Content about Biology and genomics

Imagine living next to a busy highway operating 24 hours a day for 365 days per year. That’s what life is like for ocean animals living next to busy shipping lanes.

Announcement - New European Petaflop supercomputer available in 2011

Photo courtesy PRACE

In 2011, the 1.6 Petaflop French supercomputer, Curie, will be installed and available for use. Powered by more than 90,000 processor cores, it will be exclusively dedicated to European research and available for all fields of science, including high-energy and plasma physics, climatology and much more.
“It is crucial to have high computing power to simulate, with the most possible realism, the past of our climate, the current conditions and its future evolution according to various scenarios,” said Jean Jouzel, vice-president of the IPCC (Intergovernmental Panel on Climate Change).
Scientists and engineers will also be able to use Curie’s simulations to explore the properties of various materials, improve aircraft and car construction, design better drugs, understand the intricate molecular functions of the human body and conduct simulations that are impractical in reality.
Cur

Feature - Deciphering the tree of life Image courtesy of Miriam Boon. What’s a bee without its honey, a butterfly without a flower’s nectar? It’s a pretty puzzle posed by the fossil record, which suggests that insects evolved long before flowering plants did. With the rise of genetics, a new window has opened onto evolution – one that could provide a fresh perspective on old problems such as the disparity between insect and angiosperm (flowering plant) evolution. Computational phylogenetics is the development of computational and mathematical techniques that aid in the estimation of evolutionary history, using molecular data such as protein and DNA sequences to construct a “tree of life.” To calibrate their molecular results, evolutionary biologists add the fossil record to the mix, and assume that a new species will evolve at the same rate as its ancestors. “Often they [other researchers] would force the date of angiosperms to correspond

Feature - Fighting pesticide resistance

The tobacco hornworm is a large caterpillar, that can swiftly defoliate other plants as well, such as tomato plants. Image courtesy Jan Stipala, University of Exeter

Pesticide resistance is becoming more of a problem throughout the world as the use of pesticides continues, and insects evolve to accommodate them.
Consequently, pesticides that were once effective at killing crop pests are now no longer effective, leading to an increase in damaged or destroyed crops.
To try to understand the mechanics of how this resistance develops, a group of researchers led by Richard ffrench-Constant at the University of Exeter in the UK are using the country’s National Grid Service. Wilkinson and his research group are analyzing the transcriptomes of insects that are major crop pests, such as Manduca sexta — the tobacco hornworm moth — as seen in the picture at right. (A transcriptome is the set of all messenger RNA molecules, or

Image of the week - iPlant's DNA Subway

Developed by iPlant staff at Cold Spring Harbor Laboratory’s Dolan DNA Learning Center (DNALC), DNA Subway presents complex bioinformatics and visualization tools – predominantly open-source software – in an intuitive and appealing interface.

Our regular readers may recall reading about iPlant, the international collaborative project that aims to solve the big questions of plant biology.
This spring, iPlant released beta versions of some of the planned computational environments and software frameworks. According to a press release from the Texas Advanced Computing Center, the DNA Subway, the Discovery Environment, and the Tree of Life visualization tool allow researchers at all levels to take advantage of the national cyberinfrastructure to study plant DNA.
The DNA Subway, pictured above, is the interface through which iPlant users will access a subset of the iPlant tools and data.
To read more about the iPlant beta, pleas

Link of the week - Why humans don't crash, but computers do

The hierarchical organization of the transcriptional regulatory network of bacterium E. Coli, left, shows a pyramidal structure compared to the Linux call graph, which has many more routines controlling few generic functions at the bottom. Image courtesy of Yale University.

If the human genome is our operating system, then what is it about it that prevents it from crashing as frequently as computer operating systems?
To answer that question, a team of bioinformatics researchers at Yale compared the transcriptional regulatory network of bacteria with the Linux call graph. According to the Yale press release:

The molecular networks in the bacteria are arranged in a pyramid, with a limited number of master regulatory genes at the top that control a broad base of specialized functions, which act independently. In contrast, the Linux operating system is organized more like an inverted pyramid, with many different top-level r

SAFE-BioPharma - A new domain standard for secure identity

Mollie Shields-Uehling, pictured above, is the CEO of the SAFE-BioPharma Association. Image courtesy Mollie Shields-Uehling.

