From b4780c25df4030fce2305ac1a7f381912cbba785 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 20 Jan 2025 10:47:50 +0000 Subject: [PATCH 01/10] add egg info to gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 0b8437e..f51cc53 100644 --- a/.gitignore +++ b/.gitignore @@ -46,3 +46,4 @@ venv /SBML/.DS_Store /SBML/LEMS_NML2_Ex9_FN_missing_xmlns.omex /SBML/output +*.egg-info From c52a494c015c0206a2fad6873a0a5e9fd5645fff Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 20 Jan 2025 10:48:29 +0000 Subject: [PATCH 02/10] remove commented out code --- BioModels/parse_biomodels.py | 1 - 1 file changed, 1 deletion(-) diff --git a/BioModels/parse_biomodels.py b/BioModels/parse_biomodels.py index ee434a6..9270e76 100755 --- a/BioModels/parse_biomodels.py +++ b/BioModels/parse_biomodels.py @@ -353,5 +353,4 @@ def main(): if __name__ == "__main__": use_pickles = True - # model_id_n = 443 main() From e2605d4234a0fec6fa59ee03e1d0a2b2e8ed1840 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 20 Jan 2025 11:01:40 +0000 Subject: [PATCH 03/10] draft readme --- README.md | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/README.md b/README.md index 03f6ab1..2aea59d 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,54 @@ +# SBML Showcase +This repository contains files and instructions for testing validity of Systems Biology Markup Language (SBML) and Simulation Experiment Description Markup Language (SED-ML) files, and their compatibility with different simulations engines. + +## Clone the Repository +To clone this repository to your local machine using the following command: + +```sh +git clone https://github.com/OpenSourceBrain/SBMLShowcase.git +cd SBMLShowcase +``` + +## Install requirements +To set up a conda environment for the code in the SBML, BioModels, and test_suite folders. +``` +conda create -n sbmlshowcase -c conda-forge python=3.10 +conda activate sbmlshowcase +pip install -e . +conda activate sbmlshowcase +``` +or for developers +``` +conda create -n sbmlshowcase-dev -c conda-forge python=3.10 +conda activate sbmlshowcase-dev +pip install -e .[dev] +conda activate sbmlshowcase-dev +``` +## Folders +### BioModels +Top level of this folder contains two scripts. + +#### parse_biomodels.py +Creates an overview table in `BioModels/README.md`, testing all available [BioModels](https://www.ebi.ac.uk/biomodels/). + +To run the script, navigate to the BioModels directory and run: + +``` +python parse_biomodels.py +``` + +#### test_biomodels_compatibility_biosimulators.py +Tests engine compatibility of specific [BioModels](https://www.ebi.ac.uk/biomodels/) and creates subfolders containing the results. Results can be found in `BioModels/BIOMOD_id/tests/results_BioModel_name.md`. + +For example for BioModel [BIOMD0000000001](https://www.ebi.ac.uk/biomodels/BIOMD0000000001) +`BioModels/BIOMD0000000001/tests/results_BIOMD0000000001_url.md` + +### SBML + + +### test_suite + + # Converting NeuroML2/LEMS to & from SBML [![Continuous build using OMV](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/omv-ci.yml/badge.svg)](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/omv-ci.yml) [![Testing non OMV scripts](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/non-omv.yml/badge.svg)](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/non-omv.yml) From 3500d2f7ca09788addf432cdf8b9eb8683ddb6c3 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 21 Jan 2025 12:13:40 +0000 Subject: [PATCH 04/10] bugfix level_version tag process_test_suite --- test_suite/process_test_suite.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test_suite/process_test_suite.py b/test_suite/process_test_suite.py index bbda878..0386e49 100755 --- a/test_suite/process_test_suite.py +++ b/test_suite/process_test_suite.py @@ -431,7 +431,7 @@ def process_cases(args): ) sedml_file_path = ( glob.glob(sedml_file_name)[0] - if len(glob.glob(subfolder, sedml_file_name)) > 0 + if len(glob.glob(sedml_file_name)) > 0 else [] ) From cdc7517926afb53f071b899b8a45bf631baae49c Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 21 Jan 2025 12:33:37 +0000 Subject: [PATCH 05/10] remove BIOMD files that should not be there --- SBML/BIOMD0000000127_url.xml | 262 ------------------- SBML/BIOMD0000000184.xml | 474 ----------------------------------- 2 files changed, 736 deletions(-) delete mode 100644 SBML/BIOMD0000000127_url.xml delete mode 100644 SBML/BIOMD0000000184.xml diff --git a/SBML/BIOMD0000000127_url.xml b/SBML/BIOMD0000000127_url.xml deleted file mode 100644 index 74087bf..0000000 --- a/SBML/BIOMD0000000127_url.xml +++ /dev/null @@ -1,262 +0,0 @@ - - - - - -

