Our testers didn't have any of this info when they started heel toein' down the slopes, they just knew they liked what they were riding. Sara said, "It's easy to ride, popped, and flexed good for the jibs." Emily remarked that it is an "awesome all-around board that will improve your snowboarding." Dana said, "This board rode great all over the mountain." Hmm, a twin that performs both in the park and out on the slopes-perfect.
Board length: 150
Effective edge: 113 cm
Sidecut radius: 7.2 m
Waist width: 24.1 cm
Maximum stance width: 24 in
Available sizes: 150 cm
Price: $450
Web site: burton.com
Flow Myriad 149
Talk about a company having a stellar season, the Flow team pretty much podiumed every event this winter, threw the biggest party at the Team Challenge, and made a board good enough to get the Good Wood stamp-it's one for the record books.
Our testers loved this board but couldn't agree on why. It's kind of the Transformer of snowboards. One tester thought it rode stiff; one thought it rode soft-pretty confusing. It turns out that that's what the board is built for-everything. It's a directional twin-tip board, so it comes with a set-back stance option for all-over mountain performance.
The testers only had good things to say about the Myriad, from Sara's comments about it "pressing well, but still holding an edge and turning nicely" to Emily's stoke on the twin-tip shreddability of the board: "It's fun to flip around and ride both ways."
This board is built for intermediate to expert riders. Flow teamrider Emily Akerblom helped design this board to be lighter, softer, and narrower. The Myriad leans more toward freestyle than freeride with its twin-tip shape, but the slightly set-back stance and wide variety of stance options opens the doors to really any type of terrain.
Board length: 149
Available lengths: 145, 149, 153, 157
Effective edge: 113 cm
Sidecut radius: 8.8/8/8.8 m
Waist width: 23.9 cm
Maximum stance width: 22 in
Price: $365
Web site: flow.com
its twin-tip shape, but the slightly set-back stance and wide variety of stance options opens the doors to really any type of terrain.
Board length: 149
Available lengths: 145, 149, 153, 157
Effective edge: 113 cm
Sidecut radius: 8.8/8/8.8 m
Waist width: 23.9 cm
Maximum stance width: 22 in
Price: $365
Web site: flow.com


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New assistant professor examines drug resistance through physics and biology
Research Suggests New Ways of Overcoming Resistance to Chemotherapy Drugs
University Launches Cutting-Edge Institute for AI-Driven Discovery and Innovation
Ken Dill awarded the 2019 Raymond and Beverly Sackler International Prize in Biophysics
Luca Agozzino and Evan Philip: Student Success Stories
Markus Seeliger studies cellular switch binding
Steven Skiena uses AI to find faculty
Ken Dill Awarded Max Delbruck Prize
Synthetic "Gene Thermometers" Show How Cells Endure Heat or Cold
Festschrift Issue of The Journal of Physical Chemistry B for Ken
Life's First Molecule Was Protein, Not RNA, New Model Suggests
Kellon Belfon Finds His Way from Grenada to Prestigious Fellowship
Modeling Protein Interactions Critical to Understanding Disease now Simplified With Computer Server
Ken Dill explains his research.
Physics Discovery Could Improve Solar Cells
Is the notion of a cure for cancer too simplistic?
High-Speed Protein Modeling Could Accelerate Drug Development
Study Reveals Proteins Most Associated With Aging
New Technology Tracks Cell Lineage To Watch Evolution at Work
Dill & Balazsi, Honored at SBU event
Discovery of Compound May Open New Road to Diabetes Treatment
Two SBU Professors Elected into American Academy of Arts and Sciences
Laufer Center researchers look into new ways of exploring evolution
Stony Brook Researchers Receive $3.8 Million NIH Grant to Develop Drugs for Pain, Inflammation
Research targeting endocannabinoid transporters may also help relieve symptoms of drug withdrawal
STONY BROOK, N.Y., November 6, 2013 – A multidisciplinary research team at Stony Brook University has received a five-year $3.8 million grant from the National Institute on Drug Abuse (NIDA), part of the National Institutes of Health, to develop new drugs for pain, inflammation, and potentially drug addiction. The drug development strategy is based on their discovery of intracellular transporters known as FABPs (fatty acid binding proteins) for a neurotransmitter in the body that regulates pain and stress.
The project, "Targeting FABPs," is designated to the Institute for Chemical Biology & Drug Discovery (ICB&DD) at Stony Brook. Led by Principal Investigator Dale Deutsch, Professor of Biochemistry and Cell Biology, and a member of the ICB&DD, the project involves researchers and students from four different Stony Brook University academic departments, the ICB&DD, and the Laufer Center for Quantitative and Physical Biology.
FABPs are a family of small soluble protein carriers for fatty substances in cellular metabolism that transport the neurotransmitter known as AEA (endocannabinoid anadamide) from the cell membrane to interior of the cell where the AEA is destroyed which causes pain signals to increase. AEA and other endocannabinoids are compounds in the brain, similar to THC (the active ingredient in marijuana), which plays a role in numerous physiological processes, including appetite, memory and pain. With the NIDA funding, the research team is trying to determine if by inhibiting FABPs, the breakdown of AEAs is reduced and thereby pain can be minimized.
"The major goal of our drug discovery proposal is to develop drugs that inhibit these neurotransmitter transporters," said Deutsch. "We expect that by targeting FABPs with certain compounds made by the ICB & DD group, endocannabinoid levels will increase within the brain, essentially resulting in anti-pain and anti-inflammatory effects."
Deutsch said the team's targeted strategy that reduces neurotransmitter breakdown may alleviate symptoms of drug withdrawal as does the nicotine patch for smokers or methadone for opiate replacement. He added that an additional advantage of the strategy is that by creating neurotransmitter levels to increase naturally, pain would theoretically be curbed without negative side effects, such as motor coordination problems.
A series of findings since the project began have helped to advance the research. First, in 2007 Dr. Martin Kaczocha, then a graduate student in Deutsch's laboratory, now an Assistant Professor in the Department of Anesthesiology, identified the FABPs as transporters for endocannabinoids. This discovery was published in an article that appeared in the April 14, 2009 issue of the Proceedings of the National Academy of Sciences (PNAS) entitled "Identification of intracellular carriers for the endocannabinoid anandamide."
The research project built up further momentum later that year when Deutsch and Kaczocha presented Dr. Iwao Ojima, Stony Brook University Distinguished Professor of Chemistry and Director of the ICB&DD, with the concept of the therapeutic potential of small molecules that target FABPs. Through the ICB&DD, additional researchers became involved in the project. The expanded ICB&DD research team discovered a class of compounds that display significant inhibitory activity against FABPs. By using a computer modeling process led by collaborator Dr. Robert Rizzo, Associate Professor of the Department of Applied Mathematics and Statistics and member of the Laufer Center, the team screened more than one million compounds and identified lead compounds with molecule binding profiles similar to oleic acid, a natural FABP substrate. They selected 48 of these identified compounds, and are using chemical synthesis methods to identify other potential AEA-inhibitory agents that are both effective and safe.
