Modeling Resources for Systems Biology

Modeling tools

  • CellDesigner - structured diagram editor for drawing gene regulatory and biochemical networks
  • COPASI - biochemical network simulator
  • SBW - the Systems Biology Workbench is also a collection of software tools
  • 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
  • The Software section of the systems-biology.org portal includes links and brief descriptiopns of many modeling and analsis tools.
  • While the OpenWetWare site is dedicated to Synthetic Biology it overlaps greatly with Systems Biology, and includes an extensive computing section.

Kinetic Parameters

  • Sabio-RK - is the System for the Analysis of Biochemical Pathways - Reaction Kinetics
  • BRENDA - the comprehensive enzyme information system

Model Repositories

  • BioModels database - curated repository of dynamic models with extensive annotation and other resources and information for systems modeling.
  • CellML model repository - curated repository of dynamic models in the CellML standard, along with information about modeling tools.
  • Java Web-bsed SimulationJWS is model repository with a simulation tool included.
  • The model repositories section of the systems-biology.org portal includes many links to repositories some mentioned, and others not mentioned on this page, using a looser definition of a model.

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
  • Ontologies are important in structuring and integrating information from multiple sources and to make it more easily usable by others. Two ontologies are presently prominent in systems modeling:
    • TEDDY - TErminology for the Description of DYnamics - agreed upon vocabulary to describe dynamics
    • SBO - Systems Biology Ontology is a set of controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modelling.