The model is according to the paper Simple Model of Spiking Neurons - In this paper, a simple spiking model is presented that is as biologically plausible as the Hodgkin-Huxley model, yet as computationally efficient as the integrate-and-fire model. Known types of neurons correspond to different values of the parameters a,b,c,d in the model. Figure2RS,IB,CH,FS,LTS have been simulated by MathSBML.

RS: a=0.02, b=0.2, c=-65, d=8.

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IB: a=0.02,b=0.2,c=-55,d=4

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CH: a=0.02,b=0.2,c=-50,d=2

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FS:a=0.1b=0.2c=-65,d=2

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LTS:a=0.02,b=0.25,c=-65,d=2

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To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication - for more information.

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In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.

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-

To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691. -

- - - - - - - - - - - He - Enuo - - enuo@caltech.edu - - BNMC - - - - - - 2007-07-16T09:41:14Z - - - 2014-02-14T11:28:54Z - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.04 - - - v - 2 - - - - - 5 - v - - 140 - - U - - i - - - - - - - - - - - - - - - - - - - - - a - - - - - b - v - - U - - - - - - - - - - - - - - - - - - - - - - - - - v - Vthresh - - - - - - - c - - - - - - - U - d - - - - - - - - - - - - - - - - - - - - - - - time - 10 - - - - - - - 10 - - - - - - - \ No newline at end of file diff --git a/SBML/BIOMD0000000184.xml b/SBML/BIOMD0000000184.xml deleted file mode 100644 index b217af9..0000000 --- a/SBML/BIOMD0000000184.xml +++ /dev/null @@ -1,474 +0,0 @@ - - - - - - - - - -

The model reproduces the time profile of cytoplasmic Calcium as depicted in Fig 3 of the paper. Model successfully reproduced using Jarnac and MathSBML

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This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92. -

