SED-ML and associated files*

Select a local file or enter a URL for a COMBINE/OMEX or zip archive that contains SED-ML files and associated model and metadata files

Select a method for providing a simulation project (COMBINE/OMEX or zip archive file)

Upload a local file

Enter a URL for a file

Select a simulation project (COMBINE/OMEX or zip archive file)

Enter a URL for a COMBINE/OMEX or zip archive

Select a method for providing a COMBINE/OMEX or zip archive which describes one or more simulations (in SED-ML format) of one or more models (e.g., in BNGL, SBML formats). Archives can either be uploaded from your local computer or loaded from a publicly-accessible URL.

Several example simulation projects are available from the BioSimulators test suite .

Uploaded files are limited to 64 MB. Files up to 1 GB can be submitted via URLs.

Please select a COMBINE/OMEX or zip archive file.

Currently, archive uploads are limited to 256 MB. Larger archives must be validated via URLs.

Please enter a URL for a COMBINE/OMEX or zip file.

Metadata format and minimum information convention

Indicate the format of the OMEX Metadata

files in the archive and the information convention that should be used to validate them.

Select the format of the OMEX Metadata files

Select the format of the OMEX Metadata files in the archive.

Select a minimum information convention to use to validate the metadata in the archive

The BioSimulations convention is required to publish archives to BioSimulations.

Options

Optionally, tune and disable validation of aspects of simulation project archives.

Validate the OMEX manifest

file in the archive.

Validate the simulation experiments (SED-ML

files) in the archive.

Validate the sources of the models (e.g., CellML

, SBML

files) in the simulation experiments (SED-ML files) in the archive.

Validate the metadata (OMEX Metadata

files) in the archive.

Validate the images (BMP, GIF, JPEG, PNG, TIFF, WEBP files) in the archive.

Plain zip archives can be validated by disabled validation of OMEX Manifests.

SED-ML validation is required to validate models.

Model validation is required to more comprehensively validate SED-ML files.

BioSimulations validates models using community-contributed validation tools for each model language. The thoroughness of these tools varies. In addition, some tools currently provide limited diagnostic information. We welcome contributions of improved validation tools.

This application can only validate targets for simulation observables for unchanged models. Targets for modified models cannot be validated statically, independently from executing the associated SED-ML document. Simulation tools validate such targets when they execute their parent SED-ML document. For the same reason, this application cannot validate targets for model changes. Simulation tools validate such model change targets during their execution.

Simulation projects published to BioSimulations must contain valid metadata that meets BioSimulations minimum metadata conventions.

An OMEX manifest file is required to validate metadata files. As a result, OMEX Metadata validation should generally be disabled when OMEX manifest validation is disabled.

Image validation is required to comprehensively validate thumbnail images described in OMEX Metadata files.