First, set the following environment variables
ENTREZ_EMAIL: email address to credit queries to NCBI Entrez to (e.g.,
BIOSIMULATIONS_API_CLIENT_ID: id of the client for the BioSimulations API
BIOSIMULATIONS_API_CLIENT_SECRET: secret for this client
BUCKET_ENDPOINT: Endpoint for uploading COMBINE/OMEX archives to be published to an S3 bucket
BUCKET_NAME: Name of the bucket
BUCKET_ACCESS_KEY_ID: Access key for the bucket
BUCKET_SECRET_ACCESS_KEY: Secret for the access key
Second, to optionally use Gurobi to execute simulations, encode your Gurobi license into environment variables prefixed with
GRB_. For example, to use Gurobi with a Web License Service set these environment variables:
GRB_LICENSEID: license id
GRB_WLSACCESSID: access id
Third, run the following command-line program to published the models in the BiGG repository to BioSimulations. This program downloads models from BiGG, converts them to COMBINE/OMEX archives, submits the archives to runBioSimulations, and publishes their simulation runs to BioSimulations. This program provides several optional arguments for forcing updates, skipping simulations, skipping publication, and more.:
Fourth, the following command-line program can optionally be run to publish the runs of each model to BioSimulations. This is useful if the above publication program was run with the
Fifth, run the following command-line program to verify that each model was successfully published to BioSimulations. This should be run several minutes after the publication step was run.:
Help for the command-line program is available inline by running:
The command-line program imports each BiGG models into BioSimulations as follows:
biosimulations_bigg/final/issues.ymlfor any known issues about the model which prevent it from being imported in BioSimulations (e.g., the files are not valid SBML or no reference is available). Issues with models should be reported using the BiGG issue tracker.
Checks the import status of the model in
biosimulations_bigg/final/status.ymland determines whether the model hasn’t yet been imported into BioSimuations or needs to be re-imported because it has been updated in BiGG since it was imported into BioSimulations.
Retrieves the model and metadata about the model from BiGG.
If applicable, retrieves Escher flux maps for the model from BiGG.
If possible, uses the open access subset of PubMed Central to retrive thumbnail images for the model.
Creates a Simulation Experiment Description Markup Langauge (SED-ML) file which describes a flux balance analysis simulation of the model.
Converts the Escher flux maps to Vega data visualizations.
Exports the metadata to a OMEX metadata-compliant RDF file. The list of curators is determined by
biosimulations_bigg/final/curators.yml. Individuals who contribute should add their name to this document.
Packages the model, SED-ML, Escher and Vega flux maps, images, and metadata files into a COMBINE/OMEX archive.
Uses BioSimulators-COBRApy to test the execution the COMBINE/OMEX archive.
Checks that the optimal objective value is positive.
Submits the COMBINE/OMEX archive to runBioSimulations.
Publishes the run of the archive to BioSimulations.
Updates the import status of the model in