- - - - - - - - - 2008-08-21T11:36:22Z - - - 2009-09-17T15:58:46Z - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - compartment - vin - - - - - - - - - - - - - - - - - - - - - - - - compartment - kout - X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ER - 4 - vM3 - - - k_CaA - n - - - - - - X - n - - - - - - - - X - n - - - - k_CaA - n - - - - - - - X - n - - - - k_CaI - n - - - - - - - - - Z - m - - - - - - Z - m - - - - kip3 - m - - - - - - Y - X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - compartment - vM2 - - - X - 2 - - - - - - - X - 2 - - - - k2 - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ER - kf - - - Y - X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - compartment - vp - - - X - 2 - - - - - - - X - 2 - - - - kp - 2 - - - - - - - - - - - - - - - compartment - kdeg - Z - - - - - - - From 357ae439466101cce02079271cb28acfd213c163 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 21 Jan 2025 13:54:47 +0000 Subject: [PATCH 06/10] update READMEs --- README.md | 94 +++++++++++++++++++++++++++++++++++++------- test_suite/README.md | 49 +++++++++++------------ 2 files changed, 102 insertions(+), 41 deletions(-) diff --git a/README.md b/README.md index 2aea59d..1810845 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,25 @@ # SBML Showcase +[![Continuous build using OMV](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/omv-ci.yml/badge.svg)](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/omv-ci.yml) [![Testing non OMV scripts](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/non-omv.yml/badge.svg)](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/non-omv.yml) + This repository contains files and instructions for testing validity of Systems Biology Markup Language (SBML) and Simulation Experiment Description Markup Language (SED-ML) files, and their compatibility with different simulations engines. +## Results tables + +### SBML +- [LEMS_NML2_Ex9_FN](SBML\tests\results_compatibility_biosimulators.md) + +### BioModels +- [BioModels overview table](BioModels\README.md) +- [BIOMD0000000001](BioModels\BIOMD0000000001\tests\results_BIOMD0000000001_url.md) +- [BIOMD0000000138](BioModels/BIOMD0000000138/tests/results_BIOMD0000000138_url.md) +- [BIOMD0000000724](BioModels\BIOMD0000000724\tests\results_Theinmozhi_2018.md) +- [BIOMD0000001077](BioModels\BIOMD0000001077\tests\results_Adlung2021_model_jakstat_pa.md) + +### Test Suite +- [Test Suite overview table](test_suite\results.md) +- [00001](test_suite\test_00001\tests\results_compatibility_biosimulators.md) +- [01186](test_suite\test_01186\tests\results_compatibility_biosimulators.md) + ## Clone the Repository To clone this repository to your local machine using the following command: @@ -9,7 +28,7 @@ git clone https://github.com/OpenSourceBrain/SBMLShowcase.git cd SBMLShowcase ``` -## Install requirements +## Conda environment To set up a conda environment for the code in the SBML, BioModels, and test_suite folders. ``` conda create -n sbmlshowcase -c conda-forge python=3.10 @@ -24,34 +43,79 @@ conda activate sbmlshowcase-dev pip install -e .[dev] conda activate sbmlshowcase-dev ``` -## Folders -### BioModels -Top level of this folder contains two scripts. +## Main Folders + +The repository is organized into several folders each serving a specific purpose. Some of the key folders are: + +- [**SBML**](SBML) Contains scripts and files related to a few simple SBML models and testing their compatibility with different BioSimulator engines. +- [**BioModels**](BioModels) Includes scripts for parsing and testing the compatibility of [BioModels](https://www.ebi.ac.uk/biomodels/) with various BioSimulator engines. +- [**test_suite**](test_suite) Holds test cases and scripts for validating the functionality of the repository's tools and models. +- [**utils**](utils) containing general functions. + +## SBML +[**SBML**](SBML) contains a simple SBML model [`LEMS_NML2_Ex9_FN.sbml`](SBML\LEMS_NML2_Ex9_FN.sbml) and it's simulation file [`LEMS_NML2_Ex9_FN_missing_xmlns. +sedml`](SBML\LEMS_NML2_Ex9_FN_missing_xmlns.sedml). -#### parse_biomodels.py -Creates an overview table in `BioModels/README.md`, testing all available [BioModels](https://www.ebi.ac.uk/biomodels/). +[test_compatibility_biosimulators](SBML/tests/test_compatibility_biosimulators.py) adds any missing XML or FBC namespaces to the SED-ML file, wraps up the SBML and SED-ML files into an Open Modeling EXchange format (OMEX) file, submits the OMEX file to different BioSimulator engines either locally via docker (indicated with an `L` for local in the results table), or remotely through the