Rizzo said as the research progressed he found it especially exciting to work "hand in hand with traditional experimental laboratories to identify and design inhibitors which target a specific protein."
"It turned out that the core structure of what our research team determined to be the most promising compounds, known as 'truxilloids,' are found in a traditional Chinese medicine, called 'incarvillaterine,' which have been used for centuries to treat rheumatism and pain," said Deutsch.
The investigators published their results on "truxilloids" in research article that appeared in the December 7, 2012 edition of PLOS ONE entitled, "Targeting Fatty Acid Binding Protein (FABP) Anandamide Transporters – A Novel Strategy for Development of Anti-Inflammatory and Anti-Nociceptive Drugs." They showed that inhibition of FABPs and the subsequent elevation of the neurotransmitter AEA is a promising new targeted treatment approach against pain and inflammation.
"This collaborative effort among our ICB&DD faculty has the potential to lead to new treatments for many diseases and conditions that affect millions worldwide," said Ojima. "The NIDA grant is a major step that will help provide the resources to discover and develop novel therapeutics, as well as shed light on the fascinating neurobiological processes involving FABP. This is exemplary multidisciplinary and collaborative research that the ICB&DD has been successfully promoting."
Bill Berger (BS, Chemistry '05) a PhD candidate in Dr. Ojima's laboratory who will defend his dissertation on this work in December this year, synthesized and purified a variety of truxillic acid analogs, a crucial step that led to the identification of the most promising FABP inhibitors. He described this research project "as a high point in my PhD career, especially when in 2012 I described these findings to 300 leading scientists at the International Cannabinoid Research Society in Germany."
"Bill Berger has been the driving force for the promotion of this project from the onset of his multidisciplinary collaboration," said Ojima. "He has a truly exceptional ability to execute chemical synthesis, computational biology and drug design with an excellent understanding of biology. He is an independent and creative thinker, but at the same time an excellent team player. Thus, he worked closely with Rizzo, Kaczocha, Deutsch and me without any difficulty in understanding all aspects of the project."
Brian Ralph, a junior Biology major at Stony Brook (with a focus in Quantitative Biology), a co-author on the PLOS ONE paper, biochemically screened compounds selected by the virtual program and discovered the top inhibitor, the current drug lead in the project, alpha-truxilic acid. He subsequently pursued binding studies of several alpha-truxilic acid analogues to determine how strongly each structure interacted with the target FABPs and to identify which analogue would be the best potential inhibitor of these proteins.
The research team also includes Dr. Trent Balius and William Joseph Allen in SBU's Department of Applied Mathematics and Statistics; structural biologist Dr. Huilin Li who has dual appointments in the SBU Department of Biochemistry and Brookhaven National Laboratory; and, Dr. Samir Haj-Dahmane of the Research Institute on Addictions at the University of Buffalo.
Initial funding for the research began with a SBU-BNL seed grant to Dr. Deutsch and Dr. Li from Stony Brook University and Brookhaven National Laboratory in 2010, followed by a Stony Brook University School of Medicine Targeted Research Opportunities (TRO) Fusion award to Drs. Deutsch, Li, and Ojima as well as a New York State SUNY REACH grant for Drs. Deutsch and Haj-Dahmane. Dr. Deutsch also received a previous single investigator grant from the NIH to research FABPs.
Laufer Center Researchers Find Surprising Similarities Between Genetic and Computer Codes
The term "survival of the fittest" refers to natural selection in biological systems, but Darwin's theory may apply more broadly than that. New research from the U.S. Department of Energy's Brookhaven National Laboratory shows that this evolutionary theory also applies to technological systems.
Computational biologist Sergei Maslov of Brookhaven National Laboratory and the Laufer Center worked with graduate student Tin Yau Pang from Stony Brook University to compare the frequency with which components "survive" in two complex systems: bacterial genomes and operating systems on Linux computers. Their work is published in the Proceedings of the National Academy of Sciences.
Maslov and Pang set out to determine not only why some specialized genes or computer programs are very common while others are fairly rare, but to see how many components in any system are so important that they can't be eliminated. "If a bacteria genome doesn't have a particular gene, it will be dead on arrival," Maslov said. "How many of those genes are there? The same goes for large software systems. They have multiple components that work together and the systems require just the right components working together to thrive.'"
Using data from the massive sequencing of bacterial genomes, now a part of the DOE Systems Biology Knowledgebase (KBase), Maslov and Pang examined the frequency of usage of crucial bits of genetic code in the metabolic processes of 500 bacterial species and found a surprising similarity with the frequency of installation of 200,000 Linux packages on more than 2 million individual computers. Linux is an open source software collaboration that allows designers to modify source code to create programs for public use.
The most frequently used components in both the biological and computer systems are those that allow for the most descendants. That is, the more a component is relied upon by others, the more likely it is to be required for full functionality of a system.
It may seem logical, but the surprising part of this finding is how universal it is. "It is almost expected that the frequency of usage of any component is correlated with how many other components depend on it," said Maslov. "But we found that we can determine the number of crucial components – those without which other components couldn't function – by a simple calculation that holds true both in biological systems and computer systems."For both the bacteria and the computing systems, take the square root of the interdependent components and you can find the number of key components that are so important that not a single other piece can get by without them.
Maslov's finding applies equally to these complex networks because they are both examples of open access systems with components that are independently installed. "Bacteria are the ultimate BitTorrents of biology," he said, referring to a popular file-sharing protocol. "They have this enormous common pool of genes that they are freely sharing with each other. Bacterial systems can easily add or remove genes from their genomes through what's called horizontal gene transfer, a kind of file sharing between bacteria," Maslov said.
The same goes for Linux operating systems, which allow free installation of components built and shared by a multitude of designers independently of one another. The theory wouldn't hold true for, say, a Windows operating system, which only runs proprietary programs.
Maslov is co-principal investigator in the KBase program, which is led by principal investigator Adam Arkin of DOE's Lawrence Berkeley National Laboratory, with additional co-principal investigators Rick Stevens of DOE's Argonne National Laboratory and Robert Cottingham of DOE's Oak Ridge National Laboratory. Supported by DOE's Office of Science, the KBase program provides a high-performance computing environment that enables researchers to access, integrate, analyze and share large-scale genomic data to facilitate scientific collaboration and accelerate the pace of scientific discovery.
DOE's Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.
An NPR interview with Maslov on April 2 can be found on iTunes. Articles in Phys Rev and Gismodo also describe this work.
