Researchers announce GenomeSpace environment to connect genomic tools

Apr 25, 2012

Researchers from the Broad Institute of MIT and Harvard have announced that GenomeSpace, a software environment that seamlessly connects genomic analysis tools, is now available to the scientific community. During her keynote address at Bio-IT World Conference and Expo on Tuesday, Jill Mesirov, director of computational biology and bioinformatics at the Broad Institute, invited biomedical researchers and tool developers to explore this beta release of the new resource and to use it in their work.

Currently, in order to make use of multiple and data sources, need to convert between the different data formats they use. This often involves error-prone spreadsheet manipulations or requires to write scripts. Mesirov's team and her collaborators set out to change that.

"Our goal is to bring the ever-changing wealth of genomic analysis methods and whatever data are required to the fingertips of any biologist," said Mesirov.

The GenomeSpace environment currently connects six tools: GenePattern, Galaxy, Integrative Genomics Viewer (IGV), Cytoscape, Genomica, and the UCSC Genome Browser. Many projects in genomic research rely on one or more of these tools. For instance, if researchers want to test a hypothesis about between two stages of , they might first use an analytical tool such as GenePattern to detect genes of interest; then IGV to view their ; and then Cytoscape to see protein-protein interactions. GenomeSpace allows them to seamlessly transition between all of these tools to carry a project through to completion.

But GenomeSpace can also be used for smaller inquiries or simple conversions from one tool to another. GenomeSpace's designers worked closely with scientists from the Broad Institute and beyond to determine many kinds of scientific problems for which GenomeSpace could be used. "We strove to identify a range of critical biological problems — from 'microproblems' involving a couple of steps in two tools, to complex scenarios on the scale of an extensive research paper," said Aviv Regev, a core faculty member of the Broad Institute. Regev, who is also an associate professor at MIT and an Early Career Scientist of the Howard Hughes Medical Institute, and members of her lab have made examples of ways to solve these kinds of problems available on GenomeSpace as tutorials for others.

Michael Reich, director of informatics development for the Broad Institute's Cancer Program, is one of the architects of GenomeSpace. He describes GenomeSpace as a connection layer that allows different tools to communicate – it can detect the different data formats each tool requires and make the necessary conversions. "GenomeSpace acts as a broker, automatically detecting and converting files from one format to another for the user," said Reich.

Anton Nekrutenko, an associate professor at Pennsylvania State University and one of the developers of the aggregation tool Galaxy, notes that tools like Galaxy and GenePattern already integrate hundreds of tools. GenomeSpace pulls these aggregation tools together.

"GenomeSpace is an integration of integrators," Nekrutenko said. "The benefit to the user is that this brings together distinctive collections of functionalities offered by individual tools."

"We couldn't be more pleased that Cytoscape is plugged into GenomeSpace," said Trey Ideker, Division Chief of Medical Genetics at University of California, San Diego School of Medicine. "GenomeSpace will connect our network analysis tools with hundreds of other state-of-the-art programs and enable our users quick access to expression clustering and classification and browsing, access to the genome sequence, and so on."

Mesirov, Reich, and their colleagues are eager for other biologists to test drive GenomeSpace and offer feedback on its utility. "We're committed to rapidly responding to the needs of the scientific community and supporting the widest range of genomic research," Reich said.

"GenomeSpace will empower biologists with no computational or programming background to maximize their ability to weave together biological insight with best-in-class computational tools," said Regev. "We hope it will make analyses accessible that were beyond the reach of many biologists."

Explore further: Improving the productivity of tropical potato cultivation

More information: To request an invitation to join GenomeSpace, researchers can visit: www.genomespace.org

add to favorites email to friend print save as pdf

Related Stories

Web-based tools, called 'Galaxy,' simplify genomic analysis

Feb 23, 2010

With tremendous advances in DNA sequencing and the advent of microarray technology in the 1990s, biology embarked on a new age of discovery. Researchers suddenly had access to unprecedented amounts of data -- and faced unprecedented ...

New center looks at how human systems function or fail

Oct 29, 2010

A new center called the National Resource for Network Biology (NRNB), based at the University of California, San Diego School of Medicine, will help clinicians analyze an ever-growing wealth of complex biological ...

Deeper view of HIV reveals impact of early mutations

Mar 08, 2012

Mutations in HIV that develop during the first few weeks of infection may play a critical role in undermining a successful early immune response, a finding that reveals the importance of vaccines targeting regions of the ...

On the trail of rogue genetically modified pathogens

Mar 18, 2008

Bacteria can be used to engineer genetic modifications, thereby providing scientists with a tool to combat many challenges in areas from food production to drug discovery. However, this sophisticated technology can also be ...

Recommended for you

Building better soybeans for a hot, dry, hungry world

10 hours ago

(Phys.org) —A new study shows that soybean plants can be redesigned to increase crop yields while requiring less water and helping to offset greenhouse gas warming. The study is the first to demonstrate ...

Gene removal could have implications beyond plant science

11 hours ago

(Phys.org) —For thousands of years humans have been tinkering with plant genetics, even when they didn't realize that is what they were doing, in an effort to make stronger, healthier crops that endured climates better, ...

Chrono, the last piece of the circadian clock puzzle?

Apr 15, 2014

All organisms, from mammals to fungi, have daily cycles controlled by a tightly regulated internal clock, called the circadian clock. The whole-body circadian clock, influenced by the exposure to light, dictates the wake-sleep ...

User comments : 0

More news stories

Chimpanzees prefer firm, stable beds

Chimpanzees may select a certain type of wood, Ugandan Ironwood, over other options for its firm, stable, and resilient properties to make their bed, according to a study published April 16, 2014 in the open-access ...

For cells, internal stress leads to unique shapes

From far away, the top of a leaf looks like one seamless surface; however, up close, that smooth exterior is actually made up of a patchwork of cells in a variety of shapes and sizes. Interested in how these ...

Down's chromosome cause genome-wide disruption

The extra copy of Chromosome 21 that causes Down's syndrome throws a spanner into the workings of all the other chromosomes as well, said a study published Wednesday that surprised its authors.

IBM posts lower 1Q earnings amid hardware slump

IBM's first-quarter earnings fell and revenue came in below Wall Street's expectations amid an ongoing decline in its hardware business, one that was exasperated by weaker demand in China and emerging markets.