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rxncon

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The complexity of cellular networks is an outstanding challenge for documentation, visualisation and mathematical modelling. In this project, we develop a new way to describe these networks that minimises the combinatorial complexity and allows an automatic visualisation and export of mathematical (ODE/rulebased) models.

Features:

  • Automatic visualiztion with Cytoscape.
  • Automatic generation of rule based models for BioNetGen.
  • Storage of biological facts that can be used for modelling.
Homepage: 
http://www.rxncon.org/

ParaView

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ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities.

ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

Homepage: 
http://www.paraview.org/

i2b2

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i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origins. This platform currently enjoys wide international adoption by the CTSA network, academic health centers, and industry.

Homepage: 
https://www.i2b2.org
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