Content about Biology and genomics

Image of the week - SNAREd in the biological act A schematic snapshot of the SNARE protein complex embedded between two cell membranes. The dynamic 340,000 atom simulation was conducted using the distributed resources of DEISA. Image © Marc BaadenCell membranes are a hot-zone of biological activity, allowing chemicals in and out of your cells, playing host to intra-membrane proteins, and even fusing with neighboring membranes. Disturbing any of these functions can have far-reaching consequences for your health, which is one reason why Marc Baaden is working to improve our understanding of just how cell membranes work.Baaden and a team from the Institut de Biologie Physico-Chimique, CNRS, France, are using complex computer simulations to model the function of the membrane-fusing SNARE complex.Using GROMACS software and 218,000 CPU hours from 96 distributed DEISA processors, Baaden was able to simulate the dynamic interactions of the two-membrane SNARE system, a massive task incorporating the trajectories of 340,000 atoms.

Announcement - ParaMEDIC enables worldwide supercomputer for bioinformatics Wu-chun Feng, associate professor in the departments of computer science and electrical and computer engineering at Virginia Tech (left) and Pavan Balaji, post-doctoral researcher in the mathematics and computer science division at Argonne National Laboratory.Images courtesy of Virginia TechParaMEDIC, a general software-based framework for large-scale distributed computing developed by Argonne National Laboratory and Virginia Tech, is set to have significant impact on the study of genomics.The GenBank database, a collection of all publicly available DNA sequences, doubles in size approximately every 12 months. Yet the computational capability of a compute node doubles only every 18 months. Consequently, searching for similarities between new protein or nucleotide sequences with the database of known sequences is becoming increasingly difficult. This problem becomes even more insidious when attempting a large-scale sequence-searching problem, like identifyi

Link of the week - Sharkrunners Your ship is virtual, but the sharks are real. Real-world data gathered from a network of sensors offers gamers the chance to track actual great whites.Screenshot courtesy of Sharkrunners Sharkrunners, designed for Discovery Channel’s 20th Anniversary Shark Week, is a persistent game of oceanic exploration and high stakes shark research. Players take on the role of marine biologists who must outfit their boat, map its path and then ply the oceans in the search for great white sharks, all while keeping an eye on their fuel capacity and monitoring the skill, stamina and compatibility of their crew members.The game uses real-world telemetry data collected from actual sharks, using sensors and GPS units to provide the position and movement of the sharks in the game.  Boat movement is in realtime, and if you aren’t logged in when you encounter a shark, you’ll be buzzed with an email or text message that gives you three hours to log on, then three minutes to select your approa

  Feature - The path more travelled by: grids help track human migration Nicolas Ray uses Approximate Bayesian Computation—developed in 2002—to track the migration of humans through the centuries.Images courtesy of Rakesh Rampertab Today, families interested in an intercontinental move will probably go by plane, train or automobile. Several thousand years ago, adventurers had a harder time of it. Thanks to the plucky, pioneering efforts of early families, humans have managed to explore and settle every habitable region of the globe. Surviving the “bottlenecks” Two ancient migrations have particularly affected the shape of future generations: the “Out of Africa” event and the North to South colonization of the Americas. These migrations left traces in our genes still observable today. Described as “bottlenecks”—events where only a few individuals get through—the migrations may have caused a drastic reduction in population size and a corresponding drop

  Announcement - World Community Grid migrates to BOINC Discovering Dengue Drugs – Together is the latest project to join World Community Grid and aims to identify drug leads to combat the dengue, hepatitis C, West Nile, and Yellow fever viruses. Stock image from sxc.hu World Community Grid is migrating completely to BOINC—the Berkeley Open Infrastructure for Networking Computing platform for volunteer and desktop grid computing.Previously World Community Grid members have had the option of participating using either the United Devices (UD) or BOINC clients. At the time of the migration announcement, approximately 67% of devices were running on UD and 33% on BOINC. However, a greater proportion of new registerations were opting for BOINC (80%) than UD (20%).The UD software helped launch World Community Grid with MetaProcessor 3.0. However, this version is no longer supported by United Devices. As part of the migration many BOINC enhancements and new functionality have been introduced to World Community Grid, incl

  Feature - Grids: a global home for serious science World Community Grid has more than 315,000 members, running nearly 700,000 computing devices. Image courtesy of World Community Grid Just two weeks ago, public grid project World Community Grid launched their newest project: a global computing effort to find cures for dengue, West Nile and hepatitis C diseases. Since 2004 World Community Grid has run seven projects, and already this year, science conducted using World Community Grid has resulted in the publication of two scientific papers in peer-reviewed journals, with several more papers scheduled for the latter half of 2007. The first paper detailed results from the Human Proteome Folding project and was published in PLoS Biology, a journal of the Public Library of Science; the second showcased results from Fight AIDS@Home and was published in the ACS Journal of Chemical Information and Modeling.Hot on their scientific heels are papers expected from a U.S. team working on a cancer tissue microarray project, a French

