Open source appeals to bioinformatics

Australia’s bioinformatics industry will increasingly rely on open source software as researchers look for inexpensive point solutions that are not just a “black box”, according to delegates at an Australian Technology Park Innovations bioinformatics symposium in Sydney.

Sydney University senior lecturer in bioinformatics, Dr Bret Church, said open source is undoubtedly the founding stone of bioinformatics.

“We love it,” Dr Church said. “It is made for research, and there was plenty out there when bioinformatics came along. On the way to solutions, and while exploring possibilities and avenues, open source code tends to play a leading role.”

Church believes open source and bioinformatics work well together because the industry often requires specialty solutions, for which niche open source applications exist.

“I think this is on the basis that [whenever] you are taking time writing code at an early phase, you may just be spinning your wheels,” he said. “Code produced at an early phase may not be worth much.”

Church is conducting research where “computation and neuroscience meet” and relies on open source software for everyday work.

“Students are continually suggesting ‘I’ll look at the preliminary results using Gnuplot [www.gnuplot.info], or ‘Biopython [www.biopython.org] is what I’ll use for that BLAST search’,” he said. “Traditional research from academic bioinformaticians isn’t just a matter of a highly-trained mind, or minds, churning out an elegant piece of software that solves a problem. Academics pride themselves on choosing difficult problems, so it is likely that a number of steps are anticipated.”

Regarding the prospect of developing software for the bioinformatics market, Church said: “In a specialised research area running the line that your software is assured to turn a profit for a business is plain unreasonable.”

“Why not just use software that is freely available to meet the real goal as quickly as possible, especially if you’re working on a specialised project.”

Church is also a proponent of donating resources to give back to open source software projects for bioinformatics, which he described as the “best credit or satisfaction”.

“I’ve always been comfortable with the idea of supporting open source projects,” he said. “I hope that our contributions to our field of study will benefit the community at large, and working towards treatments of neurological disorders is one of our goals.”

Also at the seminar Tim Littlejohn from IBM’s healthcare and lifesciences division said most innovation will occur through government-funded research and will be open.

“A lot of work [in bioinformatics] is done in a granular fashion, which is like open source [development],” Littlejohn said. “This is science and we want to look at the code and we don’t want a black box telling us what’s being done.”

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