Laufer Center Researchers Look Back on Scientific Advances Made as a Result of a 50-Year Old Puzzle
Effort to solve questions on protein folding created field of protein physical science that has led to major scientific advances. Fifty years after scientists first posed a question about protein folding, the search for answers has led to the creation of a full-fledged field of research that led to major advances in supercomputers, new materials and drug discovery, and shaped our understanding of the basic processes of life, including so-called "protein-folding diseases" such as Alzheimer's, Parkinson's and type II diabetes.
In a review article published in the Nov. 23, 2012 issue of the journal Science, Stony Brook University researchers reviewed the progress on a 50-year-old puzzle called the Protein Folding Problem. Ken Dill and Justin MacCallum of Stony Brook's Louis and Beatrice Laufer Center for Physical and Quantitative Biology show how a community of scientific researchers rose to tackle a grand-challenge problem of very basic science that had no obvious payoff at the time.
"Protein folding is a quintessential basic science. There has been no specific commercial target, yet the collateral payoffs have been broad and deep," the researchers said in their paper, The Protein Folding Problem, 50 Years On.
"We have learned that proteins fold rapidly because random thermal motions cause conformational changes leading energetically downhill toward the native structure, a principle that is captured in funnel-shaped energy landscapes. And thanks in part to the large Protein Data Bank of known structures, predicting protein structures is now far more successful than was thought possible in the early days. What began as three questions of basic science one half-century ago has now grown into the full-fledged research field of protein physical science."
This year marks the 50th anniversary of the 1962 Nobel Prize in Chemistry awarded to Max Perutz and John Kendrew for their pioneering work in determining the structure of globular proteins. That work laid the foundation for structural biology, which interprets molecular level biological mechanisms in terms of the structures of proteins and other biomolecules. Their work also raised the question of how protein structures are explained by physical principles.
Since Perutz and Kendrew discovered the structures of two proteins, nearly 80,000 protein structures have been discovered. The protein folding "problem" arose when Perutz and Kendrew were unable to make sense of how the folded structure of the protein molecule was related to its sequence of bead types. Ever since then, there has been great interest in understanding the protein-folding "code": how does a given string of amino acids lead to a particular balled-up ("native") structure of a protein?
Proteins are molecules that perform the basic functions in biological cells – converting food to growth, to repairing DNA molecules and damaged cell parts, to motion in muscles, to transduction of signals in the brain and light in the eye, for example. Humans have about 20,000 different types of protein molecules. Each performs a different function. The abilities of proteins to perform such a broad array of powerful chemical functions arise from a peculiar principle of chemical structure and function, namely the folding of each protein. A protein is miniature string of beads, like a pearl necklace, where the bead-like component pieces are called amino acids. Amino acids come in 20 different types. The folding principle is that different sequences of amino acids strung together cause different protein molecules to ball-up in very specific, but different, ways, giving rise to their very different functionalities.
The protein folding problem became a set of three inter-related puzzles: What is the folding code? How does the protein find its one native structure in fractions of a second inside the cell (the needle-in-a-haystack problem)? And: Can we make a computer method that can discover new structures of proteins from the large number of amino acid sequences that are now known?
Dill, Director of the Laufer Center and Distinguished Professor of Physics and Chemistry, and MacCallum, a junior fellow at the Laufer Center, describe how huge advances have been made on all three fronts. They detail some very important collateral payoffs of this work that was completely unanticipated at the time, including the development of the IBM Blue Gene computer and distributed-grid computing, computer-based methods for discovering new pharmaceuticals, a deeper understanding of molecular mechanisms in biology, a deeper understanding of the inter-atomic interactions inside proteins (that has also involved Stony Brook Laufer Center researchers Carlos Simmerling, David Green, and Rob Rizzo), and a new class of very promising polymer materials called "foldamers".
Dill and MacCallum argue that what started out as one compelling question of basic science has now become an entire field of theoretical and experimental approaches in which many questions are now leading to a few answers and many more questions.
LC Postdoc Alberto Perez is September Stony Brook Postdoc-of-the-Month
As one of the founding members of Stony Brook's Postdoc Working Group, Alberto Perez is tireless in his efforts to emphasize the importance of communicating one's science to all types of audiences.
His will be the lead-in presentation in the upcoming Postdoc Research Symposium to be held on September 20 with his talk entitled Proteins? Yes, please (but folded). Why does he so highly value the art of communication?
"It is not uncommon to go to a conference, check out all the great talks you are going to hear, be in the room excitedly anticipating what is to come on the big screen ... and then you get lost after the second slide. Scientists want to make sure there is no doubt that we know what we are talking about, but unfortunately that can result in only experts, working on exactly the same problem as we are, being able to understand our presentations. It is a frustrating experience for the listener who wants to learn about new subjects, and it is frustrating for the speaker who wants to create new opportunities for collaborations across disciplines. We need to learn how to better engage everyone while keeping the talk interesting to even the more advanced listener
"Communicating science is not about losing accuracy; you can still convey your ideas precisely but with less detail so that people understand what you are doing and why. You want to make your audience curious and then let them ask afterward for details. If you start with the details ... you'll never get your science across."
How did you get interested in science?
"Since I was small I had lots of opportunities - my dad is a scientist, and there were plenty of books around me so I guess that sparked my interest in science. I was born in Barcelona, Spain but I came to the US for middle school, which helped me learn English … which made it so much easier for me in science."
What brought you to Stony Brook?
"I did my undergrad in Chemistry and my PhD in DNA flexibility at the University of Barcelona. When I started looking for a Postdoc position I interviewed with Ken Dill at the University of California San Francisco to study protein folding. When I got to San Francisco I was told it was likely that Ken's group was going to move to Stony Brook. Ken gave me the options of looking for another group at UCSF, working remotely from UCSF or moving with him to a new center full of new opportunities … so I decided to come to Stony Brook." Alberto is now a Postdoctoral Associate in the new Laufer Center for Physical and Quantitative Biology under the direction of Professor Dill.
"Initially I was afraid of leaving UCSF because of the high level of NIH funding awarded there and because there were several Nobel Laureates on campus so I thought I might not have the same level of opportunities at SBU as I would at UCSF, but actually I've increased my network considerably since coming to Stony Brook. And also working with the Postdoc Working Group allows me to take part in shaping events for Postdocs on campus, which is a very rewarding experience."
What accomplishments are you most proud of since arriving at Stony Brook?
"I just finished participating in CASP, an event that takes place every other year, which stands for Critical Assessment for Structural Prediction. The competition runs throughout the summer and consists of regularly receiving different protein sequences for which you have three weeks to predict the structure. Basically the competition is a way of blind testing protein predictions methods from all around the world. At the present time the methods to characterize proteins directly via experiments are expensive and limited, so we are trying to use computational tools to allow us to get some insight. This competition gave us the chance to use some of the new resources at the Laufer Center and assess the effectiveness of our methods and how they compare to cheaper but less principle-based methods.
