create a minimal omex file that is accepted on https://run.biosimulations.org/

stellaprins commented 4 months ago

Biosimulators requires an omex file as input, but it does not seem to accept the omex files we created. Why are the omex files not accepted? To figure out why, create a 'minimal' omex file that has the minimal requirements to be accepted by biosimulators.

robertvi commented 4 months ago

The create_omex function currently uses the pymetadata module to create omex files containing the SBML and SEDML files. It also inserts a manifest entry to the omex file itself, which generates a warning from biosimulators that this is not part of the combine/omex standard. However this is not the main issue. Rather the biosimulators sedml parser throws an error about the model contents.

stellaprins commented 4 months ago

These are the SBML and SEDML files Ankur has successfuly used to create an omex file that Biosimulators accepts: SBML/LEMS_NML2_Ex9_FN.sbml LEMS_NML2_Ex9_FN.sedml

robertvi commented 4 months ago

Ok, then I'll use pymetadata module to create one using those as well, to check it also works. Do you know how he created the omex file?

stellaprins commented 4 months ago

I've looked at all references in the SBML Showcase to the create_omex function and it is only called in run_biosimulators_docker.

In the folder with the SBML and SEDML files Ankur used I can only find a validation of the seperate files (validateAll.sh) but not a validation of an omex file.

I will have a look here too [Wednesday 12:53] Sinha, Ankur https://github.com/NeuroML/pyNeuroML/blob/development/pyneuroml/biosimulations.py#L167 -> submitting to biosimulations

robertvi commented 4 months ago

create_omex (pymetadata) makes an omex file, which then generates errors about the sedml variables not being in the correct namespace. Same result from uploading the omex file to biosimulators.

stellaprins commented 4 months ago

Quick fix in create_omex in utils\__init__.py allows us to create a minimal omex file SBML\LEMS_NML2_Ex9_FN.omex.

The resulting minimal omex file SBML\LEMS_NML2_Ex9_FN.omex biosimulations tool was used to run simulations on https://run.biosimulations.org/

[x] Simulator: tellurium 2.2.8 (Sensible output was produced)
[x] Simulator: copasi 4.42.284 Failed
[x] Simulator: amici 0.18.1 (No output was produced)
[x] Simulator: vcell 7.5.0.127 (No output was produced)
[x] Simulator: pysces 1.2.1 Failed
[x] Simulator: gillespy2 1.6.6 (No sensible output was produced, flat line)
[x] Simulator: libsbmlsim 1.4.0 (Sensible output was produced)
[x] Simulator: masspy 0.1.6 Failed

stellaprins commented 4 months ago

Simulation Run Details

Name: test_minimal_omex_tellurium Id: #66433e6716d2b6badabf1246 Simulator: tellurium 2.2.8 CPU cores: 1 RAM: 8 GB Max time: 20 m Submitted: 2024-05-14 11:35:20 AM Updated: 2024-05-14 11:35:37 AM Status: Succeeded

Name: test_minimal_omex_copasi Id: #6643403921392a553ec4f1a2 Simulator: copasi 4.42.284 CPU cores: 1 RAM: 8 GB Max time: 20 m Submitted: 2024-05-14 11:43:06 AM Updated: 2024-05-14 11:43:23 AM Status: Failed

Name: test_minimal_omex_amici Id: #6643429507f7ec63789130fc Simulator: amici 0.18.1 CPU cores: 1 RAM: 8 GB Max time: 20 m Submitted: 2024-05-14 11:53:10 AM Updated: 2024-05-14 11:53:54 AM Status: Succeeded

Name: test_minimal_omex_virtualcell Id: #6643424d07f7ec63789130df Simulator: vcell 7.5.0.127 CPU cores: 1 RAM: 8 GB Max time: 20 m Submitted: 2024-05-14 11:51:58 AM Updated: 2024-05-14 11:52:37 AM Status: Succeeded

Name: test_minimal_omex_pysces Id: #664342d821392a553ec4f1e4 Simulator: pysces 1.2.1 CPU cores: 1 RAM: 8 GB Max time: 20 m Submitted: 2024-05-14 11:54:16 AM Updated: 2024-05-14 11:54:34 AM Status: Failed

Name: test_minimal_omex_gillespy2 Id: #6643441116d2b6badabf12ec Simulator: gillespy2 1.6.6 CPU cores: 1 RAM: 8 GB Max time: 20 m Submitted: 2024-05-14 11:59:29 AM Updated: 2024-05-14 11:59:51 AM Status: Succeeded

Name: test_minimal_omex_libsbmlsim Id: #6643443507f7ec6378913148 Simulator: libsbmlsim 1.4.0 CPU cores: 1 RAM: 8 GB Max time: 20 m Submitted: 2024-05-14 12:00:05 PM Updated: 2024-05-14 12:00:33 PM Status: Succeeded

Name: test_minimal_omex_masspy Id: #664344a816d2b6badabf1304 Simulator: masspy 0.1.6 CPU cores: 1 RAM: 8 GB Max time: 20 m Submitted: 2024-05-14 12:02:00 PM Updated: 2024-05-14 12:02:23 PM Status: Failed

robertvi commented 3 months ago

created a new branch here to preserve the local tellurium run results tables, not yet implemented any actual changes yet, but this branch is where I will roll back to the original version of the table generation scripts to preserve the results

robertvi commented 3 months ago

The changes that preserve the current markdown tables have been merged into master branch on opensourcebrain repo. For now let's make sure we don't change the generator scripts (https://github.com/robertvi/SBMLShowcase/blob/master/test_suite/process_test_suite.py) and (https://github.com/robertvi/SBMLShowcase/blob/master/BioModels/parse_biomodels.py) until we have a fully tested biosimulators method for running the test suite and biomodels

robertvi commented 3 months ago

Am going to work using the https://github.com/robertvi/SBMLShowcase/tree/test_omex branch

robertvi commented 3 months ago

I fixed the output dir is the same as the input dir problem and merged the changes back into test_omex branch

robertvi / SBMLShowcase

create a minimal omex file that is accepted on https://run.biosimulations.org/ #2