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  • richardmitnick 9:17 am on November 1, 2018 Permalink | Reply
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    From Discover Magazine: “Meet the Biochemist Engineering Proteins From Scratch” 

    DiscoverMag

    From Discover Magazine

    October 30, 2018
    Jonathon Keats

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    David Baker. Brian Dalbalcon/UW Medicine

    U Washington Dr. David Baker

    In a sleek biochemistry laboratory at the University of Washington, postdoctoral fellow Yang Hsia is watching yellowish goo — the liquefied remains of E. coli — ooze through what looks like a gob of white marshmallow. “This isn’t super exciting,” he says.

    While growing proteins in bacteria and then purifying them, using blobby white resin as a filter, doesn’t make for riveting viewing, the end product is extraordinary. Accumulating in Hsia’s resin is a totally artificial protein, unlike anything seen in nature, that might just be the ideal chassis for the first universal flu vaccine.

    David Baker, Hsia’s adviser, calls this designer protein a “Death Star.” Imaged on his computer, its structure shows some resemblance to the notorious Star Wars superweapon. Though microscopic, by protein standards it’s enormous: a sphere made out of many interlocking pieces.

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    The Death Star artificial protein. Institute for Protein Design

    “We’ve figured out a way to put these building blocks together at the right angles to form these very complex nanostructures,” Baker explains. He plans to stud the exterior with proteins from a whole suite of flu strains so that the immune system will learn to recognize them and be prepared to fend off future invaders. A single Death Star will carry 20 different strains of the influenza virus.

    Baker hopes this collection will cover the entire range of possible influenza mutation combinations. This all-in-one preview of present and future flu strains could replace annual shots: Get the Death Star vaccination, and you’ll already have the requisite antibodies in your bloodstream.

    As Baker bets on designer proteins to defeat influenza, others are betting on David Baker.

    After revolutionizing the study of proteins — molecules that perform crucial tasks in every cell of every natural organism — Baker is now engineering them from scratch to improve on nature. In late 2017, the Open Philanthropy Project gave his University of Washington Institute for Protein Design more than $10 million to develop the Death Star and support Rosetta, the software platform he conceived in the 1990s to discover how proteins are assembled. Rosetta has allowed Baker’s lab not only to advance basic science and pioneer new kinds of vaccines, but also to create drugs for genetic disorders, biosensors to detect toxins and enzymes to convert waste into biofuels.

    His team currently numbers about 80 grad students and postdocs, and Baker is in constant contact with all of them. He challenges their assumptions and tweaks their experiments while maintaining an egalitarian environment in which ideas may come from anyone. He calls his operation a “communal brain.” Over the past quarter-century, this brain has generated nearly 450 scientific papers.

    “David is literally creating a new field of chemistry right in front of our eyes,” says Raymond Deshaies, senior vice president for discovery research at the biotech company Amgen and former professor of biology at Caltech. “He’s had one first after another.”

    Nature’s Origami

    When Baker was studying philosophy at Harvard University, he took a biology class that taught him about the so-called “protein folding problem.” The year was 1983, and scientists were still trying to make sense of an experiment, carried out in the early ’60s by biochemist Christian Anfinsen, that revealed the fundamental building blocks of all life on Earth were more complex than anyone imagined.

    The experiment was relatively straightforward. Anfinsen mixed a sample of the protein ribonuclease — which breaks down RNA — with a denaturant, a chemical that deactivated it. Then he allowed the denaturant to evaporate. The protein started to function again as if nothing ever happened.

    What made this simple experiment so striking was the fact that the amino acids in protein molecules are folded in three-dimensional forms that make origami look like child’s play. When the denaturant unfolded Anfinsen’s ribonuclease, there were myriad ways it could refold, resulting in structures as different as an origami crane and a paper airplane. Much as the folds determine whether a piece of paper can fly across a room, only one fold pattern would result in functioning ribonuclease. So the puzzle was this: How do proteins “know” how to refold properly?

    “Anfinsen showed that the information for both structure and activity resided in the sequence of amino acids,” says University of California, Los Angeles, biochemist David Eisenberg, who has been researching protein folding since the 1960s. “There was a hope that it would be possible to use sequence information to get three-dimensional structural information. Well, that proved much more difficult than anticipated.”

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    Protein molecules play critical roles in every aspect of life. The way each protein folds determines its function, and the ways to fold are virtually limitless, as shown in this small selection of proteins visualized through the software platform Rosetta, born in Baker’s lab. Institute for Protein Design.

    Baker was interested enough in protein folding and other unsolved mysteries of biology to switch majors and apply to grad school. “I’d never worked in a lab before,” he recalls. He had only a vague notion of what biologists did on a daily basis, but he also sensed that the big questions in science, unlike philosophy, could actually be answered.

    Grad school plunged Baker into the tediousness and frustrations of benchwork, while also nurturing some of the qualities that would later distinguish him. He pursued his Ph.D. under Randy Schekman, who was studying how molecules move within cells, at the University of California, Berkeley. To aid in this research, students were assigned the task of dismantling living cells to observe their internal molecular traffic. Nearly half a dozen of them, frustrated by the assignment’s difficulty, had given up by the time Baker got the job.

    Baker decided to follow his instincts even though it meant going against Schekman’s instructions. Instead of attempting to keep the processes within a cell still functioning as he dissected it under his microscope, Baker concentrated on preserving cell structure. If the cell were a wristwatch, his approach would be equivalent to focusing on the relationship between gears, rather than trying to keep it ticking, while taking it apart.

    “He was completely obsessed,” recalls Deshaies, who was his labmate at the time (and one of the students who’d surrendered). Nobody could stop Baker, or dissuade him. He worked for months until he proved his approach was correct: Cell structure drove function, so maintaining its anatomy preserved the internal transportation network. Deshaies believes Baker’s methodological breakthrough was “at the core of Randy’s Nobel Prize,” awarded in 2013 for working out one of the fundamentals of cellular machinery.

    But Baker didn’t dwell on his achievement, or cell biology for that matter. By 1989, Ph.D. in hand, he’d headed across the Bay to the University of California, San Francisco, where he switched his focus to structural biology and biochemistry. There he built computer models to study the physical properties of the proteins he worked with at the bench. Anfinsen’s puzzle remained unsolved, and when Baker got his first faculty appointment at the University of Washington, he took up the protein-folding problem full time.

    From Baker’s perspective, this progression was perfectly natural: “I was getting to more and more fundamental problems.” Deshaies believes Baker’s tortuous path, from cells to atoms and from test tubes to computers, has been a factor in his success. “He just has greater breadth than most people. And you couldn’t do what he’s done without being somewhat of a polymath.”

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    Illustration above: National Science foundation. Illustrations below: Jay Smith

    Rosetta Milestone

    Every summer for more than a decade, scores of protein-folding experts convene at a resort in Washington’s Cascade Mountains for four days of hiking and shop talk. The only subject on the agenda: how to advance the software platform known as Rosetta.

    David Baker’s Rosetta@home project, a project running on BOINC software from UC Berkeley


    Rosetta@home BOINC project



    They call it Rosettacon.

    Rosetta has been the single most important tool in the quest to understand how proteins fold, and to design new proteins based on that knowledge. It is the link between Anfinsen’s ribonuclease experiment and Baker’s Death Star vaccine.