"In a nutshell, proteins do most things inside us. We want to know what proteins look like so we can better understand how they work and how to correct them when they go wrong. Basically there are two approaches for predicting a protein's structure. One approach is: if it looks like a duck and quacks like a duck then it must be a duck so it must have a duck's shape, and applying that approach to proteins means that similar protein sequences probably have the same structure.
"Our approach is based on physics. We say: here are the equations of motions and these are the laws of physics governing different kinds of interactions in a given protein. We allow these interactions to drive the protein from its initial disordered state until we get a folded protein. This approach is much more computationally intense, but the insights we get are much more realistic. We just finished the competition last week and will find out how we did in about a month."
What are your future goals?
"In the short-term I plan to continue working at the Laufer Center and to take advantage of the opportunities here to grow as a scientist and as a person, to better prepare myself for the next stage which will hopefully be a tenure track position … somewhere."
What advice might you have for other Postdocs here at Stony Brook?
"While you are a Postdoc, try to plan where you see yourself in a year's time and work towards that goal. Also keep an open mind: No matter how much you plan, things change in your life and you have to adapt. Don't get frustrated by a change in your plans … and network … a lot."
What is your favorite word or phrase?
"Move slow, think fast."
What is your favorite sound?
"Its absence."
What is your favorite hobby?
"Sports, especially soccer, reading and trying to learn Japanese."
For more information about the upcoming Postdoc Research Symposium, please visit http://www.stonybrook.edu/commcms/postdoc/archivedevents/researchsymposium/researchsymp.html.
To learn more about Alberto Perez, you can visit his website at: http://alberto4web.wordpress.com
Form, Function and Folding: In collaboration with LC Lab, a team of scientists move toward rational design of artificial proteins
In the world of proteins, form defines function. Based on interactions between their constituent amino acids, proteins form specific conformations, folding and twisting into distinct, chemically directed shapes. The resulting structure dictates the proteins' actions; thus accurate modeling of structure is vital to understanding functionality.
Peptoids, the synthetic cousins of proteins, follow similar design rules.Less vulnerable to chemical or metabolic breakdown than proteins, peptoids are promising for diagnostics, pharmaceuticals, and as a platform to build bioinspired nanomaterials, as scientists can build and manipulate peptoids with great precision. But to design peptoids for a specific function, scientists need to first untangle the complex relationship between a peptoid's composition and its function-defining folded structure.Peptoids, the synthetic cousins of proteins, follow similar design rules.
Less vulnerable to chemical or metabolic breakdown than proteins, peptoids are promising for diagnostics, pharmaceuticals, and as a platform to build bioinspired nanomaterials, as scientists can build and manipulate peptoids with great precision. But to design peptoids for a specific function, scientists need to first untangle the complex relationship between a peptoid's composition and its function-defining folded structure.
Past efforts to predict protein structure have met with limited success, but now a scientific team led by Glenn Butterfoss, and Barney Yoo, research scientists at New York University, in collaboration with investigators from the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab), Stony Brook University and Temple University have demonstrated that a computer modeling approach similar to one used to predict protein structures can accurately predict peptoid conformation as well.
The authors describe this accomplishment in a new paper in the Proceedings of the National Academy of Sciences (PNAS) titled, "De novo structure prediction and experimental characterization of folded peptoid oligomers," coauthored by Jonathan Jaworski, Ilya Chorny, Ken Dill (Director of the Laufer Center), Ronald Zuckermann, Richard Bonneau, Kent Kirshenbaum, and Vincent Voelz.
"Natural selection has engineered protein sequences that can self-assemble into molecular machines with specific functions. Why can't we do the same with biologically inspired synthetic materials?" Voelz, Principal Investigator with Temple University, explains.
With this mission in mind, the collaborative team of scientists developed the project two years ago at the 7th Peptoid Summit, a – conference devoted to peptoid research hosted by Berkeley Lab's Molecular Foundry.
"The research was carried out by a remarkable, interdisciplinary team of scientists," says Kent Kirshenbaum of NYU. "Some of the team have worked together on this truly difficult problem for almost 20 years. The researchers include both experimentalists and theorists who have been able to guide one another in discovering how these peptoid molecules fold."
Together, they proposed a 'blind structure prediction' challenge. This self-assessment technique, responsible for the enormous progress in the world of protein structure modeling, allows scientists to test the fidelity of their computational models by predicting the three-dimensional structure of a known molecule and then comparing their proposed structure to the X-ray crystallography results.
An analogous, combined experimental-computational method was employed by the peptoid team in an effort to advance the computational design of peptoid structure. X-ray crystal structures for three peptoid molecules, two small and linear and one larger and cyclical, were simultaneously determined, but not disclosed to the theoretical modelers. The experimentalists then used a combination of two simulation techniques, Replica Exchange Molecular Dynamics (REMD) simulation and Quantum Mechanical refinement (QM). REMD can efficiently predict the preferred general conformations, and the QM calculations further refine the conformational prediction. In combination, these two calculations accurately define the physical structures of molecules.
The proposed structural predictions of the peptoid molecules did exceedingly well at calculating the actual folded conformations. The first two blind predictions were calculated for two linear, small N-alkyl and N-aryl peptoid trimers. Of these, the N-aryl peptoid trimer was the best blind prediction, matching the crystal described conformation to within 0.2 Å. The N-alkyl trimer prediction matched less well with the crystal results because of its increased flexibility.
The greater challenge facing the group was structural prediction of the larger, cyclic peptoid nonamer. Six different possible conformations were considered for the final, submitted prediction and the top pick proved to agree best with the crystallography results to an accuracy of 1.0 Å.
This success suggests that reliable structure prediction for complex three-dimensional folds is within reach, an enormous step forward on the path to reliable and efficient computational peptoid design.
"This will hopefully break open the field of peptoid structure prediction and design, an area we desperately need to guide our more well-developed synthetic efforts,"
says Ron Zuckermann, co-author and director of the Biological Nanostructures Facility at Berkeley Lab's Molecular Foundry.
"It is an exciting time for peptoid research," says author Glenn Butterfoss, research scientist with NYU. "The community of labs working on these molecules is growing, and both the diversity and creativity of recent studies is quite astonishing. We hope our work here, aimed toward understanding the structural behavior of peptoids in three dimensional space, serves as a building block for future efforts to design peptoid molecules with practical functions."
Portions of this work were performed at the Molecular Foundry, Lawrence Berkeley National Laboratory, and supported by the DOE Office of Science. Additional funding came from the Defense Threat Reduction Agency, the NSF and the NIH.
Titan Supercomputer Hours Awarded to Collaborative Protein Project
Laufer Center Scientists at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory and Stony Brook University have been awarded processing time on a new supercomputer at Oak Ridge National Laboratory to study how proteins fold into their three-dimensional shapes.
