Biomedical Engineering Reference
In-Depth Information
14.10 SOME EXAMPLES OF OPEN - SOURCE SYSTEMS BIOLOGY
TOOLS IN PROTEOMICS
The world of open-source systems biology software tools is dynamic and ever
expanding. An excellent and well-maintained list of freely available tools in
the area of mass spectrometry-based proteomics is available at http://www.ms-
utils.org, and another is at http://www.expasy.ch/tools/. Some projects of note
include:
• T h e
Trans - Proteomic Pipeline
, or
TPP
[18], is a suite of proteomics tools
notable for the large and active user and developer community behind
it.
• T h e
OpenMS Proteomics Pipeline
, or
TOPP
[19], is another proteomics
suite with a smaller but still active community around it.
•
LabKey Server
is a Web-based suite of tools for organizing, processing,
and sharing “all types of biomedical data including mass spectrometry,
fl ow cytometry, microarray, microplate, ELISpot, ELISA, NAb and obser-
vational study information” [11] (Fig. 14.2). It integrates many compo-
nents of the TPP for proteomics processing. Developed and maintained
by a core group of software professionals largely funded by subcontracts
to various prominent labs, this project sets the standard for software
engineering discipline in the bioinformatics open - source world.
Figure 14.2
Labkey Server.
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