The practice of systems biology depends upon many software tools,
operating on many kinds of data from many different sources. Each of
these tools typically excels at one (or a few) types of analysis with one
(or a few) types of data. A crucial challenge, therefore, is to combine the capabilities
of these and other, forthcoming tools to create a data exploration and
analysis environment which can do justice to the variety and
complexity of systems biology.
The Gaggle is a simple, open-source Java software environment which
solves this problem. Guided by the classic software engineering
strategy of separation of concerns and a policy of semantic
flexibility, it combines existing popular programs and web resources
into a user-friendly, rich, and easily extended environment in which
to do systems biology.
We currently support a number of geese -- our name for any
open source software which is adapted to run in the gaggle. This adaptation
is generally only a small amount of programming work. Once gaggled
the program can broadcast and receive any of a small number of data types
which together constitute an adequate basis for exploratory analysis in
systems biology. These data types include:
- Name list (i.e., these genes are interesting)
- Bicluster: Name list combined with a condition list (i.e., these genes are interesting in these conditions)
- Tuple (replaces HashMap): a collection of name/value pairs
- Matrix: rows and columns, each named, containing numerical data
- Network: a collection of nodes and edges, with arbitrary hashmaps associated with each
Our current geese include:
- MeV: MultiExperiment Viewer
- a browser for KEGG,
EMBL's STRING, and other web resources
- a DataMatrixViewer
for loading &: navigating, and plotting high-throughput
experimental data (microarray, proteomics, MPSS, ...)
- R -- an indispensible tool for statistics,
graphics, and data manipulation
- Cytoscape -- the standard software for the
graphical exploration of networks
- Firegoose -- a Firefox toolbar that
enables data exchange between web resources and the Gaggle framework.