COLLABORATIVE SYSTEMS BIOLOGY: OPEN SOURCE, OPEN DATA, AND CLOUD COMPUTING - Collaborative Computational Technologies for Biomedical Research - page 218

• Skyline is “a Windows client application for building Selected Reaction
Monitoring (SRM)/Multiple Reaction Monitoring (MRM) methods and
analyzing the resulting mass spectrometer data” [12]. This project is also
notable for its very high standard for rigorous software engineering prac-
tices, which is not surprising as its lead developer is a LabKey alumnus.
• Cytoscape is “an open source bioinformatics software platform for visual-
izing molecular interaction networks and integrating these interactions
with gene expression profi les and other state data” [20]. The project is
notable for its consistent progress and support from academia and indus-
try alike.
• ProteoWizard , already discussed above, hosts several proteomics-related
projects in addition to the mzML reference implementation and convert-
ers, including the aforementioned Skyline and various tools for data
visualization and working with metabolic labeling and protein metabo-
lism experiments.

14.11 PUBLIC DATA REPOSITORIES

The ability for different research teams to assess data sets that other teams
have used is critical in evaluating the merit of new systems biology techniques.
The following list, while by no means complete, illustrates the rich and still
developing culture of public life sciences data repositories (much of which is
made possible by the emergence of open-data standards):

• PeptideAtlas is “a multi-organism, publicly accessible compendium of
peptides identifi ed in a large set of tandem mass spectrometry proteomics
experiments” [21] with many contributors. Many of the data sets are
associated with publications.
• Amazon EC2 has a growing number of data sets ready for use in its cloud
environment; the biology data sets are mostly for genomics such as
Unigene and GenBank [22] .
• Uniprot provides the Swiss-Prot and TrEMBL protein sequence data-
bases used by many protein search tools [23].
• Protein Data Bank from Research Collaboratory for Structural
Bioinformatics (RCSB) is “the single worldwide repository of informa-
tion about the 3D structures of large biological molecules, including
proteins and nucleic acids ” [24] .
• The MGED Society is “ an international organization of biologists, com-
puter scientists, and data analysts that aims to facilitate biological and
biomedical discovery through data integration” [25]. While not actually
a repository, it is notable for creating the Minimum Information About a
Microarray Experiment ( MIAME ) standard and particularly for running
a service to facilitate data deposition for published papers and a watch-