    When Baker arrived at the University of Washington in 1993, researchers knew that a protein’s function was determined by its structure, which was determined by the sequence of its amino acids. Just 20 different amino acids were known to provide all the raw ingredients. (Their particular order — specified by DNA — makes one protein fold into, say, a muscle fiber and another fold into a hormone.) Advances in X-ray crystallography, a technique for imaging molecular structure, had provided images of many proteins in all their folded splendor. Sequencing techniques had also improved, benefitting from the Human Genome Project as well as the exponential increase in raw computing power.

    “There’s a right time for things,” Baker says in retrospect. “To some extent, it’s just luck and historical circumstance. This was definitely the right time for this field.”

    Which is not to say that modeling proteins on a computer was a simple matter of plugging in the data. Proteins fold to their lowest free energy state: All of their amino acids must align in equilibrium. The trouble is that the equilibrium state is just one of hundreds of thousands of options — or millions, if the amino acid sequence is long. That’s far too many possibilities to test one at a time. Nature must have another way of operating, given that folding is almost instantaneous.

    Baker’s initial approach was to study what nature was doing. He broke apart proteins to see how individual pieces behaved, and he found that each fragment was fluctuating among many possible structures. “And then folding would occur when they all happened to be in the right geometry at the same time,” he says. Baker designed Rosetta to simulate this dance for any amino acid sequence.

    Baker wasn’t alone in trying to predict how proteins fold. In 1994, the protein research community organized a biennial competition called CASP (Critical Assessment of Protein Structure Prediction). Competitors were given the amino acid sequences of proteins and challenged to anticipate how they would fold.

    The first two contests were a flop. Structures that competitors number-crunched looked nothing like folded proteins, let alone the specific proteins they were meant to predict. Then everything changed in 1998.

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    Rosetta’s impressive computational power allows researchers to predict how proteins — long, complex chains of amino acids — will fold; the platform also helps them reverse engineer synthetic proteins to perform specific tasks in medicine and other fields. Brian Dalbalcon/UW Medicine.

    Function Follows Form

    That summer, Baker’s team received 20 sequences from CASP, a considerable number of proteins to model. But Baker was optimistic: Rosetta would transform protein-folding prediction from a parlor game into legitimate science.

    In addition to incorporating fresh insights from the bench, team members — using a janky collection of computers made of spare parts — found a way to run rough simulations tens of thousands of times to determine which fold combinations were most likely.

    They successfully predicted structures for 12 out of the 20 proteins. The predictions were the best yet, but still approximations of actual proteins. In essence, the picture was correct, but blurry.

    Improvements followed rapidly, with increased computing power contributing to higher-resolution models, as well as improved ability to predict the folding of longer amino acid chains. One major leap was the 2005 launch of Rosetta@Home, a screensaver that runs Rosetta on hundreds of thousands of networked personal computers whenever they’re not being used by their owners.

    Yet the most significant source of progress has been RosettaCommons, the community that has formed around Rosetta. Originating in Baker’s laboratory and growing with the ever-increasing number of University of Washington graduates — as well as their students and colleagues — it is Baker’s communal brain writ large.

    Dozens of labs continue to refine the software, adding insights from genetics and methods from machine learning. New ideas and applications are constantly emerging.

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    Protein (in green) enveloping fentanyl molecule. Bick et al. eLife 2017.

    The communal brain has answered Anfinsen’s big question — a protein’s specific amino acid alignment creates its unique folding structure — and is now posing even bigger ones.

    “I think the protein-folding problem is effectively solved,” Baker says. “We can’t necessarily predict every protein structure accurately, but we understand the principles.

    “There are so many things that proteins do in nature: light harvesting, energy storage, motion, computation,” he adds. “Proteins that just evolved by pure, blind chance can do all these amazing things. What happens if you actually design proteins intelligently?”

    De Novo Design

    Matthew Bick is trying to coax a protein into giving up its sugar habit for a full-blown fentanyl addiction. His computer screen shows a colorful image of ribbons and swirls representing the protein’s molecular structure. A sort of Technicolor Tinkertoy floats near the center, representing the opioid. “You see how it has really good packing?” he asks me, tracing the ribbons with his finger. “The protein kind of envelops the whole fentanyl molecule like a hot dog bun.”

    A postdoctoral fellow in Baker’s lab, Bick engineers protein biosensors using Rosetta. The project originated with the U.S. Department of Defense. “Back in 2002, Chechen rebels took a bunch of people hostage, and there was a standoff with the Russian government,” he says. The Russians released a gas, widely believed to contain a fentanyl derivative, that killed more than a hundred people. Since then, the Defense Department has been interested in simple ways to detect fentanyl in the environment in case it’s used for chemical warfare in the future.

    Proteins are ideal molecular sensors. In the natural world, they’ve evolved to bind to specific molecules like a lock and key. The body uses this system to identify substances in its environment. Scent is one example; specific volatiles from nutrients and toxins fit into dedicated proteins lining the nose, the first step in alerting the brain to their presence. With protein design, the lock can be engineered to order.

    For the fentanyl project, Bick instructed Rosetta to modify a protein with a natural affinity for the sugar xylotetraose. The software generated hundreds of thousands of designs, each representing a modification of the amino acid sequence predicted to envelop fentanyl instead of sugar molecules. An algorithm then selected the best several hundred options, which Bick evaluated by eye, eventually choosing 62 promising candidates. The protein on Bick’s screen was one of his favorites.

    “After this, we do the arduous work of testing designs in the lab,” Bick says.

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    Cassie Bryan, a senior fellow at Baker’s Institute for Protein Design at the University of Washington, checks on a tube of synthetic proteins. The proteins, not seen in nature, are in the process of thawing and being prepped to test how they perform. Brian Dalbalcon/UW Medicine.

    With another image, he reveals his results. All 62 contenders have been grown in yeast cells infused with synthetic genes that spur the yeasts’ own amino acids to produce the foreign proteins. The transgenic yeast cells have been exposed to fentanyl molecules tagged with a fluorescing chemical. By measuring the fluorescence — essentially shining ultraviolet light on the yeast cells to see how many glow with fentanyl — Bick can determine which candidates bind to the opioid with the greatest strength and consistency.

    Baker’s lab has already leveraged this research to make a practical environmental sensor. Modified to glow when fentanyl binds to the receptor site, Bick’s customized protein can now be grown in a common plant called thale cress. This transgenic weed can cover terrain where chemical weapons might get deployed, and then glow if the dangerous substances are present, providing an early warning system for soldiers and health workers.

    The concept can also be applied to other biohazards. For instance, Bick is now developing a sensor for aflatoxin, a residue of fungus that grows on grain, causing liver cancer when consumed by humans. He wants the sensor to be expressed in the grain itself, letting people know when their food is unsafe.

    But he’s going about things differently this time around. Instead of modifying an existing protein, he’s starting from scratch. “That way, we can control a lot of things better than in natural proteins,” he explains. His de novo protein can be much simpler, and have more predictable behavior, because it doesn’t carry many million years of evolutionary baggage.

    For Baker, de novo design represents the summit of his quarter-century quest. The latest advances in Rosetta allow him to work backward from a desired function to an appropriate structure to a suitable amino acid sequence. And he can use any amino acids at all — thousands of options, some already synthesized and others waiting to be designed — not only the 20 that are standard in nature for building proteins.

    Without the freedom of de novo protein design, Baker’s Death Star would never have gotten off the ground. His group is now also designing artificial viruses. Like natural viruses, these protein shells can inject genetic material into cells. But instead of infecting you with a pathogen, their imported DNA would patch dangerous inherited mutations. Other projects aim to take on diseases ranging from malaria to Alzheimer’s.

