General Technique
BioTapestry, which is a joint effort between the Bolouri Lab at the Institute for Systems Biology (ISB) and the Dr. Eric Davidson Lab at Caltech, is an interactive tool for building, visualizing, and simulating genetic regulatory networks (GRNs). Since it is written in Java, and is available as open-source software, it is available for use by any project that needs a cross-platform, web-deployed visualization and modeling tool for GRNs. It is available on the web at BioTapestry project home page.
Purpose/use/application of the technique:
BioTapestry is designed around the concept of a developmental network model, and is intended to deal with large scale models with consistency and clarity. It is capable of representing systems that exhibit increasing complexity over time, such as the genetic regulatory network controlling endomesoderm development in sea urchin embryos. Significant features include:
- Supporting data resulting from the perturbation of expression of specific genes, measured in any way (Quantitative Polymerase Chain Reaction - QPCR, genetics, etc.), can be easily accessed for each gene. Temporal and spatial expression results are also accessible.
- BioTapestry can portray hourly, localized views of the network during development based on data tables describing the network's local and temporal states.
Twork during development based on data tables describing the network's local and temporal states.
- BioTapestry can automatically layout the set of network models from lists of interactions provided either through interactive dialogs or comma-separated value (CSV) files exported by spreadsheet programs.
Example(s) of projects at ISB that use this technique:
While BioTapestry is being used to visualize genetic regulatory networks for ongoing projects at the ISB, the best publicly available example depicts the development of the endomesoderm in S. purpuratus at the Davidson Lab. See example.
Ongoing area of technology development:
Development of BioTapestry is ongoing. The first publicly available version allowed users to draw up a network and show how it develops over time. A more recent release concentrated on automating the layout process and allowed the network to be built from a list of interactions. The current version also provides more features to help the user draw and reorganize network layouts, including automatic link layout support, network expansion and compression, layout synchronization.
In the next major release, BioTapestry will analyze experimental spatial/temporal expression data and raw perturbation data, and then help the user decide what network connections should be included in the network diagram.
Other planned enhancements include:
- Making the creation of submodels easier, more intuitive, and more flexible.
- Making the ties to experimental data more flexible, thus allowing BioTapestry to handle a wider range of experimental data types.
- Tying the abstract network representations to 2D and 3D models of the developing organism.
- Addressing scalability issues, including adding support for arbitrary groupings of network elements.
- Significantly improved support for Systems Biology Markup Language (SBML) export and ties to the Dizzy simulation engine.
Representative publication(s):
Longabaugh, W.J.R., Davidson, E.H., Bolouri, H.
Computational representation of developmental genetic regulatory
networks. Dev. Biol. 283, 1-16, 2005.
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