Mathematical models describing biological/biomedical systems can be submitted to BioModels, irrespective of the modelling formats they are encoded in or the modelling approaches (ODE, FBA, logical, agent-based, etc.) used for assessing the biological mechanism. The new infrastructure for BioModels form a flexible platform and can handle models of any formats (eg. SBML, CellML, matlab, mathematica, etc.), but only minimum support will be provided for non-SBML models at the level of curation. An extensive model checking procedure (curation) will be undertaken for models submitted in SBML.The model files along with the supporting documents such as SED-ML file, experimental data, simulation results, etc., can also be submitted in COMBINE archive format.
For SBML models: Models encoded in any level and version of SBML are accepted. The following SBML formats are currently accepted:
- SBML Level 3: Version 1 and Version 2 (including any packages)
- SBML Level 2: Version 1, Version 2, Version 3, Version 4 and Version 5
- SBML Level 1: Version 1 and Version 2
Please contact us if you have any queries regarding depositing your models to BioModels.
The submitted model will not be publicly available from BioModels straightaway. If you wish to know more about the submission, curation and annotation processes, please refer to the relevant sections of the Frequently Asked Questions.
To ensure a prompt processing of your model, please go through the following check-list before submission.
- Check that your model is valid according to the format you chose. If your model is encoded in SBML, you can use the official online validator.
- Enter all relevant information in appropriate fields in the submission pipeline, which would be useful for processing your models.
- If you created the model (or collaborated to its creation) but are not an author of the associated publication, please add your personnal information (first and last name, organisation and email address) in the model, so that your contribution can be acknowledged. If you used SBML, this can be done by adding to the model element a dc:creator annotation, as in this which you can re-use (skip the blue part if already present).
- Choose a meaningful name for your model. You can follow the pattern AuthorNameYear - Topic, Method, for example: Kim2007 - Crosstalk between Wnt and ERK pathways.
- Please check the file names of your submission only containing acceptable characters: alphanumeric characters, spaces, hyphens and underscores.
All models in BioModels are available under the terms of the Creative Commons CC0 1.0 (Public Domain Dedication). Therefore you need to agree to release the encoded model in the Public Domain before submitting it to BioModels.
Thank you for contributing to BioModels!
<?xml version="1.0" encoding="UTF-8"?>
<sbml level="2" version="1" xmlns="http://www.sbml.org/sbml/level2">
<model id="my_id" name="my_name" metaid="my_metaid">