    In Baker’s presence, protein design no longer seems so extraordinary. Coming out of a brainstorming session — his third or fourth of the day — he pulls me aside and makes the case that his calling is essentially the destiny of our species.

    “All the proteins in the world today are the product of natural selection,” he tells me. “But the current world is quite a bit different than the world in which we evolved. We live much longer, so we have a whole new class of diseases. We put all these nasty chemicals into the environment. We have new needs for capturing energy.

    “Novel proteins could solve a lot of the problems that we face today,” he says, already moving to his next meeting. “The goal of protein design is to bring those into existence.”

    See the full article here .

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  • richardmitnick 4:51 pm on September 28, 2018 Permalink | Reply
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    From World Community Grid (WCG): “A Graduation, a Paper, and a Continuing Search for the ‘Help Stop TB’ Researchers” 

    New WCG Logo

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    From World Community Grid (WCG)

    By: Dr. Anna Croft
    University of Nottingham, UK
    28 Sep 2018

    Summary
    In this update, principal investigator Dr. Anna Croft shares two recent milestones for the Help Stop TB research team, and discusses their continuing search for additional researchers.

    The Help Stop TB (HSTB) project uses the massive computing power of World Community Grid to examine part of the coating of Mycobacterium tuberculosis, the bacterium that causes tuberculosis. We hope that by learning more about the mycolic acids that are part of this coating, we can contribute to the search for better treatments for tuberculosis, which is one of the world’s deadliest diseases.

    Graduation Ceremony for Dr. Athina Meletiou

    In recent news for the HSTB project, Dr. Athina Meletiou has now officially graduated. It was a lovely day, finished off with some Pimms and Lemonade in the British tradition.

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    Athina (center) with supervisors Christof (left) and Anna (right)

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    Athina and her scientific “body-guard,” Christof

    Search for New Team Members Continues

    We are still looking for suitably qualified chemists, biochemists, mathematicians, engineers and computer scientists to join our team, especially to develop the new analytical approaches (including machine-learning approaches) to understand the substantial data generated by the World Community Grid volunteers.

    We will be talking to students from our BBSRC-funded doctoral training scheme in the next few days and encouraging them to join the project. Click here for more details.

    Paper Published

    Dr. Wilma Groenwald, one of the founding researchers for the HSTB project, recently published a paper describing some of the precursor work to the project. The paper, which discusses the folding behavior of mycolic acids, is now freely available on ChemRXiv Revealing Solvent-Dependent Folding Behavior of Mycolic Acids from Mycobacterium Tuberculosis by Advanced Simulation Analysis.

    We hope to have Athina’s first papers with World Community Grid data available later in the year, and will keep you updated.

    Thank you to all volunteers for your support.

    See the full article here.


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    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
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    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

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    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
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    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Microbiome Immunity Project

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    Outsmart Ebola together

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    Mapping Cancer Markers
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    Uncovering Genome Mysteries
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    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

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  • richardmitnick 1:49 pm on August 8, 2018 Permalink | Reply
    Tags: , , BOINC-Berkeley Open Infrastructure for Network Computing, Maping Cancer Markets project takes on sarcoma, ,   

    From World Community Grid (WCG): “Sarcoma Dataset Coming Soon to Mapping Cancer Markers Project” 

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    From World Community Grid (WCG)

    8 Aug 2018
    Dr. Igor Jurisica

    In this comprehensive update, the Mapping Cancer Markers team explains how they are determining which genes and gene signatures carry the greatest promise for lung cancer diagnosis. They also introduce the next type of cancer–sarcoma–to be added soon to the project.

    The Mapping Cancer Markers (MCM) project continues to process work units for the ovarian cancer dataset. As we accumulate these outcomes, we continue to analyze MCM results from the lung cancer dataset. In this update, we discuss preliminary findings from this analysis. In addition, we introduce the sarcoma dataset that will be our focus in the next stage.

    Patterns of gene-family biomarkers in lung cancer

    In cancer, and human biology in general, multiple groups of biomarkers (genes, protein, microRNAs, etc.) can have similar patterns of activity and thus clinical utility, helping diagnosis, prognosis or predicting treatment outcome. For each cancer subtype, one could find large number of such groups of biomarkers, each having similar predictive power; yet current statistical and AI-based methods identify only one from a given data set.

    We have two primary goals in MCM: 1) to find good groups of biomarkers for the cancers we study, and 2) to identify how and why these biomarkers form useful groups, so we can build a heuristic approach that will find such groups for any disease without needing months of computation on World Community Grid. The first goal will give us not only information that after validation may be useful in clinical practice, but importantly, it will generate data that we will use to validate our heuristics.

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    Illustration 1: Proteins group by similar interactions and similar biological functions.

    Multiple groups of biomarkers exist primarily due to the redundancy and complex wiring of the biological system. For example, the highly interconnected human protein-protein interaction network enables us to see how individual proteins perform diverse molecular functions and together contribute to a specific biological process, as shown above in Illustration 1. Many of these interactions change between healthy and disease states, which in turn affects the functions these proteins carry. Through these analyses, we aim to build models of these processes that in turn could be used to design new therapeutic approaches.

    Two specific groups of biomarkers may appear different from each other, yet perform equivalently because the proteins perform similar molecular functions. However, using these groups of biomarkers for patient stratification may not be straightforward. Groups of biomarkers often do not validate in new patient cohorts or when measured by different biological assays, and there are thousands of possible combinations to consider. Some groups of biomarkers may have all reagents available while others may need to be develop (or be more expensive); they may also have different robustness, sensitivity and accuracy, affecting their potential as clinically useful biomarkers.

    At the present time, there is no effective approach to find all good groups of biomarkers necessary to achieve the defined goal, such as accurately predicting patient risk or response to treatment.

    The first goal of the Mapping Cancer Markers project is to gain a deeper understanding of the “rules” of why and how proteins interact and can be combined to form a group of biomarkers, which is essential to understanding their role and applicability. Therefore, we are using the unique computational resource of World Community Grid to systematically survey the landscape of useful groups of biomarkers for multiple cancers and purposes (diagnosis and prognosis). Thereby, we established a benchmark for cancer gene biomarker identification and validation. Simultaneously, we are applying unsupervised learning methods such as hierarchical clustering to proteins that group by predictive power and biological function.

    The combination of this clustering and the World Community Grid patterns enables us to identify generalized gene clusters that provide deeper insights to the molecular background of cancers, and give rise to more reliable groups of gene biomarkers for cancer detection and prognosis.

    Currently, we are focusing on the first-phase results from the lung cancer dataset, which focused on a systematic exploration of the entire space of potential fixed-length groups of biomarkers.

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    Illustration 2: Workflow of the MCM-gene-pattern-family search. The results of the World Community Grid analysis combined with the unsupervised clustering of genes identifies a set of gene-pattern-families, generalizing the groups of biomarkers. Finally, the results are evaluated using known cancer biomarkers and by using functional annotations, such as signaling pathways, gene ontology function and processes.

    As depicted above in Illustration 2, World Community Grid computed about 10 billion randomly selected groups of biomarkers, to help us understand the distribution of which group sizes and biomarker combinations perform well, which in turn we will use to validate heuristic approaches. Analysis showed that about 45 million groups of biomarkers had a high predictive power and passed the quality threshold. This evaluation gives us a detailed and systematic picture of which genes and gene groups carry the most valuable information for lung cancer diagnosis. Adding pathway and protein interaction network data enables us to further interpret and fathom how and why these groups of biomarkers perform well, and what processes and functions these proteins carry.

