Content about Biology and genomics

Ion channel simulations and free energy calculations on the grid Visualization of the KcsA ion channel.  Image courtesy of National Grid Service Philip Fowler had a problem. He wanted to find out how selective a certain ion channel is for potassium over sodium—vital for its function—via a process known as "computational chemistry." Unfortunately, while the techniques used to get such results are well-known and well-established, they are extremely time-consuming. Sometimes, he needed to do as many as 34 parallel simulations, and with each one taking one to two days, that could take over two months. But by accessing the grid via the UK’s National Grid Service, Fowler -- previously at University College London and now at the University of Oxford -- found he could complete the entire job in less than two weeks.Fowler uses classical molecular dynamics to study membrane proteins, in particular the proteins that allow ions such as potassium to diffuse in and out of cells, otherwise known as ion chan

Fight AIDS at home, via unused computer time World Community Grid is helping “FightAIDS@Home” by completing computational calculations related to molecular structures of potential anti-HIV drugs..  Image courtesy of World Community Grid Starting on World AIDS Day on 1 December, the World Community Grid will sponsor a month-long challenge via its FightAIDS@home project, with the goal of increasing the number of computers and computer cycles available to researchers conducting HIV/AIDS research.Like all molecules, HIV—the virus that causes AIDS—is dependent upon its three-dimensional shape to attack the human immune system, in much the same way that a key must fit into a lock in order to gain entry. If the lock can be blocked—with a drug, for example—then the key cannot fit, and the virus is prevented from maturing. Such blockers, known as “protease inhibitors,” are one way of avoiding the onset of AIDS.Researchers have been able to determine by trial-and-error the shapes of a

Image of the week - Molecular dynamics on DEISA: lipids, licorice and lines A single snapshot of a coarse-grained molecular dynamics simulation of a protein (Synaptobrevin transmembrane domain) in a lipid bilayer. The protein is shown as licorice, lipids as lines and water as points. The red arrows show the user external forces applied interactively in the simulation. Here, the membrane anchoring of protein is probed by pulling on one particular side (on tryptophane residues). Image courtesy of deisa.eu. From the DEISA Newsletter, Vol. 5, 2008 Coupled applicationsMany complex systems can be viewed as sets of components that obey their own physical laws and interact weakly with one another. Code-coupling, which deals with multi-physics, multi-models and multi-scale numerical simulations, is well-suited for inter-disciplinary research projects in which different legacy codes cooperate within the whole coupled application.Generally, due to the complexity of these applications, coupled codes run with a moderate efficiency on parallel

Feature - Anthrax and the grid Researchers used Taverna to model molecules such as the anthrax bacillum. Image courtesy of EPSRC Bacillus anthracis, the bug that causes anthrax, is a peculiar creature.Even though it resembles a soil-growing bacterium, it just hibernates when in the ground, in some cases lying dormant for hundreds of years until ingested by a suitable animal host. Then it springs to life, often causing rapid, even fatal, illness. For years, scientists have wondered how and why this occurs. Now, using Taverna workflow technology developed under myGrid—an e-Science project funded by the Engineering and Physical Sciences Research Council (EPSRC)—researchers Anil Wipat, Colin Harwood and colleagues at the North East Regional e-Science Center in Newcastle, UK, think that they have puzzled out the answer, by sequencing its genome and thus characterizing the proteins it secretes Proteins equip a bacterium to survive in its environment and reveal much about its lifestyle.  A soil-living bacterium, for exa

Feature - Electron tomography without the headaches Image courtesy of Belin Czechowicz, sxc.hu Seeing is understanding For biologists, seeing a structure's shape is the all-important step to understanding how it works. Just as in the architecture of a well-designed building, form follows function. So, when a 17th century Dutch draper who enjoyed grinding lenses as a hobby invented the microscope, Anton van Leeuwenhoek revolutionized biology. Microbiologists today may find their next tool coming from a source just as unlikely—academic computing.By using the grid and a number of super-slim electron scans of an object taken at a variety of angles, researchers can create 3-D views up to 2 million times real size. In spite of its usefulness for the field of microbiology, this process, known as electron tomography, has long remained unpractical for many researchers, as it is too computationally expensive.But a project called EGEETomo, centered at University of Almería, in Spain, is building a tool to make

Feature - The deep in 3-D A two-dimensional representation of a three-dimensional holograph of water. Image courtesy of Peter Hobson, Brunel University Grid-powered holography In recent years, biologists have used holograms to visualize predator-prey encounters, fragile  marine snows (“snowflakes” of detritus showering down through the water column) and other phenomena at high resolution in 3-D without harming the denizens of the deep.As camera technology improves, images become bigger and more complex and consequently take longer to process and store. A single charge-coupled-device (CCD) chip captures as many as 100,000,000 pixels.The result? A single desktop machine often takes 12 hours to replay one 3-D image.Using the grid, Peter Hobson and Henry Nebrensky of Brunel University, U.K., have found a way to replay holographic images of water samples in 66 percent less time than it takes with conventional, single-desktop machines. Slice and diceThe researchers captured the information about a particle’s

