Systems Biology Intro and Tools
Systems Biology - Overview, Resources, Standards and Tools
Overview
- Intro & Resources
- Books
- Groups
Resources
- Systems Biology Portal Site - includes many links in a number of categories
- BioModels database - curated repository of dynamic models in the CellML standard
- CellML model repository - curated repository of dynamic models in the CellML standard
- Sabio-RK - System for the Analysis of Biochemical Pathways - Reaction Kinetics
- The Gene Ontology - the ongoing effort to standardize the names of genes
- KEGG - Kyoto Encyclopedia of Genes and Genomes - is amassive collection of databases (perhaps the "mothership" for systems biology
- Reactome - curated resource of core pathways and reactions in human biology
Standards
- BioModels.net - Site describing the various standards movements in systems biology
- SBML - systems biology markup language - XML specification for dynamic models
- CellML - cell markup language - - a competing XML specification for dynamic models, with greater depth to the handling of the mathematics of the model
- SBGN - systems biology graphical notation - a standard notation for drawing systems models diagramatically
- SBW - an software standard (API standard) to allow different software tools to work together to design, simulate and analyze models
- MIRIAM - Minimal Information Required In the Annotation of Models - this is one of a large number of minimum information standards being developed to make the reporting of experimental unambiguous and reproducible
- TEDDY - TErminology for the Description of DYnamics - agreed upon vocabulary to describe dynamics
Tools
- SBW - the Systems Biology Workbench is also a collection of software tools
- CellDesigner - structured diagram editor for drawing gene regulatory and biochemical networks
- Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
- Cell Net Analyzer is a package for MATLAB and provides a comprehensive and user-friendly environment for structural and functional analysis of biochemical networks.
- Virtual Cell Modeling and Analysis Software - this is a modeling environment hosted on a high-performance computing resource
- OpenCell - a new tool for systems biology modeling being developed around the CellML standard