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There is an old saying that if you can’t measure it, you can’t manage it. When it comes to scientific puzzles, especially those specific to bioinformatics, that adage could well be that if you cannot see it, you cannot solve it. Although still under development, the Microsoft Biology Foundation (MBF), the beta 2 version of which was recently released as open source is already helping researchers address visualization challenges by providing a language-neutral bioinformatics toolkit that’s an extension to the Microsoft .NET Framework. To date, MBF implements a range of parsers for common bioinformatics file formats and a range of algorithms used to manipulate DNA, RNA and protein sequences.
Perhaps most critically, in addition to allowing scientists to easily and quickly view their data within Excel, MBF provides a set of connectors to biological Web services such as the Basic Local Alignment Search Tool, or BLAST. Alignments, for readers who aren’t familiar with research methodology, are valuable to researchers as they work with large sets of data, searching for similarities and differences throughout the discovery process.
Drawing on what’s already within MBF, researchers at Queensland University of Technology in Australia have developed the BLAST Explorer, which uses SilverMap, a display technology based on SilverLight. Among many other benefits, the BLAST Explorer allows scientists to retrieve BLAST results on demand via Web services and easily share their work with colleagues and other researchers worldwide.
Jim Hogan, associate professor at Queensland University of Technology, says that having BLAST-related visualization tools that are simple and easy to use is an important part of managing large and complex sets of data. “Since it’s a very standard tool that is used by many people, the people developing MBF have incorporated BLAST into the technology, which means that rather than manually editing data you can have direct access to BLAST from within MBF,” he says. “It eliminates the middle man.” And in a business where looking at massive data from hundreds of genes and dozens of organisms is the norm, eliminating the middle man makes the once complex process of analysis far more simple.
In addition to its work on BLAST Explorer, Hogan’s team is working with Microsoft to develop and contribute extensions for those who use MBF within Excel.
Hogan says that the BLAST Explorer is a work in progress, with future development plans that call for an overall extension of capabilities, specifically enhancing input and output of BLAST results – especially the use of custom BLAST collections – improved collaboration and exchange with other tools, such as Excel and sequence and alignment viewers.
Derick Campell, Microsoft External Research