Biomedical Engineering Reference
In-Depth Information
dog service calling out authors who fail to provide data as required by
its funders or publishing journals.
•
BioTorrents
[26] and
ProteoCommons
[27] are two different projects
looking to apply peer - to - peer fi le-sharing technologies to sharing biologi-
cal data sets.
•
PRoteomics IDEntifi cations database
(
PRIDE
) is a public data repository
for proteomics data “developed to provide the proteomics community
with a public repository for protein and peptide identifi cations together
with the evidence supporting these identifi cations. ” [28] .
• Sage BioNetworks is developing
Sage Commons
, an ambitious open
repository for systems biology tools and datasets: “The Commons will be
a novel computational environment for shared research and develop-
ment of biological network models and their application to human disease
and biology. It will consist of very large network datasets, tools and
models organized within conventions governing user participation” [29].
While in its infancy, this should be an interesting project to watch as its
backers are well connected and well funded.
14.12
CONCLUSION
Perhaps it is no surprise that many scientists working in systems biology are
comfortable operating in and contributing to its open-source and open-data
ecosystems. While it is diffi cult to say precisely what one will get back when
one puts one's energy into extending or simply supporting others in the use
of the available open offerings, the understanding that it
is a system
which
requires feeding seems to motivate many to be active in the community. As a
young discipline attacking problems of breathtaking complexity and scope and
with many young researchers who have never experienced a world without an
Internet and open source, in systems biology collaboration may be the instinc-
tive norm.
REFERENCES
1. Asay M. Intel claims No. 2 Linux contributor spot as hedge against Microsoft.
Available: http://news.cnet.com/8301 - 13505_3 - 10288910 - 16.html .
2. Pryor G. Multi - scale data sharing in the life sciences: Some lessons for policy
makers .
Int J Digital Curation
2009 ; 4 : 71 - 82 .
3. Smith B , et al. The OBO Foundry: Coordinated evolution of ontologies to support
biomedical data integration.
Nat Biotechnol
2007 ; 25 : 1251 - 1255 .
4. HUPO Proteomics Standards Initiative mzML 1.1.0 Specifi cation . Available: http://
www.psidev.info/index.php?q=node/257.
5. SBML.org The Systems Biology Markup Language. Available: http://www.sbml.org .
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