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Biodatomics’ Open Source Approach

Maxim Mikheev is a co-founder and CEO of Biodatomics, gene informatics software companies. Mikheev is a molecular biologist, computer programmer, and aggressive entrepreneur. More uniquely, he is also an active member of the open source community, and BioDT, the platform his company unveiled two weeks ago at the ASHG conference in Boston, is open source from top to bottom. None of the roughly 400 distinct tools included in BioDT are exclusive to Biodatomics; instead, popular open source tools like the Galaxy suite, Bowtie, and the Broad Institute’s Genome Analysis Toolkit are collected on a common platform to be stitched together however the user likes. BioDT’s own source code, of course, is also freely available to view and modify – as is legally required of any program that uses preexisting open source tools – and anyone is welcome to use the community version of the platform at no charge.

There are good reasons one would want to, say the creators. Without the need to build tools from scratch, Biodatomics’ programmers have instead focused on creating a top-of-the-line interface, with visualized results and intuitive operations. Even for sophisticated workflows and queries, says Mikheev, “end users don’t need to know programming languages.” Instead, workflows are created in a drag-and-drop manner, with users choosing from BioDT’s arsenal of tools and placing their operations in order – if desired, feeding the output data from one analysis as input data into another. BioDT also incorporates Impala, a query execution program that frees users from writing PERL scripts to search through their tables. (BioDT allows users to display results either graphically or in the traditional table format.) Impala not only allows queries to be written in natural language, but also returns information at a greatly accelerated rate, on the order of just seconds. “We have virtually real-time queries,” Alan Taffel, Biodatomics’ Chief Marketing Officer, told Bio-IT World. “You just enter [your search term] into a field, and the table, or the subset of a table, that you’re looking for pops right up. That makes getting insights out of the data a lot quicker and easier.”

BioIT World