[ox] Fwd: open source bioinformatik
- From: Stefan Merten <smerten oekonux.de>
- Date: Sat, 12 Jul 2003 19:52:17 +0200
Hi!
Hier eine (unabgesprochene, deswegen anonymisierte) News aus der
wak-Liste aus dem Feld Freie Software, Wissenschaft, Genforschung,
offene Standards.
Seid Jahren haben zu diesem Thema auch einen Link in der Link-Liste:
* Nachdem er mit Patentierung seiner eigenen Idee durch eine andere
Firma bedroht wurde, hat der Erfinder seine Erfindung als
{{2:Freien Microarrayer für die Molekularbiologie}}
{{[jump="http://cmgm.stanford.edu/pbrown/"]veröffentlicht}}, zu
dem es auch einen
{{[jump="http://opencollector.org/news/Archives/2000/Feb/951242884.html";]
Kommentar}} gibt.
Ausführliche Bauanleitung:
http://cmgm.stanford.edu/pbrown/mguide/index.html
Das wiederum ein Beitrag zum Thema Freie Hardware :-) .
Mit Freien Grüßen
Stefan
------- Forwarded Message
/Nature/ *424*, 119 (10 July 2003); doi:10.1[PHONE NUMBER REMOVED]a
* DNA-chip firm backs down over upgrade*
JOHN WHITFIELD
[LONDON]Biotechnology company Affymetrix is retreating from a plan that
would have made it tougher for biologists to use open-source computer
software to analyse results from its ubiquitous microarray chips.
The firm, based in Santa Clara, California, had planned to upgrade its
microarrays, which are used by thousands of molecular biologists to
detect gene activity. It hoped that the upgrade would have made the
output files from its chips smaller and faster to process.
But researchers energetically protested that the new files would be
incompatible with open-source software that has been developed by
academics to work with the company's microarrays. Such software is free
for everyone to use.
On 2 July, Affymetrix said that it would change course to ensure that
its upgraded technology would not render the free software obsolete.
Microarray chips are covered in thousands of strands of DNA, each
corresponding to a known gene and marked with a fluorescent molecular
tag. Researchers add a sample of biological material to the chip, and
the DNA in the sample bonds to the sequences on the chip. The chip
outputs its results -- a record of which dots are glowing, and how
brightly -- as a computer file. At present, these files can be opened on
almost any computer.
Affymetrix announced late last year that it would upgrade its
microarrays to produce data as smaller files in a proprietary format.
The change would have made it easier to modify formats in the future
without disrupting the analysis software, says David Kulp, a
bioinformaticist at the company.
But the move would have placed the microarray data files off-limits to
the developers of open-source software. It would also have rendered
useless many existing tools for interpreting the data, including a
popular one called Bioconductor.
Many molecular biologists are happy with the simple file format produced
by Bioconductor. "The file is readable by a human," says James
MacDonald, who uses Bioconductor to analyse output from chips at the
University of Michigan's microarray facility at Ann Arbor.
Researchers' worries were increased by the fact that US law now makes it
difficult to write open-source software to interface with proprietary
formats. On 27 June, 21 members of the group that develops Bioconductor
announced that they would not develop software for a private file format.
"We wouldn't be willing to do anything that was marginally legal," says
group member Robert Gentleman, a statistician at the Harvard School of
Public Health. Researchers working on software in their spare time lack
the resources to deal with proprietary file formats, he adds.
Besides the inconvenience to researchers forced to use new software,
losing the efforts of a large group working out how best to analyse
microarray data would have damaged the field as a whole, Gentleman
argues. "The technology isn't mature yet. We need a lot of clever people
working on these problems," he says.
Last week, after conferring with the Bioconductor team, Affymetrix
announced that its new compressed format will be made public. "We don't
have any trouble with this," says Kulp. "Clearly, some developers prefer
to write their own file readers, which is more work on their part, but
has advantages to open-source software distribution."
"I think that science won," says Gentleman. But he doubts that the issue
will go away: "The clash between open source and commercialization will
probably be a constant minefield for both sides."
------- End of Forwarded Message
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