Proteins, which account for one-quarter of our dry body mass, are made up of different sequences of amino acids. While these sequences are relatively well understood, the myriad ways in which the amino acid chains fold into a functional structure are still difficult to predict.
"This is not a matter of just curiosity. Most medicines interact with proteins and alter their behavior," explained Stony Brook biochemist Alberto Perez, one of the lead researchers on the project. "If we want to design better medicines, we need to know what proteins look like."
The award, which comes from the DOE's Advanced Scientific Computing Research Leadership Computing Challenge, is for up to two million processing hours on the Titan supercomputer at Oak Ridge. Titan is an upgrade of Jaguar, a supercomputer that was recently named the sixth most powerful in the world by the TOP500 ranking system. Some scientists believe that Titan will contend for the number-one spot when it comes online later this year.
Titan has an unusual configuration: it will run on graphical processing units (GPUs) i addition to central processing units (CPUs). GPUs, originally developed by the technology company NVIDIA to render images in video games, are particularly efficient for repetitive tasks. By re-appropriating GPUs to solve scientific problems, Titan will become part of a burgeoning new approach in computational analysis.
Perez's team will use Titan to run AMBER, a software package that simulates the effect of different force fields on organic molecules such as proteins to determine the most likely folding configuration. This method is a fast and effective complement to conventional protein imaging methods such as x-ray crystallography or nuclear magnetic resonance imaging.
"With the GPU port to AMBER, we are able to obtain in days in one single GPU the sampling that we were able to accomplish in several months of simulation using multiple CPUs," said Perez.
The trick is finding the right set of rules to limit AMBER's massive search. The team believes they will be successful by focusing on the "first principles" that govern physical interactions in molecules while simplifying the representation of electron and nucleus behavior. These restraints are built into AMBER's classical molecular dynamics machinery.
The team plans to test their approach in the Critical Assessment of Protein Structure (CASP), a competition in which groups have just three weeks to guess at a particular protein's folds. Having the opportunity to run a simulation on Titan will be a big advantage.
"Getting into the competition is part of the motivation, but it's not the whole story," said Yan Li, a physicist at Brookhaven. If their model scores well against CASP's experimentally derived structure, then they want to apply their approach to membrane proteins, which are important therapeutic targets that are particularly difficult to crystallize. "Eventually, we want to make the method more rigorous," Li said.
Perez and Li are joined on the project by Stony Brook's Laufer Center Director Ken A. Dill and Junior Fellow Justin MacCallum; Brookhaven Computational Science Interim Director Mike McGuigan; and Vageli Coutsias, a mathematics professor at the University of New Mexico.
"It's not just inter-institutional. It's interdisciplinary. We want to take advantage of the expertise of biology, chemistry, and physics," Li said.
Study Finds Parasitic Plants Steal Nutrients and Genes from Their Hosts
Joshua Rest, assistant professor in the Department of Ecology and Evolution at Stony Brook, has co-authored an article appearing in BMC Genomics , "Horizontal transfer of expressed genes in a parasitic flowering plant," detailing the first evidence of substantial horizontal gene transfer from a host to the parasitic flowering plant Rafflesia cantleyi. Professor Rest was co-leader of the project along with Professor Charles Davis from Harvard University.
The plant, Rafflesia cantleyi, is an obligate holoparasite dependent on its host, Tetrastigma rafflesiae, a member of the grape family, for sustenance. Rafflesias have the largest known flowers at approximately three feet across.
A team of researchers led by Professor Rest and Professor Davis collaborated to systematically investigate the extent of horizontal gene transfer between these two plants. By looking at the transcriptome, the transcribed products of switched on genes, they found 49 genes transcribed by the parasite, accounting for 2% of their total transcriptome, which originally belonged to the host. Three quarters of these transcripts appear to have replaced the parasites' own version.
"This research suggests that this horizontal gene transfer may be important to the parasitic lifestyle of this very unusual plant," said Professor Rest. "These transferred genes have been integrated and are expressed in the host genome." The transferred genes have a wide range of functions, appear to be fully operational, and have become integrated into the nuclei of the parasite's cells. Such gene transfer between species is common in bacteria, but rare in more complex organisms.
"Our study suggests that the Rafflesia genome may have evolved to mimic the genome of its host," said Professor Rest. "This study highlights the power of genomics to learn about the life history and evolutionary strategies of the diversity of life."
Professor Rest's lab uses both bioinformatic and experimental approaches to study the evolution of gene regulation and the consequences of variation in gene expression on the fitness of organisms. He is an associate member of the Laufer Center for Physical and Quantitative Biology <http://laufercenter.stonybrook.edu/> at Stony Brook and has published 18 articles in various publications, including: PLoS ONE, Human Molecular Genetics, Journal of Molecular Evolution, BMC Biology, Infection, Genetics and Evolution and more. He received his BS in Biology from Drake University (1999) and his PhD in Ecology and Evolutionary Biology from the University of Michigan (2004).
Opening of the Laufer Center for Physical and Quantitative Biology
The new home of the Louis and Beatrice Laufer Center for Physical and Quantitative Biology at Stony Brook University was officially dedicated at a celebratory event on May 7. Nearly 40 extended members of the Laufer family from across the United States joined Stony Brook officials, research faculty and staff, and local elected representatives for the commemorative ceremony.
The Laufer Center, which is housed in a newly remodeled building (formerly the Stony Brook University Life Sciences Library), started operation in February of 2011 with a major philanthropic gift in loving memory of Louis and Beatrice Laufer by their children Henry and Marsha Laufer, Helen Laufer Kaplan and Howard Kaplan, and Jeffrey and Barbara Laufer. The Center supports two endowed professorships and an endowed chair.
The Laufer family is very pleased to partner with Stony Brook University in creating the Louis and Beatrice Laufer Center for Physical and Quantitative Biology," said Drs. Henry and Marsha Laufer in a joint statement. "This new facility that houses the Center is not only spacious and lovely, but is also ideally located adjacent to the Life Sciences Building and across the street from the Health Sciences Center. We wish the very best to the faculty and staff of the Laufer Center, and look forward to the excellent science that they will produce here. We thank Stony Brook University for all that they have done to make possible the Laufer Center."
The Laufer Center was designed by architect Jim Braddock of the New York City architectural firm of Mitchell-Giurgola. The Center houses a 73-seat teleconferencing auditorium, a Mediascape collaborative research station and an advanced GPU + CPU computing cluster that currently gives the Center the power of nearly 9000 computer cores.
Research at the Center focuses on solving challenging problems at the interface between the physical and life sciences. As an example, a deeper knowledge of the physical bonding forces within molecules will help to improve the computer algorithms that are increasingly used to design next-generation pharmaceuticals and biotech drugs, and to understand the mechanisms of action of proteins. In addition, a deeper understanding of the mathematical principles that describe the network of interrelationships among the thousands of biochemical reactions and genetic control circuits inside cells will aid in developing next-generation approaches for curing diseases.
