Simulation Experiment Description Markup Language
|SED-ML Script Editor||http://libsedml.sourceforge.net/libSedML/SedMLScript.html|
|SED-ML Web Tools||http://sysbioapps.dyndns.org/SED-ML_Web_Tools|
|SBW Simulation Tool||https://sourceforge.net/p/sbwsimtool/wiki/Home/|
|Systems Biology Simulation Core Library||http://sourceforge.net/projects/simulation-core/|
Conditions of Use
Models and Formats
BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-linked to publicly available reference information.
WholeCellSimDB is a database of whole-cell model simulations designed to make it easy for researchers to explore and analyze whole-cell model predictions including predicted: - Metabolite concentrations, - DNA, RNA and protein expression, - DNA-bound protein positions, - DNA modification positions, and - Ribome positions.
Physiome Model Repository
The Physiome Model Repository (PMR) is the main online repository for the IUPS Physiome Project, providing version and access controlled repositories, called workspaces, for users to store their data. PMR also provides a mechanism to create persistent access to specific revisions of a workspace, termed exposures. Exposure plugins are available for specific types of data (e.g., CellML or FieldML documents) which enable customizable views of the data when browsing the repository via a web browser, or an application accessing the repository’s content via web services.
JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.
This record is not implemented by any policy.
031 6194 (Bundesministerium fur Bildung und Forschung (BMBF), Germany)
BB/D019621/1 (Biotechnology and Biological Sciences Research Council)
DFG Research Training Group 1387/1 (Deutsche Forschungsgemeinschaft)
GM070923 (NIGMS NIH)
GM081070 (NIGMS NIH)
P41-RR013186 (National Institutes of Health)
U54-RR022232 (National Institutes of Health)
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.
Waltemath D,Adams R,Bergmann FT,Hucka M,Kolpakov F,Miller AK,Moraru II,Nickerson D,Sahle S,Snoep JL,Le Novere N
BMC Syst Biol 2011