Gaggle Components
Data Standards

What is the Gaggle?

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:

  1. Name list (i.e., these genes are interesting)
  2. Bicluster: Name list combined with a condition list (i.e., these genes are interesting in these conditions)
  3. Tuple (replaces HashMap): a collection of name/value pairs
  4. Matrix: rows and columns, each named, containing numerical data
  5. Network: a collection of nodes and edges, with arbitrary hashmaps associated with each

Our current geese include:

  1. MeV: MultiExperiment Viewer
  2. a browser for KEGG, EMBL's STRING, and other web resources
  3. a DataMatrixViewer for loading &: navigating, and plotting high-throughput experimental data (microarray, proteomics, MPSS, ...)
  4. R -- an indispensible tool for statistics, graphics, and data manipulation
  5. Cytoscape -- the standard software for the graphical exploration of networks
  6. Firegoose -- a Firefox toolbar that enables data exchange between web resources and the Gaggle framework.
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