"On behalf of Stony Brook University, we are deeply honored that the Laufer Family is tying the legacy of their parents to the future of Stony Brook with the establishment of the Louis and Beatrice Laufer Center for Physical and Quantitative Biology," said Samuel L. Stanley Jr., MD, President of Stony Brook University. "There is no doubt that this state of the art Center, under the direction of Ken Dill, creates a new nexus for excellence in the studies at the intersection of physics, mathematics, chemistry, computational science and biology. This is a place where we can assemble the brightest minds and provide them with the opportunity to succeed so they can discover new medicines, continue to decipher the human genome and further our understanding of how healthy biological cells work and how diseased cells fail, and we thank the Laufer family for making it possible."
Laufer Center researchers come from a broad community including Stony Brook departments of chemistry, physics, applied mathematics and statistics, computer science, molecular genetics and microbiology; Cold Spring Harbor Laboratory and Brookhaven National Laboratory. A novel aspect of the Center's research is a core-team approach to problem solving and outreach.
"The Laufer Center provides us with a tremendous opportunity for the development of interdisciplinary approaches to advance biology and medicine through discoveries in physics, mathematics, and computational science," said Dennis N. Assanis, Stony Brook University Provost and Senior Vice President for Academic Affairs. "Stony Brook's west campus has strengths in many of the critically important areas needed to support scientific inquiry and new discovery, such as outstanding departments of physics, applied math, computer science, chemistry, microbiology, and evolution and ecology. By partnering the strengths of these areas with SBU's distinguished medical school, as well as Brookhaven National Laboratory and Cold Spring Harbor Laboratory, the Laufer Center will help us provide fundamental solutions to some of the most difficult medical problems facing us today--problems that will require expertise in both the life sciences and physical sciences."
"In addition to performing research, we train Ph.D. students, mentor postdoctoral researchers, and host regular scientific seminars from distinguished outside scientists," said Ken A. Dill, Director of the Center, a member of the National Academy of Sciences and a past president of the Biophysical Society. He is known internationally for his pioneering work on the physical forces that give rise to the structures and properties of protein molecules. Dr. Dill has dual faculty appointments at Stony Brook in the Department of Physics and Astronomy and the Department of Chemistry.
The Center will house four to six research groups under the Directorship of Dr. Dill and Associate Director, Carlos Simmerling, an Associate Professor in Computational Structural Biology. It serves as a core on Long Island of scientific and educational activity in computational and physical biology. The Center's 13 affiliated faculty lead research groups from physics, mathematics, chemistry, computer science and biology at Stony Brook, as well as Brookhaven National Laboratory and Cold Spring Harbor Laboratory.
The Laufer Center also will sponsor an interdisciplinary graduate training program, directed by David Green, a computational biophysicist and Assistant Professor of Applied Mathematics and Statistics at Stony Brook.
The article above comes from SBU's General University News. The Opening was also covered in Newsday.
Reaping Knowledge from a Deluge of Data
Gene sequencing data is now accumulating at a phenomenal rate, and that rate is increasing faster than Moore's law. This makes computer storage, management and analysis into bottlenecks in the process of reaping knowledge from all that data.In the December first, 2011 New York Times, Michael Schatz of the Laufer Center and Cold Spring Harbor Laboratory (CSHL) explained that the world's annual production of DNA sequencing data today is 13 quadrillion DNA bases, enough to fill a stack of DVDs two miles high. This is a $12-million program to create, not a database, but a knowledgebase (called Kbase) of genetic and other high-throughput information on plant and microbial communities. Michael Schatz of the Laufer Center and CSHL is a co-investigator.
The Kbase will enable scientists to develop new knowledge through free and open access to diverse biological data and models, modeling, analytical and simulation software and inventories of results (described in the DOE's Systems Biology Knowledgebase for a New Era in Biology workshop report.
Department of Energy Funds a Knowledgebase of Plant and Microbial Life
In July, 2011, the U.S. Energy Department (DOE) named Sergei Maslov of the Laufer Center and Brookhaven National Laboratory to be one of four co-principal investigators to create a knowledgebase of plant and microbial life. This is a $12-million program to create, not a database, but a knowledgebase (called Kbase) of genetic and other high-throughput information on plant and microbial communities. Michael Schatz of the Laufer Center and CSHL is a co-investigator.
The Kbase will enable scientists to develop new knowledge through free and open access to diverse biological data and models, modeling, analytical and simulation software and inventories of results (described in the DOE's Systems Biology Knowledgebase for a New Era in Biology workshop report).


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Reward systems - to motivate participation.
Games and songs - to make the lesson fun
I absolutely love what I do and would love to meet you and embark on this exciting journey through the English language with your treasured child.
Teresa was so polite, knowledgeable and well prepared. She made the lesson super fun for my son, and he learnt so much even though it was such a short time. Well done on recruiting such a gem!
Teresa C.
It was such a pleasure giving a lesson to Ethan. I'm so glad it was thoroughly enjoyed.
Hi! My name is Elisabetta, I'm from Italy and I can provide professional Italian, Spanish and English language lessons for all levels. I am an open and friendly person, but also very rigorous with my job and I expect my students be the same, that is positive and committed. The language course I am offering will be tailored to your specific needs and we'll together find the best way to reach your goal: learn a new language and enjoying while doing it!
Elisabetta is a teacher who manages to convey love for her work. It follows you on your path of growth and strongly supports you. He follows different teaching methods according to the needs and priorities of the moment. Punctual, precise and super helpful. That's what I was looking for! Thanks
Elisabetta .
Thank you very much dear, I send you a hug :)
Hi, welcome to my profile!
My name is Alessia and I currently live in Italy. I lived some years in America where I deepened my knowledge of English and American dialects. I am currently specializing in the Spanish and German. In all these years I have given private lessons of Italian, English, Spanish and Japanese, at the moment the most required language. Regarding Japanese, I had the opportunity to experience the teaching of the language in an American College with a native Japanese teacher, implementing the method that they themselves use to learn their language. I will help you in a simple way; conversation is really important to learn a language and even more a good method. No days spent on textbooks are needed, constancy and fun during lessons are the most important part for learning. You will see the results immediately! I am patient, flexible and I will adapt in all ways to your personal needs. I'll wait for you on my profile for the trial lesson and discover an easy and fun method to learn a language as soon as possible.
The teacher is always on time and uses perfect learning materials to learn the language. Very prepared in what she teaches and in the way she does it; very useful lessons!
Alessia T.
Thank you Hilary!
