open-source software for bioinformatics (was Re: Unix vs Linux - the movie.)

Sean Eddy eddy at wol.wustl.edu
Thu Jul 27 16:18:52 EST 2000

In article <398069d7$1 at news.ucsc.edu> karplus at cse.ucsc.edu (Kevin Karplus) writes:
  >I'm generally in favor of having source code available for any
  >software I buy or use, but reluctant to part with source code that I
  >have spent years working on.  

Kevin, why should your source code be treated as a different kind of
scientific information than a genome center's DNA sequence, or a
crystallographer's coordinates?

I'm not sure that your argument -- though very human and
understandable -- is consistent with the ethics of publicly funded
scientific research, which dictate the open dissemination of results
and techniques in a form that most enables reproduction and rapid
improvement. People have worked very hard to try to make sure that we
get open access to sequences and structure coordinates, for instance,
both of which (like source code) are examples of results too
voluminous to publish in a journal.

It is also unclear to me that the bioinformatics community -- being
heavily reliant on early and open access to incredibly expensive
genome sequence data, such as dictated by the visionary Bermuda
Principles of the NHGRI -- is going to be well-served by a proprietary
attitude towards our software. I don't see how people will be able to
argue with a straight face that science will be best served by rapid
Genbank deposition of genome sequences, while they keep their source
code closed behind glacially slow tech transfer office licensing

- Sean Eddy
- HHMI/Dept. of Genetics, Washington University in St. Louis
- http://www.genetics.wustl.edu/eddy/

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