    Simultaneously, we used the described lung cancer data to discover groups of similar genes. We assume that these genes or the encoded proteins fulfill similar biological functions or are involved in the same molecular processes.

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    Illustration 3: Evaluation of the hierarchical clustering of the lung cancer data, using the complete linkage parameter, for different numbers of groups indicated by the K-values (100 to 1000). The first plot shows the silhouette value – a quality metric in this clustering, i.e., measure of how well each object relates to its cluster compared to other clusters. The second plot depicts the inter- and intra-cluster distance and the ratio of intra/inter cluster distance.

    To find the appropriate clustering algorithms and the right number of gene groups (clusters) we use different measures to evaluate the quality of each of the individual clustering. For instance, Illustration 3 (above) shows the results of the evaluation of the hierarchical clustering for different numbers of clusters. To evaluate clustering quality, we used silhouette value (method for assessing consistency within clusters of data, i.e., measure of how well each object relates to its own cluster compared to other clusters). A high silhouette value indicates good clustering configuration, and the figure shows a large increase in the silhouette value at 700 gene groups. Since this indicates a significant increase in quality, we subsequently select this clustering for further analysis.

    Not all combinations of biological functions or the lack of it will lead to cancer development and will be biologically important. In the next step, we apply a statistical search to investigate which combinations of clusters are most common among the well-preforming biomarkers, and therefore result in gene groups or pattern families. Since some gene-pattern-families are likely to occur even at random, we use enrichment analysis to ensure the selection only contains families that occur significantly more often than random.

    In the subsequent step we validated the selected generalized gene-pattern-families using an independent set of 28 lung cancer data sets. Each of these studies report one or several groups of biomarkers of up- or down-regulated genes that are indicative for lung cancer.


    Illustration 4: Shown is a selection of high performing pattern families and how they are supported by 28 previously published gene signatures. Each circle in the figure indicates the strength of the support: The size of the circle represents the number of clusters in the family that where found significantly more often in the signature of this study. The color of the circle indicates the average significance calculated for all clusters in the pattern-family.

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    Illustration 5: One of the most frequent gene-pattern-families, is a combination of cluster 1, 7 and 21. We annotated each cluster with pathways using pathDIP and visualized it using word clouds (the larger the word/phrase, the most frequently it occurs).

    The word cloud visualization indicates that cluster 7 is involved in pathways related to GPCRs (G protein–coupled receptor) and NHRs (nuclear hormone receptors). In contrast, the genes in cluster 1 are highly enriched in EGFR1 (epidermal growth factor receptor) as well as translational regulation pathways. Mutations affecting the expression of EGFR1, a transmembrane protein, have shown to result in different types of cancer, and in particular lung cancer (as we have shown earlier, e.g., (Petschnigg et al., J Mol Biol 2017; Petschnigg et al., Nat Methods 2014)). The aberrations increase the kinase activity of EGFR1, leading to hyperactivation of downstream pro-survival signaling pathways and a subsequent uncontrolled cell division. The discovery of EGFR1 initiated the development of therapeutic approaches against various cancer types including lung cancer. The third group of genes are common targets of microRNAs. Cluster 21 indicates strong involvement with microRNAs, as we and others have shown before (Tokar et al., Oncotarget 2018; Becker-Santos et al., J Pathology, 2016; Cinegaglia et al., Oncotarget 2016).

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    Illustration 6: Evaluation of enriched pathways for cluster 1. Here we used our publicly available pathway enrichment analysis portal pathDIP (Rahmati et al., NAR 2017). The network was generated with our network visualization and analysis tool NAViGaTOR 3 (http://ophid.utoronto.ca/navigator).

    The final illustration evaluates the 20 most significantly enriched pathways for cluster 1. The size of the pathway nodes corresponds to the number of involved genes, and the width of the edges corresponds the number genes of overlapping between pathways. One can see that all pathways involved in translation are highly overlapping. mRNA-related pathways form another highly connected component in the graph. The EGFR1 pathway is strongly overlapping with many of the other pathways, indicating that genes that are affected by those pathways are involved in a similar molecular mechanism.

    Sarcoma

    After lung and ovarian cancers, next we will focus on sarcoma. Sarcomas are a heterogeneous group of malignant tumors that are relatively rare. They are typically categorized according to the morphology and type of connective tissues that they arise in, including fat, muscle, blood vessels, deep skin tissues, nerves, bones and cartilage, which comprises less than 10% of all malignancies (Jain 2010). Sarcomas can occur anywhere in the human body, from head to foot, can develop in patients of any age including children, and often vary in aggressiveness, even within the same organ or tissue subtype (Honore 2015). This suggests that a histological description by organ and tissue type is neither sufficient for categorization of the disease nor does it help in selecting the most optimal treatment.

    Diagnosing sarcomas poses a particular dilemma, not only due to their rarity, but also due to their diversity, with more than 70 histological subtypes, and our insufficient understanding of the molecular characteristics of these subtypes (Jain 2010).

    Therefore, recent research studies focused on molecular classifications of sarcomas based on genetic alterations, such as fusion genes or oncogenic mutations. While research achieved major developments in local control/limb salvage, the survival rate for “high-risk” soft tissue sarcomas (STSs) has not improved significantly, especially in patients with a large, deep, high-grade sarcoma (stage III) (Kane III 2018).

    For these reasons, in the next phase of World Community Grid analysis, we will focus on the evaluation of the genomic background of sarcoma. We will utilize different sequencing information and technologies to gain a broader knowledge between the different levels of genetic aberrations and the regulational implications. We will provide a more detailed description of the data and the incentives in the next update.

    Petschnigg J, Kotlyar M, Blair L, Jurisica I, Stagljar I, and Ketteler R, Systematic identification of oncogenic EGFR interaction partners, J Mol Biol, 429(2): 280-294, 2017.
    Petschnigg, J., Groisman, B., Kotlyar, M., Taipale, M., Zheng, Y., Kurat, C., Sayad, A., Sierra, J., Mattiazzi Usaj, M., Snider, J., Nachman, A., Krykbaeva, I., Tsao, M.S., Moffat, J., Pawson, T., Lindquist, S., Jurisica, I., Stagljar, I. Mammalian Membrane Two-Hybrid assay (MaMTH): a novel split-ubiquitin two-hybrid tool for functional investigation of signaling pathways in human cells; Nat Methods, 11(5):585-92, 2014.
    Rahmati, S., Abovsky, M., Pastrello, C., Jurisica, I. pathDIP: An annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. Nucl Acids Res, 45(D1): D419-D426, 2017.
    Kane, John M., et al. “Correlation of High-Risk Soft Tissue Sarcoma Biomarker Expression Patterns with Outcome following Neoadjuvant Chemoradiation.” Sarcoma 2018 (2018).
    Jain, Shilpa, et al. “Molecular classification of soft tissue sarcomas and its clinical applications.” International journal of clinical and experimental pathology 3.4 (2010): 416.
    Honore, C., et al. “Soft tissue sarcoma in France in 2015: epidemiology, classification and organization of clinical care.” Journal of visceral surgery 152.4 (2015): 223-230.
    Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor L, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes. Oncotarget. 9(10):9137-9155, 2018
    Becker-Santos, D.D., Thu, K.L, English, J.C., Pikor, L.A., Chari, R., Lonergan, K.M., Martinez, V.D., Zhang, M., Vucic, E.A., Luk, M.T.Y., Carraro, A., Korbelik, J., Piga, D., Lhomme, N.M., Tsay, M.J., Yee, J., MacAulay, C.E., Lockwood, W.W., Robinson, W.P., Jurisica, I., Lam, W.L., Developmental transcription factor NFIB is a putative target of oncofetal miRNAs and is associated with tumour aggressiveness in lung adenocarcinoma, J Pathology, 240(2):161-72, 2016.
    Cinegaglia, N.C., Andrade, S.C.S., Tokar, T., Pinheiro, M., Severino, F. E., Oliveira, R. A., Hasimoto, E. N., Cataneo, D. C., Cataneo, A.J.M., Defaveri, J., Souza, C.P., Marques, M.M.C, Carvalho, R. F., Coutinho, L.L., Gross, J.L., Rogatto, S.R., Lam, W.L., Jurisica, I., Reis, P.P. Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung, adenocarcinoma, Oncotarget, 7(20): 28920-34, 2016.

