UNC Scientists Open Source Their Genomic Research

ectoman writes: The human genome specifies more than 500 "kinases," enzymes that spur protein synthesis. Four hundred of them are still mysteries to us, even though knowledge about them could spark serious medical innovations. But scientists at the University of North Carolina, Chapel Hill, have initiated an open source effort to map them all—research they think could pioneer a new generation of drug discovery. As members of the Structural Genomics Consortium, the chemical biologists are spearheading a worldwide community project. "We need a community to build a map of what kinases do in biology," one said. "It has to be a community-generated map to get the richness and detail we need to be able to move some of these kinases into drug facilities. But we're just doing the source code. Until someone puts the source code out there and makes it available to everybody, people won't have anything to modify."

Spur protein synthesis?

[Alopex]

Kinases do much more than just spur protein synthesis. They are among the primary signaling enzymes in the body, involved in turning on and off a multitude of cellular processes by attaching phosphate groups to various targets. Some enzymes simply don't function without being triggered by a kinase. The summary just irks me when it's misleading or wrong

Re:

[Anonymous Coward]

They are important for life. It's pretty much impossible for life to exist without them.

Open source isn't the exception, it's the norm

[avarus]

I work in this field, and outside of the commercial pharma companies, the general rule is that all the data goes public and that all the code written is open source. All the big publicly funded agencies, and certainly all the research councils here in the UK, follow this principle. Admittedly some people do sit on the data a bit longer than they should before releasing it, but in principle it all goes public and freely available.

Want to find open, public data in genomic science, or contribute to an open database? - fill your boots: http://www.oxfordjournals.org/... [oxfordjournals.org]
Want to find new open-source algorithms for genome analysis? There are so many it's hard to keep up - http://blends.debian.org/med/t... [debian.org]

In the EU, there is so much data in public databases they had to start a pan-European effort called ELIXIR just to try and work out how they were going to handle all the data curation work.

So, not to take anything away from this fine project, the idea that it's special because it's open source or because scientists are collaborating widely is just plain silly.

TIM

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[the gnat]

I agree that this isn't an extraordinary example, but I have to take issue with this:

the general rule is that all the data goes public and that all the code written is open source

The first part is correct in the literal sense (this is an absolute requirement of public funding agencies and journals), but that doesn't mean they're unencumbered by patents. The second part, unfortunately, is incorrect: open source is getting more common and scientists are slowly coming around to the idea that this shouldn't be

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[the gnat]

It seems to me that fewer people may want to contribute to the effort if they think their freely-contributed work could be subsumed by a patent fence that (e.g.) GlaxoSmithKline might decide to slap around a derivative discovery.

In practice, you are almost certainly incorrect. Scientists working in basic research - the ones I've met, anyway - are almost universally thrilled if their research leads to improvements in human health, regardless of whether or not they or someone else profits from it. (In fact,

It will not spur anything other than greed.

[deviated_prevert]

Most medical research that is publicly funded winds up being used by the drug corporations to line the pockets of a few very rich people. Take for example the recent cures for hep c. Much of the primary research into the HCV rna structure and thus the secondary chemical binding processes was done on the public purse. The result is medicines that can cure the disease at over 1000 dollars a pill that in reality cost the company very small amounts of money to actually produce. One company even paid 11 billion

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[the gnat]

Much of the primary research into the HCV rna structure and thus the secondary chemical binding processes was done on the public purse

A huge fraction of it was done privately as well, but that's still just one tiny piece in a much larger project. Solving a structure isn't that difficult or expensive for a well-validated experimental system, and the end result helps you guess at what chemical syntheses to try, but actually putting something on the market takes the better part of a decade and hundreds of mil