Content about Biology and genomics

Video of the Week - Preventing bird strikes

The Bird Avoidance Model could help to cut down on collisions between birds and planes at busy airports. Video and image courtesy Virtual Laboratory for e-Science. Click on the above and go to section that begins at 2 mins 45 seconds.

Encounters between birds and planes have the potential to be disastrous — just ask Chesley Sullenberger, pilot of the US Airways flight that just barely managed to land on New York City’s Hudson River after colliding with a flock of geese on 15 January.
Such “bird strikes” are a continuing problem, with about 4,000 of them occurring in the United States alone in a single year, says the Federal Aviation Authority.
The FAA and others would like to be able to forecast when and where dangerous  concentrations of birds will form — similar to meteorologists predicting the weather.
Researchers at the Virtual Laboratory for e-Science (vl-e), The Net

Feature - Asian computers join forces against avian flu

Computer simulation of potential drug candidate attacking avian flu virus. Image courtesy Dr. Ying-Ta Wu, Academia Sinica, Taiwan 

Dealing with deadly diseases is not just a matter of test-tubes and petri dishes. Increasingly, grid computing is being used to simulate the ways that new drugs could attack viruses, looking for a magic bullet that could cure diseases or even prevent epidemics.
Computers can simulate a large number of chemical compounds and measure their ability to fit snugly into the chemical coating of a virus, thereby blocking its ability to function properly. Launched in March 2009, this so-called “Avian Flu DC2 Refinement” is the latest attack on avian flu using grid computing power. This initiative is supported by the EUAsiaGrid community, a partnership of Asian and European research institutions co-funded by the European commission to foster new uses of grid computing for science and society

Feature - Common cheap chips get jobs done faster

Although much of today’s most interesting research requires immense amounts of computational power, many scientists don’t have the funds to access expensive supercomputers or clusters. Now, a commonplace computer chip may provide a thrifty way to get those jobs done.
Graphics processing units (GPUs) are found in most computers and are designed to render 3-D computer graphics. They contain hundreds of processing cores on a single chip, and several chips can fit into a single desktop. Computational geneticists Marc Suchard of the University of California Los Angeles and Andrew Rambaut of the University of Edinburgh were able to use GPUs to speed up their computations by a factor of 100.

This tree shows how a population of viruses evolved over a 10-year period within an infected patient. The branch colors reflect relative rates of evolution along each branch.
Courtesy of Marc Suchard of UCLA.

Suchard and Ramba

Feature - Supercomputing promises super-insight into human evolution

Visualization by John L. Moreland.

Humans and chimpanzees are closely related – even closer than mice are to rats. That’s why the slight differences between the two species could provide valuable insight into the origin and evolution of humans.
But it isn’t always easy for researchers to get access to the data they need to see those differences. Researchers at the Center for Academic Research and Training in Anthropogeny are using San Diego Supercomputer Center resources to change that. They are in the process of digitizing an extensive collection of skeletons and medical records from more than two dozen chimpanzees; eventually, the results will be made available to researchers for study.
The specimens and records were donated to CARTA by the Primate Foundation of Arizona, which cares for retired zoo primates and primates whose owners can no longer care for them. Jo Fritz, PFA’s director,

Feature - Cancer Knowledge Cloud for a new generation of medicine

Kenneth Buetow, shown speaking at a conference in 2005.Image courtesy of NCRI.

Kenneth Buetow is the National Cancer Institute’s Associate Director of Bioinformatics and IT, and Director of the Center for Biomedical Informatics and IT, where he initiated and oversees the caBIG (cancer Biomedical Informatics Grid) program. He spoke last April at the Bio-IT World conference on caBIG: An interoperable IT framework for uniting research and care.
Thinking BIGKen Buetow thinks BIG.  He envisions what he calls a Cancer Knowledge Cloud — an IT environment designed to foster information connectivity among cancer patients, cancer researchers and clinical care providers. This environment, powered by caBIG tools and infrastructure, would enable a continuous and accelerated cycle of discovery, diagnostic and pharmaceutical product development, and improved clinical care.Cancer care and research still operate on a lin

Feature - Swine flu and the grid: A researcher’s view As the name suggests, “Swine Flu” may have its origins among pigs, and then may have made the jump across species to humans. Image courtesy Janne Brodin, stock.exchng (Editor's note: Swine Flu — or H1N1 influenza A — has been in the headlines lately. The World Health Organization has officially classified the latest outbreak a “pandemic,” in response to its world-wide geographic spread. To find out more about how the grid fits in with research to fight this virus, we asked Ana Lucia Da Costa of HealthGrid, who formerly worked at CNRS France, to give her viewpoint from the lab.) The emergence of a new influenza epidemic such as this is an opportunity for the grid to contribute to international public health response. It has highlighted the importance of providing the right information to decision-makers as quickly as possible. Grid technology is particularly well fitted to

