Biomedical Engineering Reference
In-Depth Information
14
COLLABORATIVE SYSTEMS
BIOLOGY: OPEN SOURCE, OPEN
DATA, AND CLOUD COMPUTING
BRIAN PRATT
14.1
Introduction 209
14.2
Tradition of Not Very Collaborative Science 210
14.3
Impact of Open - Source Software on Truly Collaborative Science 210
14.4
Open Data Standards: Ontologies and Interchange Formats 211
14.4.1
Some Notable Standards Efforts in Life Sciences 212
14.5
Note on Assessing Open - Source Software 213
14.6
Constraints on Open - Source Science 214
14.7
Using Cloud Computing to Eliminate Barriers to Collaboration 214
14.8
Additional Benefi ts of Cloud Computing for Systems Biology 216
14.9
Some Examples of Cloud - Based Systems Biology Tools 216
14.10
Some Examples of Open - Source Systems Biology Tools in Proteomics 217
14.11
Public Data Repositories 218
14.12
Conclusion 219
References 219
14.1
INTRODUCTION
The term
systems biology
is a relatively recent coinage, and its meaning is still
evolving. Here it is understood to encompass what some call “the omics”—
genomics, proteomics, metabolomics, and so on, and the effort to synthe-
size knowledge gained about genes, proteins, metabolism, and so on, into an
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