    Other news

    We have secured a major funding from Ontario Government for our research: The Next Generation Signalling Biology Platform. The main goal of the project is developing novel integrated analytical platform and workflow for precision medicine. This project will create an internationally accessible resource that unifies different types of biological data, including personal health information—unlocking its full potential and making it more usable for research across the health continuum: from genes and proteins to pathways, drugs and humans.

    We have also published papers describing several tools, portals and applications with our collaborators. Below we list those most related directly or indirectly to work on World Community Grid:

    Wong, S., Pastrello, C., Kotlyar, M., Faloutsos, C., Jurisica, I. SDREGION: Fast spotting of changing communities in biological networks. ACM KDD Proceedings, 2018. In press. BMC Cancer, 18(1):408, 2018.
    Kotlyar, M., Pastrello, C., Rossos, A., Jurisica, I. Protein-protein interaction databases. Eds. Cannataro, M. et al. Encyclopedia of Bioinformatics and Computational Biology, 81, Elsevier. In press. doi.org/10.1016/B978-0-12-811414-8.20495-1
    Rahmati, S., Pastrello, C., Rossos, A., Jurisica, I. Two Decades of Biological Pathway Databases: Results and Challenges, Eds. Cannataro, M. et al. Encyclopedia of Bioinformatics and Computational Biology, 81, Elsevier. In press.
    Hauschild, AC, Pastrello, C., Rossos, A., Jurisica, I. Visualization of Biomedical Networks, Eds. Cannataro, M. et al. Encyclopedia of Bioinformatics and Computational Biology, 81, Elsevier. In press.
    Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S. Encompassing new use cases – level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics, 19(1):134, 2018.
    Minatel BC, Martinez VD, Ng KW, Sage AP, Tokar T, Marshall EA, Anderson C, Enfield KSS, Stewart GL, Reis PP, Jurisica I, Lam WL., Large-scale discovery of previously undetected microRNAs specific to human liver. Hum Genomics, 12(1):16, 2018.
    Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor L, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica, I. Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes. Oncotarget. 9(10):9137-9155, 2018.
    Paulitti A, Corallo D, Andreuzzi E, Bizzotto D, Marastoni S, Pellicani R, Tarticchio G, Pastrello C, Jurisica I, Ligresti G, Bucciotti F, Doliana R, Colladel R, Braghetta P, Di Silvestre A, Bressan G, Colombatti A, Bonaldo P, Mongiat M. Matricellular EMILIN2 protein ablation ca 1 uses defective vascularization due to impaired EGFR-dependent IL-8 production, Oncogene, Feb 27. doi: 10.1038/s41388-017-0107-x. [Epub ahead of print] 2018.
    Tokar, T., Pastrello, C., Rossos, A., Abovsky, M., Hauschild, A.C., Tsay, M., Lu, R., Jurisica. I. mirDIP 4.1 – Integrative database of human microRNA target predictions, Nucl Acids Res, D1(46): D360-D370, 2018.
    Kotlyar M., Pastrello, C., Rossos, A., Jurisica, I., Prediction of protein-protein interactions, Current Protocols in Bioinf, 60, 8.2.1–8.2.14., 2017.
    Singh, M., Venugopal, C., Tokar, T., Brown, K.B., McFarlane, N., Bakhshinyan, D., Vijayakumar, T., Manoranjan, B., Mahendram, S., Vora, P., Qazi, M., Dhillon, M., Tong, A., Durrer, K., Murty, N., Hallet, R., Hassell, J.A., Kaplan, D., Jurisica, I., Cutz, J-C., Moffat, J., Singh, D.K., RNAi screen identifies essential regulators of human brain metastasis initiating cells, Acta Neuropathologica, 134(6):923-940, 2017.

    Thank you.

    This work would not be possible without the participation of World Community Grid Members. Thank you for generously contributing CPU cycles, and for your interest in this and other World Community Grid projects.

    See the full article here.


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings
    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Microbiome Immunity Project

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 9:29 am on July 4, 2018 Permalink | Reply
    Tags: BOINC-Berkeley Open Infrastructure for Network Computing, Carbon nanostructures, ,   

    From World Community Grid (WCG): “The Expanding Frontiers of Carbon Nanotube Technology” 

    New WCG Logo

    WCGLarge

    From World Community Grid (WCG)

    3 Jul 2018

    Summary
    The Clean Water Project made an exciting discovery about the possible applications of carbon nanostructures to water purification, biomedical research, and energy research. Dr. Ming Ma, one of the scientists on the project, recently published a paper that summarizes the current status of work in this field.

    1
    The team at Tsinghua University includes (left to right) Ming Ma, Kunqi Wang, Wei Cao, and Jin Wang. Not pictured: Yao Cheng

    Dr. Ming Ma (of the Computing for Clean Water project) at Tsinghua University recently published a paper in the Journal of Micromechanics and Microengineering entitled “Carbon nanostructure based mechano-nanofluidics.” The paper is a thorough survey of all the recent research work on fluid flow in carbon nanostructures, such as carbon nanotubes and graphene sheets.

    Carbon atoms can form single-atom thick sheets known as graphene. When these are rolled into tube shape, they are called carbon nanotubes. In recent years, there has been a flurry of research work with these nanostructures, called that because they deal with very tiny atomic structures measured in nanometers (billionths of a meter). The Computing for Clean Water project is one example of recent research in this area: By using World Community Grid to simulate water flow through carbon nanotubes at an unprecedented level of detail, the project’s research team discovered that under specific conditions, certain kinds of natural vibrations of atoms inside the nanotubes can lead to a 300% increased rate of diffusion (a kind of flow) of water through the nanotubes.

    Among their many surprising properties are the ability to dramatically enhance water flow through or past the nanostructures. There is much research being conducted to understand how this happens and ultimately how to make best use of this property to potentially purify water, desalinate water, and meet other goals in biomedical and energy research. Challenges remain in how to efficiently manufacture these materials and how to adjust their structures to achieve the best results.

    Thanks to everyone who supported this project.

    See the full article here.


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings
    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Microbiome Immunity Project

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 3:07 pm on June 27, 2018 Permalink | Reply
    Tags: BOINC-Berkeley Open Infrastructure for Network Computing, Help Cure Muscular Dystrophy project,   

    From World Community Grid (WCG): “Data from Help Cure Muscular Dystrophy Project Helps Shed Light on the Mysteries of Protein Interactions” 

    New WCG Logo

    WCGLarge

    From World Community Grid (WCG)

    26 Jun 2018
    Dr. Alessandra Carbone
    Sorbonne Université

    Summary
    Protein-protein interactions are the basis of cellular structure and function, and understanding these interactions is key to understanding cell life itself. Dr. Alessandra Carbone and her team continue to analyze data on these interactions from the Help Cure Muscular Dystrophy project, and they recently published a new paper to contribute to the body of knowledge in this field.