In medical and pharmaceutical research, researchers deal with sensitive private information on a daily basis. That makes secure identity management a crucial need. Mollie Shields-Uehling is the CEO of the SAFE-BioPharma Association, a non-profit organization charged with creating a standard that meets that need.
iSGTW: Thank you for joining us for this discussion, Mollie. Could you tell us a little bit about SAFE-BioPharma?
Shields-Uehling: SAFE-BioPharma Association is a non-profit industry collaboration established by the world's leading biopharmaceutical companies to develop and maintain a global interoperable digital identity and signature standard for the biopharmaceutical and healthcare communities. The purpose of the standard is to allow the transformation of business and regulatory process to

Announcement - Call for papers: Life Sciences Workshop

The workshop on Emerging Computational Methods for the Life Sciences is now accepting paper submissions.
The event will take place 21-25 June 2010 in Chicago, Illinois, as part of the International Symposium on High Performance Distributed Computing.
The purpose of this the workshop is to provide the opportunity for researchers, scientists, engineers, and students to discuss and share the latest research in parallel and distributed high performance systems applied to Life Science problems. It aims to offer an interactive environment for investigators working on novel “computational thinking” for (Systems) Biology, Bioinformatics, Biocomplexity, and Cheminformatics, so that future activities and collaborations will be initiated, as well as fostering discussions about the utilization of HPDC systems in their respective research initiatives. Selected papers will be published in a special issue of Journal Concurrency and Compu

Feature - Keeping an eye on the skies with LifeWatch, poster winner of EGEE 09

Bird encounters jets. According to the photographer, “This was not done in Photoshop. The bird was certainly a lot closer than the planes, but the depth of field was deep enough to capture everything in focus.” Image courtesy Flickr/Kent Smith

Reports of ‘bird strikes’ in recent years are on the rise. According to Scientific American, in 1990 there were only 1,750 incidents in which birds struck a plane, whereas the number for 2008 was close to 8,000. While these encounters never work out well for the bird, normally the plane and passengers escape unharmed — although sometimes a lot of luck is involved. A small percentage of the time, the plane becomes seriously damaged and its engines fail, forcing an emergency landing (as happened last January with US Airways Flight 1549).
Several factors are contributing to the rise in bird strikes. For one thing, migratory bird popu

Biology group issues challenge to computing

The O6-methylguanine DNA methyltransferase protein from Vibrio parahaemolyticus. This protein methylates DNA and is associated with DNA repair. Vibrio is a bacterium in the family that causes cholera. Image courtesy eNMR.

The famous Chicago architect Louis Sullivan — arguably the founder of the modern skyscraper — once said that “Form follows function.”
And what is true of architecture is true of chemistry and structural biology as well: a molecule’s function — how it behaves, and what it causes to be produced — can be deduced by its form. Knowing a molecule’s precise, three-dimensional geometry tells researcheers how and where it will bind to some other molecule, and what effects the two combined molecules will have when they are united.
Or, as Timothy Lovell, a computational chemist at a pharmaceutical company, summed it up: “Once you have the structure down on p

Feature - Big science facilities meet the cloud

Dylan Maxwell explains the Science Studio system to a bystander at Summit 2009 in Banff, Alberta. Photo by Miriam Boon.

Lab notebooks are so passé. In the brave new world of cloud computing, the entire experimental process will take place in your web browser.
And if a team of Canadian researchers at the University of Western Ontario and the Canadian Light Source in Saskatchewan has anything to say about it, researchers around the world will be using a web platform called Science Studio.
“One of the aims of Science Studio is to be able to access big science facilities such as the Canadian Light Source,” said Marina Fuller, a chemistry researcher with the project. “It’s a complete experiment management system.”
The test case for Science Studio is the VESPERS beamline at the Canadian Light Source synchrotron. When Science Studio is complete in 2011, researchers will be able to use the platform to apply