BioSimulators API (indicated with an `R`). The results table created by this script can be found in [here](SBML\tests\results_compatibility_biosimulators.md). -To run the script, navigate to the BioModels directory and run: +To run the script, change your directory to the SBML folder and run: + +``` +python test_compatibility_biosimulators.py +``` + +The following scripts test specific components the process described above and are mainly run as workflows in GitHub Actions. +- [test_biosimulators_api](SBML/tests/test_biosimulators_api.py) +- [test_biosimulators_docker](SBML/tests/test_biosimulators_docker.py) +- [test_biosimulators_local](SBML/tests/test_biosimulators_local.py) +- [test_biosimulators_remote](SBML/tests/test_biosimulators_remote.py) +- [test_compatibility_biosimulators](SBML/tests/test_compatibility_biosimulators.py) +- [test_tellurium](SBML/tests/test_tellurium.py) + +## BioModels +### Overview with all curated BioModels + +[parse_biomodels](BioModels\parse_biomodels.py) creates an overview table in [`BioModels/README.md`](BioModels\README.md), testing curated [BioModels](https://www.ebi.ac.uk/biomodels/). + +To run the script, change your directory to the BioModels folder and run: ``` python parse_biomodels.py ``` +### Test specific BioModels +[test_biomodels_compatibility_biosimulators](BioModels\test_biomodels_compatibility_biosimulators.py) +tests engine compatibility of BioModels listed in `biomodel_id_list` ([BIOMD0000000001](https://www.ebi.ac.uk/biomodels/BIOMD0000000001), [BIOMD0000000138](https://www.ebi.ac.uk/biomodels/BIOMD0000000138), [BIOMD0000000724](https://www.ebi.ac.uk/biomodels/BIOMD0000000724), [BIOMD0000001077](https://www.ebi.ac.uk/biomodels/BIOMD0000001077)) and creates subfolders containing the results. Results can be found in `BioModels/BIOMOD_id/tests/results_BioModel_name.md`. -#### test_biomodels_compatibility_biosimulators.py -Tests engine compatibility of specific [BioModels](https://www.ebi.ac.uk/biomodels/) and creates subfolders containing the results. Results can be found in `BioModels/BIOMOD_id/tests/results_BioModel_name.md`. +For example for BioModel [BIOMD0000000001](https://www.ebi.ac.uk/biomodels/BIOMD0000000001), results can be found [here](BioModels\BIOMD0000000001\tests\results_BIOMD0000000001_url.md). -For example for BioModel [BIOMD0000000001](https://www.ebi.ac.uk/biomodels/BIOMD0000000001) -`BioModels/BIOMD0000000001/tests/results_BIOMD0000000001_url.md` +## test_suite +### Overview with semantic test suite cases +Processes the [semantic](https://github.com/sbmlteam/sbml-test-suite/tree/release/cases/semantic) [SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite?tab=readme-ov-file) test cases which should all be valid SBML models with deterministic simulation results. -### SBML +[process_test_suite](test_suite\process_test_suite.py) creates an overview table summarising whether the SBML files, SBML units, and SED-ML files are valid. In addition to that it shows whether the XML SBML namespaces (`xmlns-sbml`) are missing, and whether the models can be run (`pass` / `FAIL`) in tellurium natively, or remotely through the BioSimulators API. The table can be found [here](test_suite\results.md). +To run the script, change your directory to the test_suite folder and run: -### test_suite +``` +python process_test_suite.py +``` +There are several command line options for testing a limited amount of cases or specific test suite cases, see the [test_suite README](test_suite\README.md) for more information. -# Converting NeuroML2/LEMS to & from SBML -[![Continuous build using OMV](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/omv-ci.yml/badge.svg)](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/omv-ci.yml) [![Testing non OMV scripts](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/non-omv.yml/badge.svg)](https://github.com/OpenSourceBrain/SBMLShowcase/actions/workflows/non-omv.yml) +### Testing specific test suite cases +[test_test_suite_compatibility_biosimulators](test_suite\test_test_suite_compatibility_biosimulators.py) tests engine compatibility of specific semantic test suite cases (00001, 01186) Results can be found in `test_suite/test_case_id/tests/results_compatibility_biosimulators.md`. + +For example for for semantic test case [00001](https://www.ebi.ac.uk/biomodels/BIOMD0000000001), results can be found [here](test_suite\test_00001\tests\results_compatibility_biosimulators.md). + +To run the script, change your directory to the test_suite folder and run: + +``` +python test_test_suite_compatibility_biosimulators.py +``` +There are several command line