    29 mminutes

    Dr. Alessandra Carbone (principal investigator of the Help Cure Muscular Dystrophy project) and team have published a paper entitled “Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions” in the journal Proteins.

    Protein interactions are the basis for most biological functions. How they interact with each other and other compounds (such as DNA, RNA, and ligands) in the cell is key to understanding life and disease functions. Complicating things, proteins often interact with more than one other kind of protein. To better understand protein functions, tools are required to uncover these potential interactions.

    Different parts (surfaces) of the protein can be binding sites that attract another protein. This paper describes a methodology the research team developed to better predict these alternative binding sites. A subset of the Help Cure Muscular Dystrophy project data was used to validate their technique, which will be subsequently applied to the whole dataset computed via World Community Grid.

    See the full article here.


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Microbiome Immunity Project

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 3:19 pm on June 19, 2018 Permalink | Reply
    Tags: , BOINC-Berkeley Open Infrastructure for Network Computing, ,   

    From World Community Grid (WCG): “Microbiome Immunity Project Researchers Create Ambitious Plans for Data” 

    New WCG Logo

    WCGLarge

    From World Community Grid (WCG)

    By: Dr. Tomasz Kościółek and Bryn Taylor
    University of California San Diego
    19 Jun 2018

    Summary
    The Microbiome Immunity Project researchers—from Boston, New York, and San Diego—met in person a few weeks ago to make plans that include a 3D map of the protein universe and other far-ranging uses for the data from the project.


    The research team members pictured above are (from left to right): Vladimir Gligorijevic (Simons Foundation’s Flatiron Institute), Tommi Vatanen (Broad Institute of MIT and Harvard), Tomasz Kosciolek (University of California San Diego), Rob Knight (University of California San Diego), Rich Bonneau (Simons Foundation’s Flatiron Institute), Doug Renfrew (Simons Foundation’s Flatiron Institute), Bryn Taylor (University of California San Diego), Julia Koehler Leman (Simons Foundation’s Flatiron Institute). Visit the project’s Research Participants page for additional team members.

    During the week of May 28, researchers from all Microbiome Immunity Project (MIP) institutions (University of California San Diego, Broad Institute of MIT and Harvard, and the Simons Foundation’s Flatiron Institute) met in San Diego to discuss updates on the project and plan future work.

    Our technical discussions included a complete overview of the practical aspects of the project, including data preparation, pre-processing, grid computations, and post-processing on our machines.

    We were excited to notice that if we keep the current momentum of producing new structures for the project, we will double the universe of known protein structures (compared to the Protein Data Bank) by mid-2019! We also planned how to extract the most useful information from our data, store it effectively for future use, and extend our exploration strategies.

    We outlined three major areas we want to focus on over the next six months.

    Structure-Aided Function Predictions

    We can use the structures of proteins to gain insight into protein function—or what the proteins actually do. Building on research from MIP co-principal investigator Richard Bonneau’s lab, we will extend their state-of-the-art algorithms to predict protein function using structural models generated through MIP. Using this new methodology based on deep learning, akin to the artificial intelligence algorithms of IBM, we hope to see improvements over more simplistic methods and provide interesting examples from the microbiome (e.g., discover new genes creating antibiotic resistance).

    Map of the Protein Universe

    Together we produce hundreds of high-quality protein models every month! To help researchers navigate this ever-growing space, we need to put them into perspective of what we already know about protein structures and create a 3D map of the “protein universe.” This map will illustrate how the MIP has eliminated the “dark matter” from this space one structure at a time. It will also be made available as a resource for other researchers to explore interactively.

    Structural and Functional Landscape of the Human Gut Microbiome

    We want to show what is currently known about the gut microbiome in terms of functional annotations and how our function prediction methods can help us bridge the gap in understanding of gene functions. Specifically, we want to follow up with examples from early childhood microbiome cohorts (relevant to Type-1 diabetes, or T1D) and discuss how our methodology can help us to better understand T1D and inflammatory bowel disease.

    The future of the Microbiome Immunity Project is really exciting, thanks to everyone who makes our research possible. Together we are making meaningful contributions to not one, but many scientific problems!

    See the full article here.


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Microbiome Immunity Project

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 8:43 am on May 23, 2018 Permalink | Reply
    Tags: , BOINC-Berkeley Open Infrastructure for Network Computing, , ,   

    From World Community Grid (WCG): “FightAIDS@Home – Phase 2 Prepares for A New Stage” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    By: The FightAIDS@Home research team
    22 May 2018

    Summary
    The FightAIDS@Home – Phase 2 researchers are making plans to write a paper and to test new compounds as part of the continuing search for new and better treatments.

    1
    No image caption or credit.

    Background

    Researchers all over the world have been making advances in the battle against HIV/AIDS for many years. However, AIDS-related complications still affect far too many people. UNAIDS estimates that 36.7 million people were living with HIV in 2016. And while AIDS-related deaths have decreased significantly since their peak in 2005, approximately 1 million people died of causes related to AIDS in 2016. (See the UNAIDS website for more statistics.)

    HIV continues to be a challenge because it quickly mutates in ways that make existing drug treatments ineffective. FightAIDS@Home joined World Community Grid more than a decade ago with the simple but challenging goal of finding new treatments for HIV. During Phase 1 of the project, the team identified thousands of potentially promising candidates to be confirmed experimentally in the lab. However, because it’s cost and time prohibitive to lab test all the potential candidates, Phase 2 was created to prioritize the candidate compounds by evaluating them with more accurate methods.

    Current Work

    Our team is processing the current type of work units through World Community Grid as quickly as possible. Once these work units are completed, we plan to write a paper about the process, including its strengths, limitations, and lessons learned.

    We are also planning to use World Community Grid’s computing power to analyze new compounds that are important to our work with the HIVE Center at the Scripps Research Institute. This work will begin after we run a sample of these new compounds on our own grid computing network.

    Thank You

    We appreciate everyone who continues to donate their computing power to the search for better anti-HIV treatments. We also encourage everyone to opt in to Phase 2 of the project—the more quickly we can run through the current work units, the sooner we can move ahead to new compounds.

    See the full article here.

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.
    stem
    Stem Education Coalition

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 1:53 pm on April 29, 2018 Permalink | Reply
    Tags: BOINC-Berkeley Open Infrastructure for Network Computing, Impact of atmospheric aerosols on climate change (Far Eastern Federal University- Russia), Impact of climate change on public health (Emory University USA), Rainfall modeling in Africa (Delft University of Technology- Netherlands),   

    From World Community Grid (WCG): “Announcing Three Winning Climate Change Projects” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    Announcing Three Winning Climate Change Projects

    26 Apr 2018

    Summary
    After a rigorous review of dozens of applications from all over the world, we’re excited to announce the research groups who will receive supercomputing power, weather data, and cloud storage from IBM to accelerate climate change science.

    1

    As our planet faces the mounting impacts of climate change, scientists are on the front lines of understanding complex consequences and developing solutions.

    We’ve heard from climate change scientists that common bottlenecks they face include limited access to weather data, and insufficient computing power and data storage capacity to accurately simulate the impacts of climate change.

    These are some of the reasons why IBM Corporate Citizenship recently invited scientists to apply for grants of massive computing power from World Community Grid, meteorological data from The Weather Company, and data storage from IBM Cloud Object Storage to support their climate change or environmental research projects. (More information about these IBM resources can be found here.)