Hello, my name is Corinne and I am a qualified ESL English teacher from England. I have been teaching in classrooms and online for over 3 years and I have many satisfied students. My lessons generally consist of a mixture of conversation and set exercises to help to improve both vocabulary and grammar. I encourage a lot of talking from my students and I give instant written correction so that they are able to recognise any grammatical errors they are making. I take note of repeated mistakes and set exercises for following lessons to address these mistakes accordingly. You will quickly notice an increase in your confidence in speaking English from our lessons, your vocabulary will increase and your grammar and sentence structure will improve. Together, we will reach your goals.
It is always a pleasure to have English lessons with Corinne. The lessons are always a lot of fun and extremely interesting concerning on current affairs and unfortunately the time always ends too early. Very recommended.
Corinne P.
Thank you, Danilo. It is always a pleasure having lessons with you and I have enjoyed our many conversations together. And what a joy that over time they have become easier for both of us to understand! :D
Hi! I've been teaching Dutch, Spanish and Italian for many years, in The Netherlands, for private institutes, for the integration of foreigners into society, and online from Italy, where I currently live.
I will help you, in a simple but effective way, to learn your favorite language(s). By focusing on conversation from the very beginning, I will help you in becoming confident with the language so that you will learn it faster.
Learning a foreign language is not a matter of doing much effort, but rather of being consistent, enjoying the lessons and allowing your intuition to work with you. You will book immediate results while having fun!
I offer you general language courses Italian (A1-C2), Dutch (A1-C1) and Spanish (A1-C1), as well as courses "Basisinburgering" "Inburgeringsexamen A1 and A2".
For English I offer ONLY pronunciation exercises. If you struggle with your pronunciation and you want to become more confident, I can help you achieve your goal. We will practice by reading texts together and you will see amazing results in a very short time.
So if you want to learn a language or improve the one you already speak, whether it is for work, to move abroad or just because you love languages, contact me for a free trial and let me know how I can help you.
I'm looking forward to meeting you!
Serious and professional. Very clear in the explanation and very patient in explaining the uncertainties. Path taken constructive. I am very satisfied.
Elena P.
Hi Vanessa and thank you for your feedback! I am happy to know that you are satisfied and to witness your progress, class after class. It's a pleasure to work with you!
I am a BELIEVER!. Each of you has something to share, give and communicate with others. It's my job to help you do just that!.
English shouldn't be scary. Let me help you become more fluid and spontaneous. Let's break those barriers you've built over time and git rid of those nasty limitations you've created.
Professionals, adults and young adults are my specialties. I've been teaching, coaching, motivating for more than 18 years in a number of different situations: small businesses, multinational companies, the Italian Army, private and public schools, associations, as well as with professionals and individuals. I've also trained teachers working specifically with children and bilingualism and worked many students preparing for traditional language exams and certifications. If you need a personalized program, that's not a problem either!
My own personal experience with learning Italian helps me understand the challenges linked with learning a new language.
I can't wait to meet you! :-)
Marissa is a very professional teacher who can put the student at ease. It is precise, effective and oriented towards achieving the objectives: highly recommended.
Marissa F.
Thanks so much Paola!!! I LOVE working with you guys and have enjoyed every moment. Even after this brief period, we can already start to see some changes. :-)
After living and working in the UK and Germany for many years, I moved to Spain where I have been living for the past sixteen years. Certified in London, I taught for language schools in Frankfurt and worked freelance in Spain teaching all levels. I try to get my students to talk as much as possible because in my experience there is often so much emphasis on learning all language rules that being able to communicate disappears into the background. Depending on the student´s goal, I adjust my classes so that we can achieve that goal as much as possible!
Very happy with teacher Eline! The lesson was very well prepared and a lot of fun. I recommend her to anyone who wants to learn the English language.
Eline E.
Thank you for your feedback Noelle, I will continue to do my very best for you!
Hello my dear future student!
It doesn't matter how old you are, what is your level of a foreign language and why you want to learn it. If you are already here, then you are ready to plunge into the world of other cultures and this is without any doubt a really cool thing.
I can offer you lessons for any taste and purpose of English, Spanish, French or Russian. I am a diplomated translator with working experience as a tutor (including via Skype) and as a language school teacher. In the course of my professional activity, I worked with children from 6 years old, teenagers and adults up to 65 years old.
I love languages and I want to make YOU loving them as much as I do.
Let's start this adventure together cause "there's no better time than now".
See you soon!
Very good teacher. Listening to our expectations, give good explanations and always smiling. Very flexible in terms of schedules!
Krystyna K.
Thank you Kelly! The pleasure is mine to work with you :)
I am an experienced English tutor specialized in IELTS and TOEFL exam preparation. My main focus is on speaking and writing section with additional focus or reading and listening.I offer a result oriented learning plan to achieve your desired score. The student will have homework after every lesson and ample opportunity to practice speaking during the lesson. I prepare a custom learning plan for every student depending on their present English level. I am an easy going and jovial personality and i make the lessons interesting by including real life examples. The student can expect smooth learning to achieve their goal. I also teach basic conversational English and prepare students for interview or presentation. For further information , the students are requested to take the trial lesson and contact me by message.
Great teacher, lovely person, smart and open minded. I also like the fact that he is aware of cultural differences and his methodology of teaching is actually so effective. I was very happy to have selected him, he did an amazing job!
If you are looking for a teacher who knows exactly what you should know before the exam, I strongly recommended contacting Tapas. He will show you the ingredients needed to write a good essay, report and proposal and pay attention to the rules of constructing statements in specific parts required during the exam.
I Highly recommend him if you are looking for....
Catherine is very professional, I found the class very helpful and would fully recommend her as a teacher Thanks Catherine !
I am Yora, a self-employed English tutor. I have been working with adults searching for tailor-made English totorials or/and flexible learning schedule since 2013. The lessons I offer are pretty much focussed on good communication and natural learning in a modern way, i.e. with using IT everywhere we can.
My methods
I am a proponent of learner-centred approaches and methods which are non-directive and rely on learners' intrinsic motivation. They usually learn a foreign language because they need it for their work, study, travel, etc.. At the same time, when they do it in an enjoyable manner, in accordance with their nature, interests, and style, and with opportunities to choose their activities and learning materials themselves, it is also intrinsically motivated learning.
In professional terms, I try to creatively implement ideas and methods from approaches such as Direct one, Natural Learning, Democratic Education, and in particular Suggestopedia, Montessori pedagogy, Summerhill and Sudbury Schools.
In practical terms, it may mean providing learner colleagues with choices and often asking them what they want to do, and whether they want to do one or another task. For instance, they can choose whether to use a student's book or not, and if yes, to choose among at least two alternatives. My primary focus is LEARNING, and I encourage the colleagues to be active and increasingly independent learners to the point they can confidently manage their own language learning themselves. Of course, efficient communication and IT are natural components of my tutorials because they are part of life.
