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Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification.
Pubmed ID: 20587024 RIS Download
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Repository of mathematical models of biological and biomedical systems. Hosts selection of existing literature based physiologically and pharmaceutically relevant mechanistic models in standard formats. Features programmatic access via Web Services. Each model is curated to verify that it corresponds to reference publication and gives proper numerical results. Curators also annotate components of models with terms from controlled vocabularies and links to other relevant data resources allowing users to search accurately for models they need. Models can be retrieved in SBML format and import/export facilities are being developed to extend spectrum of formats supported by resource.
View all literature mentionsA software package for numerical computation providing a powerful computing environment for engineering and scientific applications. It includes hundreds of mathematical functions and has a high level programming language allowing access to advanced data structures, 2D and 3D graphical functions.
View all literature mentionsA programming library to help users read, write, manipulate, translate, and validate SBML files and data streams. Specifically, it is a library that users may embed into their own applications.
View all literature mentionsSoftware application for simulation and analysis of biochemical network models and their dynamics. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespies stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. Models in COPASI are based on reactions that convert a set of species into another set of species. Simulation can be performed either with stochastic kinetics or with differential equations. COPASI also includes various methods of analysis and data visualization.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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