    As our planet faces the mounting impacts of climate change, scientists are on the front lines of understanding complex consequences and developing solutions. Common bottlenecks facing scientists conducting foundational research include limited access to weather data, and insufficient computing power and data storage capacity to accurately simulate the impacts of climate change.

    To build on IBM’s decades-long commitment to environmental stewardship, IBM Corporate Citizenship is helping overcome these roadblocks by donating technology and data to three foundational climate change research projects.

    Groundbreaking Research Projects

    These IBM resources–crowdsourced computing power through World Community Grid, weather data from The Weather Company, and IBM Cloud Object Storage–will support three groundbreaking new research projects, chosen from over 70 applications for their potential to make a significant contribution to our understanding of climate change impacts and potential solutions.

    Impact of climate change on public health (Emory University, USA)

    This project will examine the impact of climate change on temperature and air pollution at local levels, helping researchers understand the impact of a changing climate on human health.

    Impact of atmospheric aerosols on climate change (Far Eastern Federal University, Russia)

    Atmospheric aerosols, such as dust, smoke and pollution, both absorb and reflect sunlight in the atmosphere, and represent the greatest area of uncertainty in climate science today, according to the UN Intergovernmental Panel on Climate Change (IPCC). This project aims to determine how super-micron particles (6 to 12 micrometers in diameter) interact with sunlight and how they contribute to atmospheric temperatures – information that will improve the accuracy of climate models.

    Rainfall modeling in Africa (Delft University of Technology, Netherlands)

    In Africa, agriculture relies heavily on localized rainfall, which is difficult to predict. In collaboration with the Trans-African Hydro-Meteorological Observatory, researchers will simulate rainfall on the continent – information that could help farmers be more resilient, among other weather and hydrology applications.

    In return for this support, the winning scientists agree to publicly release the data from their collaboration with IBM, enabling the global community to benefit from and build upon their findings.

    Supercharged by IBM Resources

    Each of these three winning projects will use one or more of these resources:
    Crowdsourced computing power

    Scientists receive free, 24/7 access to computing power through World Community Grid, a philanthropic initiative of IBM that enables anyone with a computer or Android device to support scientific research by carrying out virtual research experiments on their devices.

    Through the contributions of over 740,000 individuals and 440 organizations, the initiative has enabled a number of breakthrough discoveries in environmental research by helping scientists discover new materials for efficient solar energy, study the impact of management policies on large watershed areas and uncover more efficient ways to filter water.

    “World Community Grid enabled us to find
    new possibilities for solar cells on a
    timescale that matters to humanity–in other
    words, in a few years instead of decades.”

    Dr. Alan Aspuru-Guzik
    Professor of Chemistry and Chemical Biology
    Harvard University

    Weather data

    The historical and real-time weather data of The Weather Company, an IBM business, can help scientists advance our understanding of environmental systems and support the design of solutions to prevent, mitigate against, and adapt to climate change.

    Cloud storage

    For scientists who work on environmental research initiatives with very large data sets, IBM Cloud Object Storage provides a scalable platform to store and analyze the results of virtual experiments on World Community Grid and conduct further investigations.
    Frequently Asked Questions
    What is World Community Grid?
    We’re a philanthropic initiative of IBM that connects researchers with free and massive computing power, donated by volunteers around the world, to advance scientific research on our planet’s most pressing issues. Anyone with a computer or Android device can sign up to participate. To date, over 740,000 individuals and 430 organizations have contributed over a billion years of computing power to support 29 research projects, including studies about low-cost water filtration systems and new materials for capturing solar energy efficiently.

    Our research partners have published over 50 peer-reviewed scientific papers in journals including Science, Nature and PLOS. This crowdsourced computing power, which is provided to researchers for free, often allows them to take on research efforts at an unprecedented scale, pursue new research approaches and get the work done in years instead of decades.

    How does World Community Grid work?
    Scientists from institutions all over the world come to us with research projects that need massive amounts of computing power. Using their research simulation or modeling software tool of choice, we integrate that software into our platform and distribute millions of virtual research experiments to thousands of World Community Grid volunteers, who perform these calculations on their computers and Android devices. World Community Grid validates and bundles the results of these calculations and sends them back to the researchers. Through World Community Grid, scientists can not only access massive computing power at no cost, but can also engage the public in their research.

    What climate and environmental research has World Community Grid supported to date?

    Since 2004, World Community Grid has supported a number of environmental research efforts including:

    Clean Energy Project – In what is believed to be the largest quantum chemistry experiment ever performed, researchers at Harvard University screened millions of organic photovoltaic compounds to predict their potential for converting sunlight into electricity. Amongst these, 36,000 were predicted to double the efficiency of most carbon-based solar cells currently in production.
    Computing for Clean Water – Researchers at Tsinghua University in Beijing used World Community Grid to simulate the flow of water through carbon nanotubes at an unprecedented level of detail. In doing so, they discovered a phenomenon that points to a new possibility for water filtration which could one day improve access to clean water for the nearly one billion people around the world who lack access to it.

    Computing for Sustainable Water – Scientists at University of Virginia studied the impact of management policies on water quality in the Chesapeake Bay to gain deeper insights into what actions can lead to restoration, health and sustainability of this important water resource.
    Uncovering Genome Mysteries – Researchers examined 200 million genes from a wide variety of life forms, such as microorganisms found on seaweed from Australian coastlines and in the Amazon river. The goal of their work is to augment knowledge about biochemical processes in general, identify how organisms interact with each other and the environment, and document the current baseline microbial diversity, allowing a better understanding of how microorganisms change under environmental stresses, such as climate change.

    What kind of computing power is being made available with the grant?

    Scientists who receive these awards will use World Community Grid, a philanthropic IBM initiative that provides scientists with massive amounts of computing power, for free. Through World Community Grid, computational research calculations are distributed to thousands of volunteers around the world who perform these calculations on their computer or Android devices.

    In addition, we carry out the technical work to integrate the researchers’ computational research tool of choice into the World Community Grid platform. We also provide communications and outreach support to engage and educate the public in this research.

    How is the computing power being made available by World Community Grid different from a supercomputer?
    As one of the researchers who has used World Community Grid for several years once said, “It turns out that having hundreds of thousands of computers in parallel accelerates things more than having a supercomputer.” World Community Grid provides scientists with 24/7 access to enough computing power to match some of the world’s most powerful supercomputers. But unlike a traditional supercomputer, World Community Grid distributes the computational work to thousands of computers worldwide, each of which is provided by a volunteer who chooses to make their device available to conduct scientific calculations. For our research partners, this means not having to wait in line for computing resources as they would with most supercomputers at their own institutions. Instead, they receive free access to massive amounts of computing power, while engaging the public in their research.

    What weather data is being made available to grant recipients?
    Grant recipients have free access to weather data from The Weather Company, an IBM business, to support their research. The data may include global weather forecasts, historical observations, and current weather conditions. Access to the data will be provided through web-based APIs, while the project runs on World Community Grid.

    What cloud storage capabilities are being made available to grantees?
    Grant recipients have free access to IBM Cloud Object Storage for all data storage needs related to their IBM-supported project, while the project runs on World Community Grid. Technical assistance will also be provided to assess their data storage needs and determine appropriate storage solutions.

    What were the criteria for successful proposals?
    Successful proposals met the following criteria:

    Not for profit: conducted by public or nonprofit organizations
    Tackle climate change: Advance understanding of the impacts of climate change, and/or strategies to adapt to or mitigate the impacts of climate change.
    Contribute to open science: all data generated by World Community Grid volunteers must be made freely available to the scientific community.
    Enabled, accelerated or enhanced by the resources we offer: climate or environmental computational studies that require significant computer processing power and can be divided into small independent computations, may need weather data, and/or could benefit from large amounts of cloud-based storage.