  Feature - Cell biologists dig new DiGS Cell biologists at the University of Edinburgh and University of Oxford are using grid technology called DiGS to support their investigation into the transport and anchoring of mRNA in Drosophila flies. Image courtesy of Wikipedia As cell biology moves from labs to computer desktops, researchers must deal with increasingly vast volumes of data. Traditional ways of sharing this data—such as physically shipping hard drives—just cannot keep up. UK Quantum Chromodynamics has been working to solve these data management challenges using grid technology since 2002, developing QCDGrid to share, publish and preserve their large datasets. And although UKQCD are a physics outfit, they’ve made their software—renamed DiGS or Distributed Grid Storage—available to the wider scientific community.First off the block: biology“The EPCC team focused initially on the needs of particle physicists,” explains George Beckett of the Edinburgh P

Image of the week - Shave hundreds of years off your research life The villin protein is presented here in two superimposed forms: the first predicted using BEMusE on EU-IndiaGrid, and the second measured experimentally. The similarity demonstrates the algorithm’s accuracy.Image courtesy of Stefano Cozzini, EU-IndiaGrid BEMusE— or the Bias-Exchange Metadynamics Submission Environment—is a grid-enabled tool able to fold a 36-residue protein in less than a year of single CPU time: a vast improvement on the hundreds or thousands of CPU years required by other grid-based techniques.Bedazzling researchers with its accuracy and speed, BEMusE scooped the poster prize at December’s eScience 2007 conference.Biased towards gridBEMusE evolved from the Bias-Exchange Metadynamics algorithm, developed by Alessandro Laio and Stefano Piana, which folds proteins with increased accuracy. “It was immediately clear how much the algorithm would benefit from the grid,” says BEMusE researcher Stefano Cozzini, of Democ

  Image of the week - The micro-world of muscle cells These four visualizations show four sections of a muscle cell, each comprising several saromeres. Different colours indicate different organelles, including the myofibrillar system, sarcoplasmic reticulum, mitochondria and t-tubules. The cell envelope is rendered transparently.Image courtesy of GeomCell Enter the micro-world of your muscle cells, and you’ll find the entire length of a muscle “fiber” is actually a single cell. Called “skeletal muscle cells,” these giants are comprised of a number of repeating units, called sarcomeres, which contain cellular organelles such as myofibrils, mitochondria, t-tubules and sarcoplasmic reticulum.These organelles, even if of the same type, vary widely in their size, shape and location within the cell. Moreover, they often display complex spatial relationships. To understand the complexity of a muscle cell, realistic computer models are instrumental and may serve as a virtual cell

Feature - Never-born proteins: predicting protein structures from your web browser By predicting the structure and functional properties of “never born proteins” scientists can learn more about the structure and function of actual existing proteins.Image courtesy of INFN While the number of known natural protein sequences is quite large, it is infinitely small compared to the number of proteins theoretically possible using the 20 natural amino acids. Thus, there exist a huge number of protein sequences that have never been observed in nature, the so-called “never born proteins.” If we can study the structural and functional properties of these “never born proteins,” we can improve our knowledge of the fundamental properties that make existing protein sequences so unique. Where these studies would take years on a single CPU, grid infrastructures make it feasible to approach this problem in an acceptable time frame. The Rosetta softwareThe Rosetta ab initio module is a software application developed by David Baker at the Univers

Feature - Cutting edge computing helps discover the origin of life A snapshot from a large-scale molecular dynamics simulation of a 480 base pair DNA plasmid sandwiched between two sheets of a clay mineral. The plasmid structure remains essentially stable and intact at the elevated temperatures and pressures of deep ocean hydrothermal vents, where life on Earth may have originated. Image courtesy of P V Coveney. The National Grid Service in the UK and the TeraGrid in the U.S. have joined forces to help University College London scientists shed light on how life on earth may have originated.  Deep undersea secretsDeep ocean hydrothermal vents have long been suggested as possible sources of biological molecules, such as RNA and DNA, but it was unclear how they could survive the high temperatures and pressures that occur round these vents.Peter Coveney and colleagues at the UCL Centre for Computational Science have used computer simulation to provide insight into the structure and stability of DNA while inserted into layered

Image of the week - Window to a molecular world  The Vaccinia virus, a bundle of DNA comprising 250 genes, is a member of the poxvirus family and was key to World Health Organization efforts to eradicate smallpox. This image was produced using EGEETomo: grid-powered electron tomography.Image courtesy of Fernández, J.J.Electron tomography, also known as ET, provides researchers with a tiny window on to the alien world of molecular biology. The technology works by shooting electron beams through super-slim samples at different angles, producing data that can be pieced together to produce a three-dimensional structure. The technology is well suited to biological specimens such as chromosomes and viruses, providing nano-scale resolution for an all-new look at these target macromolecules.To achieve such resolution, ET demands sophisticated reconstruction algorithms. Where iterative algebraic algorithms yield high quality reconstructions, they are computationally expensive and their use requires high performance techniques.