Systems Biology

Systems biology is an emergent field focused on advancing the understanding of biological systems. By studying the relationships and interactions between various parts of a biological system, researchers hope to develop a model of the system as a whole.

The ESCHER systems biology basic tools and core technologies provide a suite of biology-inspired analytical, simulation, and visualization tools and services. These support a comprehensive software development environment that aids biological researchers engaged in building computable descriptions of cellular functions.

Links to other systems biology-related resources are provided to further aid researchers in their work and promote the findings and results of other organizations.

Basic Tools

SBML2 Extension API - Systems Biology Markup Language (Extension API)
GeneTF - Gene Transcription Factor Connectivity Network
GeneTRE - Gene Transcription Regulatory Elements
TimeSeries - TimeSeries Data Format for Bio-SPICE Dashboard
MageML - MageML Data Format for Bio-SPICE Dashboard

Core Technologies

UDM - Universal Data Model
jUDM - Java Wrapper for UDM
GReAT - Graph Rewrite And Transformation
WOTIF - Web-based Open Tool Integration Framework

Other Resources

Systems Biology Markup Language (SBML) Homepage - Website supervised by The SBML Team to promote research and software development for systems biology
Bio-SPICE.org - Website with information on Bio-SPICE, an open source framework and software toolset for systems biology
Institute for Software Integrated Systems (ISIS), Vanderbilt University - Website for the BioCOMP Tool Integration Framework for Systems Biology project
Biocomputation Group, University of Pennsylvania - Systems biology research group within the Computer and Information Sciences department
DARPA BioCOMP Program - Homepage for the Defense Advanced Research Agency (DARPA) Bio Computation program

ESCHER Research Institute

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Systems Biology

Systems Biology

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Core Technologies

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