  Image of the week - Anti-cancer agent in watery bind Water molecules bind to anti-cancer agent 5-fluorouracil to prevent formation of a newly discovered form II polymorph. All molecules are immersed in liquid nitromethane, which is not shown for reasons of clarity. Image courtesy of Said Hamad These images show the interactions of water molecules with each other and with molecules of anti-cancer agent 5-fluorouracil in nitromethane solution. These interactions are strong enough to prevent the formation of 5-fluorouracil clusters, which in turn prevents the formation of a more stable 5-fluorouracil polymorph: the elusive “form II”. Only when water molecules are completely absent from the system will “form II” crystals appear. This molecular dynamics investigation was carried out by investigators now at the University College London, as part of the Control and Prediction of the Organic Solid State project.CPOSS is dedicated to predicting the crystalline structures of organic molecules and uses the e-sc

  Feature - Many millions of manuscripts: data mining and digitized objects As this Computation Institute conference room wall suggests, pen and “paper” is still a popular way to record information. But, as is also suggested, digitization can offer much in the way of improving the accessibility and utility of written materials.Image courtesy of the Computation Institute. Just three years old, the Computation Institute’s Teraport has already consumed 2.5 million hours of computing time on more than 800,000 jobs.James Evans, Assistant Professor in Sociology at the University of Chicago, is a Teraport regular, routinely occupying up to 30 processors at a time for his work on citation network analysis.Multiplying resultsCrunching through hundreds of CPU hours, Evans identifies patterns of interaction between universities and the biotechnology industry, using Teraport to compare the citations of every article with those of every other article in his database—more than 25 million citations.In work that re

  Feature - To bee or not to bee? Bee society and the human condition The honey bee’s “waggle dance” is the only symbolic language found beyond the primates. New genomic data yielded by grid-powered research could help reveal the basis for this and other social interactions.Stock image from sxc.hu The humble honey bee: pollinator, producer of honey, and potential key to unlocking the secrets of human social interaction. Why is it some bees can be queen? How can a nurse bee suddenly transform into a forager, just when foragers are needed most? And how can these furry flying insects cast light on our own human behaviors? The answers lie in the interactions of genes in the honey bee genome. And Saurabh Sinha needs grid computing to seek these answers out. “The honey bee can be a model to understand complex societies,” explains Sinha, a professor of computer science and affiliate of the University of Illinois’s Institute for Genomic Biology. “By studying the social regulation of gene ex

  Feature - Protein origami: function follows form One protein can fold in many ways. This computationally designed protein switches between a zinc finger structure and a coiled-coil structure, depending on its environment.Image courtesy of Kuhlman LaboratoryScientists in the Kuhlman Laboratory at the University of North Carolina at Chapel Hill are using the Open Science Grid to perform protein origami. They’re running Rosetta: a powerful tool for predicting and designing the incredibly complex three-dimensional structures that proteins can adopt.Why does protein folding matter? If you change the way a protein is folded, you can change the way it functions, and can even stop it from functioning at all.Nature’s ultimate nano-machinesProteins are nature’s ultimate nano-machines, performing sophisticated functions on a scale much smaller than any machine we can construct.  They can speed up chemical reactions, turn chemical energy into mechanical force, regulate the way cells grow and divide, and even fo

Image of the Week - Studying the Process of Learning   A simulation by the Virtual Cell project of a membrane reaction in a neuronal dentritic spine, one of the key aspects of learning and memory.Image courtesy of Virtual CellWant to learn more about how you learn? Our neuronal system lies at the root of learning and thought. Neurons communicate among themselves and with rest of our bodies using electrical and chemical signals. The points of communication between neurons are synapses. At a synapse, a signal received from outside the cell may or may not trigger a chain reaction that propagates the signal to other cells. After a time, synapses, on tiny protrusions called spines, can become sensitized or desensitized to certain chemical signals, known as neurotransmitters. The next time that synapse receives that neurotransmitter it may be extra responsive, or it may ignore it completely. This helps our brain organize itself in to neuronal circuits—paths of often-used neurons. Currently, researchers

Feature - New Weapons Identified in the Battle Against Hospital Superbugs Each point represents a protein expressed in the bacterium Pseudomonas aeruginosa; each line represents known interactions between these proteins. This network shows the structure of interactions the cell depends upon, giving researchers a head start in the search for anti-bacterial drugs. Image courtesy of e-TherapeuticsFor the first time in decades researchers have announced the discovery of new antibiotics that use a truly novel approach in attacking bacteria. The grid-powered drug searches were conducted by a spin-out company from Newcastle University in the United Kingdom. E-Therapeutics found three new drugs that are effective against antibiotic-resistant superbugs, such as that scourge of hospitals, methicillin-resistant Staphylococcus aureus.The drugs entered clinical trials in February and should be available for use within two to three years. The techniques that enabled this discovery were developed by the UK e-Science Programme,