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{bio,medical} informatics

Saturday, July 27, 2002

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O'Reilly Network I Hack the Body Electric

"Birney's willingness to dangle jobs in front of the OSCON audience was itself a sign of bioinformatics researchers' extreme regard for open source technologies. Birney described his ENSEMBL project, a joint effort to develop a software program to sort through and annote eukaryotic genome data, as "open source to the core" and described himself as a "Perl addict." Beyond that, Birney said, the chief advantage of open source software in the bioinformatics sphere is the ethical overlap between peer-reviewed software and peer-reviewed research.

"For us, it's straight scientific principles," Birney said. "If you want to be a scientist, open up your data and open up the code that helps you work with that data.""

ITWorld Human genome is open source, too
""You can't do science without having reproducible results," Kent said, explaining that scientists employ a system under which they conduct peer reviews on scientific discoveries before accepting them as sound. "People can't do that unless they can see your source."

Some open source developers argue that the same standards that are used for testing scientific experiments should also be used for testing software. Having access to code gives programmers the ability to dissect a software program and identify bugs, many attendees here say."

redux [05.09.01]
IEEE Spectrum Open-Source Biology And Its Impact on Industry
"The toolbox of biochemistry, the parts list--"the kernel," to stretch the software analogy--is shared by all organisms on the planet. In general, organisms differ from one another because of their order of gene expression or because of relatively subtle perturbations to protein structures common to all forms of terrestrial life. That is, innovation in the natural world in some sense has always followed the idea of a service and flow economy. If the environment is static, only when an organism figures out how to use the old toolbox to provide itself, or another organism, with a new service is advantage conferred.

The analogy to future industrial applications of biology is clear: When molecular biologists figure out the kernel of biology, innovation by humans will consist of tweaking the parts to provide new services. Because of the sheer amount of information, it is unlikely that a single corporate entity could maintain a monopoly on the kernel. Eventually, as design tasks increase in number and sophistication, corporations will have to share techniques and this information will inevitably spread widely, reaching all levels of technical ability--the currency of the day will be innovation and design. As with every other technology developed by humans, biological technology will be broadly disseminated."

Technology based on intentional, open-source biology is on its way, whether we like it or not, and the opportunity it represents will just begin to emerge in the next 50 years."

[ rhetoric ]

“Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.”

BIOINFORMATICS IN THE 21st CENTURY

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