    How were applications evaluated?
    A team of IBM scientists and outside scientists with expertise in environmental and climate change science reviewed each application for:

    Scientific merit
    Potential to contribute to the global community’s understanding of specific climate change and/or environmental science challenges
    Capacity of the research team to manage a sustained research project
    Demonstrated need for IBM resources

    What commitment do scientists make in return?
    In return for these free resources, scientists agree to support our open data policy by publicly releasing the research data from their World Community Grid project, to enable the global scientific community to benefit from and build upon their findings. Research teams also agree to engage the volunteers in their research through regular communications through World Community Grid communication channels.

    When will these projects begin running on World Community Grid?
    We have begun the onboarding process for the projects, and are planning to launch the first project later in 2018. We will be posting updates about this process on our website.

    Can researchers still apply for these resources?
    We’re not currently accepting applications that include data from The Weather Company and storage from IBM Cloud, but any researchers who are interested in using World Community Grid’s computing power are welcome to submit an application.

    How do I make sure that I start contributing to these projects as soon as they’re launched?

    If you are already a World Community Grid volunteer, go to the My Projects page, where you can choose to opt in to new projects as they become available.

    If you’re not yet a World Community Grid volunteer, you can sign up to be notified as soon as the first of these three projects is launched. You can also join World Community Grid right now and support our existing projects.

    NOTIFY ME OF PROJECT LAUNCHES

    See the full article here.

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 9:48 am on April 21, 2018 Permalink | Reply
    Tags: BOINC-Berkeley Open Infrastructure for Network Computing, , , , What's tech got to do with it?   

    From World Community Grid (WCG): “What’s tech got to do with it?” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    We went to SXSW to talk about how volunteer computing can help save the planet.

    20 Apr 2018
    Summary
    World Community was invited to give two presentations on the power of crowdsourced computing power at SXSW 2018 in Austin, Texas. See the full presentations, as well as a short video with excerpts from both, in this article.

    We were thrilled to be invited to give two presentations in the Code and Programming track at SXSW 2018. You can see both presentations in full, as well as a few excerpts in the first video below.

    In this short video, two scientists talk about the crucial issues they’re researching: climate change and clean energy. World Community Grid project manager Juan Hindo and software developer Jonathan Armstrong explain the important role of volunteers in accelerating research.

    Last year, IBM issued a call for proposals to climate change and environmental researchers, offering them not only World Community Grid supercomputing power, but also data from The Weather Company and storage on IBM Cloud Object Storage. In this video, IBM Distinguished Engineer and Chief Scientist Lloyd Treinish joins Juan and Jonathan to talk about the most pressing issues in climate change, the extent of the climate change science community’s technical needs, and the opportunity for the tech community to help.

    Dr. Alan Aspuru-Guzik was the lead researcher for the Clean Energy Project, which uncovered a large number of potential new and improved solar cells. In this presentation, Alan gave an overview of the work so far, and talked about his plans for further extending his collaboration with World Community Grid and other organizations.

    See the full article here.

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-
    Smash Childhood Cancer4

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 10:08 am on March 29, 2018 Permalink | Reply
    Tags: , , Bloomberg View, BOINC-Berkeley Open Infrastructure for Network Computing, , ,   

    From Rosetta@home via Bloomberg View: “Protein Engineering May Be the Future of Science” 

    Rosetta@home

    Rosetta@home

    2

    Bloomberg View

    March 27, 2018
    Faye Flam

    Some scientists think designing new proteins could become as significant as tweaking DNA.

    3
    Let’s build a better sperm whale. Photograph: SSPL/Getty Images

    Scientists are increasingly betting their time and effort that the way to control the world is through proteins. Proteins are what makes life animated. They take information encoded in DNA and turn it into intricate three-dimensional structures, many of which act as tiny machines. Proteins work to ferry oxygen through the bloodstream, extract energy from food, fire neurons, and attack invaders. One can think of DNA as working in the service of the proteins, carrying the information on how, when and in what quantities to make them.

    Living things make thousands of different proteins, but soon there could be many more, as scientists are starting to learn to design new ones from scratch with specific purposes in mind. Some are looking to design new proteins for drugs and vaccines, while others are seeking cleaner catalysts for the chemical industry and new materials.

    David Baker, director for the Institute for Protein Design at the University of Washington, compares protein design to the advent of custom tool-making. At some point, proto-humans went beyond merely finding uses for pieces of wood, rock or bone, and started designing tools to suit specific needs — from screwdrivers to sports cars.

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s (See our Disease Related Research for more information). Please join us in our efforts! Rosetta@home is not for profit.

    About Rosetta

    One of the major goals of Rosetta is to predict the shapes that proteins fold up into in nature. Proteins are linear polymer molecules made up of amino acid monomers and are often refered to as “chains.” Amino acids can be considered as the “links” in a protein “chain”. Here is a simple analogy. When considering a metal chain, it can have many different shapes depending on the forces exerted upon it. For example, if you pull its ends, the chain will extend to a straight line and if you drop it on the floor, it will take on a unique shape. Unlike metal chains that are made of identical links, proteins are made of 20 different amino acids that each have their own unique properties (different shapes, and attractive and repulsive forces, for example), and in combination, the amino acids exert forces on the chain to make it take on a specific shape, which we call a “fold.” The order in which the amino acids are linked determines the protein’s fold. There are many kinds of proteins that vary in the number and order of their amino acids.

    To predict the shape that a particular protein adopts in nature, what we are really trying to do is find the fold with the lowest energy. The energy is determined by a number of factors. For example, some amino acids are attracted to each other so when they are close in space, their interaction provides a favorable contribution to the energy. Rosetta’s strategy for finding low energy shapes looks like this:

    Start with a fully unfolded chain (like a metal chain with its ends pulled).
    Move a part of the chain to create a new shape.
    Calculate the energy of the new shape.
    Accept or reject the move depending on the change in energy.
    Repeat 2 through 4 until every part of the chain has been moved a lot of times.

    We call this a trajectory. The end result of a trajectory is a predicted structure. Rosetta keeps track of the lowest energy shape found in each trajectory. Each trajectory is unique, because the attempted moves are determined by a random number. They do not always find the same low energy shape because there are so many possibilities.

    A trajectory may consist of two stages. The first stage uses a simplified representation of amino acids which allows us to try many different possible shapes rapidly. This stage is regarded as a low resolution search and on the screen saver you will see the protein chain jumping around a lot. In the second stage, Rosetta uses a full representation of amino acids. This stage is refered to as “relaxation.” Instead of moving around a lot, the protein tries smaller changes in an attempt to move the amino acids to their correct arrangment. This stage is regarded as a high resolution search and on the screen saver, you will see the protein chain jiggle around a little. Rosetta can do the first stage in a few minutes on a modern computer. The second stage takes longer because of the increased complexity when considering the full representation (all atoms) of amino acids.

    Your computer typically generates 5-20 of these trajectories (per work unit) and then sends us back the lowest energy shape seen in each one. We then look at all of the low energy shapes, generated by all of your computers, to find the very lowest ones. This becomes our prediction for the fold of that protein.

    To join this project, download and install the BOINC software on which it runs. Then attach to the project. While you are at BOINC, look at some of the other projects to see what else might be of interest to you.

    U Washington Dr. David Baker

    Rosetta screensaver

    BOINC

    My BOINC

     
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