Feature - Amoolya Singh, computation and biology

Amoolya Singh in her office at EMBL.  All images courtesy of SET-Routes

Editor's note: Readers may recall our series on women in grid computing last March. ISGTW interviewed more enterprising, trailblazing women in science and computing than our month-long series could accommodate! We will continue to bring you these and other personal profiles occasionally.
iSGTW: What do you do?
Amoolya Singh: I'm a computational biologist at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, which is a fancy way of saying I use computers to understand living things. 
iSGTW: How did you get interested in this field?
Singh: My interest in science has been mainly shaped by my family origins. I was born and raised in India, in a family of scientists and artists. I remember at the age of five going with my mother to her laboratory and asking what she did. She explained that she took very detailed pictures of the insides o

Feature - Grid promotes diversity in biotechnology at Virginia State

Image courtesy of VSU, Biology department.

Biotechnology is one of the fastest-growing sectors in science, but it suffers from a lack of diversity in its workforce, as do many other scientific fields.  Recent studies* suggest that African-Americans and Hispanics lag behind whites for higher-paying biotech jobs by the largest margins in about a decade.Researchers at Virginia State University, an institution designated by the U.S. Department of Education as one of the Historically Black Colleges and Universities (HBCU), are addressing this imbalance by using grid technology as a resource to teach students and educators about bioinformatics.  Glenn Harris, an assistant professor in the Department of Biology at VSU, used grant funding from the U.S. Department of Agriculture and the National Institutes of Health to obtain a 12-node cluster server and the iNquiry bioinformatics software suite developed by The BioTe

Link of the week - The Dagdigian Doctrine

Image courtesy of Bio-ITWorld.com

What's old news? What's exciting now? What's down the road? What's just hype?In the opening keynote of the 2009 Bio-IT World Conference & Expo last April in Boston, Chris Dagdigian told it as he saw it. A founding partner for the BioTeam IT consultancy, he delivered an educated assessment of the best, the worthwhile, and the most overhyped information technologies  for the life sciences.Ken Davies covers Dagdigian's talk in Bio-ITWorld.com. You'll only find a few highlights from the article here . . .What does Dagdigian think is dead?“Unlimited data storage is over,” he noted, according to Davies. Dagdigian asserted that it is simply not possible to back up all data and keep it safe. “Sometimes it’s better to go back to the -40 F freezer and repeat the experiment.”What's hot now?  He offered virtualization as the “lowest hanging fruit.” Not coming soon,

Feature - EDGeS helps us all talk to each other

With AutoDock, biologists can predict how small molecules will interact with known larger molecules - vital to evaluating candidates for new drugs. Image courtesy www.YASARA.org

Like Bill Murray adrift in Japan in the movie “Lost in Translation,” things can go awry when service grids and volunteer grids try to talk to each other.
Service grids, such as EGEE, often involve large institutions whose work method is centered around collaboration — to the point where participants often know each other personally. To ensure security, resources and users pass through an accreditation process, and the resulting “certificate” provides proof that this occurred successfully. The certificate is key to allowing jobs to be submitted and completed.
On the other hand, volunteer systems — such as BOINC or XtremWeb-based desktop grids — consist of large numbers of personal computers linked together by individuals w

Feature - Sharing in the Taverna

Researchers used Taverna to model molecules such as bacteria. Image courtesy of Engineering and Physical Sciences Research Council

Grids are powerful tools, but for many scientists they remain too complex to easily adopt. Now the KnowARC project’s work with the Taverna tool has taken the first steps toward making grid integration a seamless experience for the bioinformatics community.Taverna, developed by the myGrid project, is a multiplatform system for designing and executing bioinformatics workflows.“The Taverna workbench gives biological scientists the means to rapidly assemble data analysis pipelines,” explained Carole Goble, project leader of myGrid. “It repeatedly and systematically gets results that used to take days in mere hours.”Taverna caught the interest of Steffen Möller, a bioinformatics expert at the University of Lubeck, Germany. Möller and Hajo Krabbenhoft, a member of his team, started looking in

Announcement - Biomed grid school May 2009: Call for participation Image courtesy of Biomed grid school  After the success of the previous two editions of the Biomed Grid School, the thrid edition will be held, again in Varenna on Lake Como, Italy, 10-15 May 2009. The Biomed Grid School is aimed at biomedical research students, post-docs, and senior researchers from any country with an interest in using or developing biomedical applications for distributed data integration and distributed computing environments.School dates: 10-15 May 2009School location: Varenna on Lake Como, ItalySchool Web site RegistrationContact email: biomedgrid at itb.cnr.it Participation limited to 20 students The aim of the school is to provide bioinformatics and biomedical developers the opportunity:to learn how to use new services and functionalities made available by gLite middleware releasesto implement applications on grid infrastructures (EGEE, EGEE related projects) using gLite to build high level interfaces for data provision and management us