So my pillars are:
1. Reliance on the intrinsic motivation (self-driven and self-determined learning); my role is to be learner's guide, to facilitate their learning, and encourage their independence;
2. Good communication;
3. eLearning (IT as inherent component);
4. Creativity and art.
What my students will learn
Firstly, my learner colleagues will achieve their learning goals, be they to cover a relevant student's book material necessary for passing an English level test, or to advance with their language command in areas they want or find necessary for their work, travel, study, etc., in a rather tailor made manner.
Secondly, my learner colleagues will learn to become more independent English learners. As the language is everywhere nowadays, there are countless accessible learning options, and it is usually a matter of motivation, knowing how to learn, and good self-management to go as far as they need in it
My teaching experience
My English teaching career started in private language centres in Sofia in 2013. I have been working independently as an online English tutor since 2015.. Among my students, there have been from pre-school children (with the youngest one aged four) through teenagers to adults just before retirement. However I have specialized in and feel most comfortable tutoring English to adults. Currently, my online learner colleagues are usually white-collar workers and pink-collar ones investing in their English skills for the sake of their career.
Apart from it, I have been in the field of learning for almost thirty years starting with my university studies in education, and then focusing on non-formal learning (outside school) and lifelong learning. The latter covers seven years as a professional in staff qualification and career guidance in National Institute for Education in Sofia, as well as fourteen years as an independent expert for the European Commission under their programmes related to education, lifelong learning, youth, and European Citizenship.
As the first lesson, the teaching strategy was excellent prepared. Also we used a lot of websites to make reading , answering and discussions.
I am very good with beginners and intermediate students. I help with pronunciation, learning new vocabulary and grammar. I always offer corrections and offer endless speaking opportunities.
I enjoy teaching and more than anything I enjoy teaching English, but as much as I teach I am always looking for an opportunity to learn. I allow myself to learn something from my students as many times as they are willing to teach. Together with my students, we create an atmosphere of on-going conversation around our class topic.
I have a Bachelor of English degree, as well as a 120-HOUR TEFL Certificate. I am mostly fluent in English, as it has the language medium throughout my entire life and school career.
My experience with teacher Comfort was excellent. She is patient, kind and explains in a way that is very easy to understand, giving you support tools for learning. I highly recommend her. Thank you so much Comfort.
Hello, my name is Allison! I have been teaching German for four years and English for two. I work to fit my lessons my students' needs as well as trying to make them enjoyable.
In terms of special topics, I have experience giving lessons in German pronunciation. Also, in addition to my BA in German Studies, I also have an undergraduate degree in music.
Thank you for your time. I look forward to meeting you!


text:
JACKSONVILLE, Fla. – Circuit Judge Mark Hulsey on Monday denied a 32-year-old woman charged with second-degree murder a motion for a "stand your ground" defense in the stabbing death of her ex-boyfriend.
Jennifer Goodman's motion would have given her immunity from the murder charge in the September 2011 killing of 33-year-old Anthony Norman.
Goodman claims she was a victim of physical abuse and feared for her life during confrontation. She said she suffered years of physical abuse at the hands of her ex, which is why she claims she retaliated.
Overcome with disappointment at the judge's decision Monday, Goodman was consoled by her family, knowing her murder case will indeed go to trial.
"Of course she's sad because she was hoping and depending that the law would have been in place for her," family spokeswoman Linda Dayson said.
According to testimony at the "stand your ground" hearing last month, Norman left the Shortreed Street home after beating Goodman during an argument.
"He had me by my hair and he just kept punching me in my face," Goodman testified last month. "I guess he kept hitting me until he got tired of hitting, and blood was everywhere. Then he left. He left. He walked out the door. He left. No, he didn't leave. He went in the room and got my phone and he got my money. And then he left."
According to the "stand your ground" petition, after the fight that night, Goodman left the house and reported the incident to family members.
"Her brother and his friend returned back to the house to retaliate, striking Norman at least six times in the face," the petition reads.
At one point, Goodman said she went outside with a knife to protect herself and her family, and when Norman turned around, the knife went into his chest. Goodman testified that Norman "ran into the knife" she was holding.
"Jennifer had a reasonable fear of imminent peril or death, which is why she chose to use deadly force," according to the petition.
Legal experts say when Norman left the scene and Goodman went looking for him, she essentially became the aggressor and provoked another altercation.
"At that point and time, when the victim had retreated from the scene, her fear, her reasonable fear of imminent injury of death, was ended at the moment and time when she was there," said attorney Gene Nichols, who's not affiliated with the case.
Nichols said "stand your ground" immunity is rare, adding that most judges would rather leave the decision up to a jury. But Goodman's family says she had no other choice than to defend herself.
"I'm really not understanding what the system is wanting," Dayson said. "Do they want them to continue to be battered by these men? I mean, especially when you have paperwork, restraining orders, and the police have been called out."
Norman was Goodman's on-again, off-again boyfriend since she was 14, and the two had a child together.
Goodman's next court hearing is scheduled for Feb. 11.


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This is a tremendous website
I have been very fortunate to find 7 useful records from this website – this is the kind of
information I've got just from one of them:
'Number on Index 1883 CROMPTON JAMES Born 1821 (Ch. mem., Cannon Street Preston). Died 9 January 1898 Cheetham Hill (Manchester)
1840-1843 Blackburn Academy; rem. to Lancashire 1843-45
1843 Lancashire Independent College
Did not enter the Ministry but became Deacon and prominent Sunday School
worker at Cannon Street, Preston where he followed teaching profession.
Subsequently removed from Preston to Manchester, where known in scholastic
circles as a Professor of English. Died at home of his son-in-law at Cheetham Hill, 9 January 1898 age 76; buried Preston Cemetery. B. Nightingale in Blackburn Times March 192.'
Charles Surman's extraordinary biographical card index of Congregational ministers was given to Dr Williams's Library in 1960. The Surman Index Online makes the contents available electronically via the internet for the first time. The index includes the names of about 32,000 ministers, and, where known, their dates, details of their education, ministries or other employment, together with the sources used. It covers the period from the mid-seventeenth century to 1972, and though it focuses on England and Wales, it includes Congregational ministers serving abroad provided they trained or served as ministers in Britain. Although intended as an index of Congregational ministers, it also gives details of seventeenth- and eighteenth-century Presbyterians. The card index has been much used by academics and by local and family historians.
This open access online edition has been funded by a Small Research Grant from the British Academy with further grants from the Congregational Memorial Hall Trust and Dr Williams's Trust. We gratefully acknowledge the financial support received from these bodies, without which the work could not have been undertaken.
Do have a look at it and see if you can find any records for your own research.
Related articles
- Cheetham Lancashire Imperial Gazetteer of England and Wales Circa 1870 (parishmouse.wordpress.com)