options in the [test_suite README](test_suite\README.md). + +# Converting NeuroML2/LEMS to & from SBML Most of the interactions between [SBML](https://sbml.org) and LEMS/NeuroML showcased here are enabled by: diff --git a/test_suite/README.md b/test_suite/README.md index 6526fd7..835571a 100644 --- a/test_suite/README.md +++ b/test_suite/README.md @@ -9,57 +9,49 @@ It currently runs three validation tests: The output is a markdown file containing a simple table of the results obtained on each file, where each test result is recorded as either a `pass` or `FAIL`. -## Getting Started +## Run the Validation Script -### Step 1: Download the Test Suite -Download the [zipfile](https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip) (or the latest equivalent) of the [SBML test suite](https://github.com/sbmlteam/sbml-test-suite) that includes [SEDML](https://github.com/SED-ML/sed-ml) files. +Navigate to the test_suite directory and run for example -### Step 2: Extract the Files -Extract the downloaded ZIP file to a desired location, for example using the `unzip` command: - -```bash -unzip semantic_tests_with_sedml_and_graphs.v3.4.0.zip -d /path_to_extraction_folder ``` + python process_test_suite.py --cases 00001 00002 00011 --sbml-level_version l1v2 --output-file results_00001_00002_00011.md +``` +or to run all test cases using the highest SBML versions available navigate to the test_suite directory and run (overwrites `results.md`) -### Step 3: Set up the right environment ``` -pip install matplotlib -pip install pyneuroml -pip install pyneuroml[combine] -pip install pyneuroml[tellurium] -pip install pymetadata -pip install docker + python process_test_suite.py ``` +## Test specific cases +Navigate to the test_suite directory and run for example -### Step 3: Run the Validation Script -Navigate to the directory containing the `process_test_suite.py` script and execute it, specifying the path to the extracted test files. For example if the extraction folder is `C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic` and the `process_test_suite.py` script is in the current directory. +``` +test_test_suite_compatibility_biosimulators.py --cases 00006 01280 --sbml-level_version highest +``` +or to run test cases 00001 and 01186 (tested in this repository) using the highest SBML versions available navigate to the test_suite directory and run ``` - python process_test_suite.py --suite-path C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic --sbml-level_version 'sbml-l3v2' --output-file ./results_test.md --limit 5 +test_test_suite_compatibility_biosimulators.py ``` ## Command Line Options -The `process_test_suite.py` script provides various command-line options to customize the execution of the tests. Below are the available options. - - `--limit` **Description:** Limits the number of test cases processed. **Usage:** `--limit ` **Default:** `0` (no limit) - `--cases` - **Description:** list specific cases to process +- `--cases` + **Description:** List specific cases to process. **Usage:** `--cases ` **Default:** `[]` (no limit) - - `--suite-path` **Description:** Specifies the path to the directory containing the test suite files. **Usage:** `--suite-path ` **Default:** `.` (current directory) -- `--sbml-level_version' - **Description:** String that specifies level and version of files to select for processing (e.g. 'l3v2') +- `--sbml-level_version` + **Description:** String that specifies the level and version of files to select for processing (e.g., 'l3v2'). **Usage:** `--sbml-level_version ` **Default:** `highest` @@ -68,9 +60,14 @@ The `process_test_suite.py` script provides various command-line options to cust **Usage:** `--suite-url-base ` **Default:** `https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic` + ### process_test_suite only +- `--skip` + **Description:** Skip cases listed. + **Usage:** `--skip ` + **Default:** `[]` (no skip) + - `--output-file` **Description:** Specifies the path to the output file where the results will be written. **Usage:** `--output-file ` **Default:** `results.md` -Each option can be used to modify the behavior of the script to fit specific needs, such as limiting the number of cases to process for testing purposes or specifying a different output file for the results. From 2320d6118df9914dbfd326b6129064fc2e6e5247 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 21 Jan 2025 13:55:46 +0000 Subject: [PATCH 07/10] bugfix command line options overrule main script --- BioModels/test_biomodels_compatibility_biosimulators.py | 2 +- test_suite/process_test_suite.py | 3 ++- .../test_test_suite_compatibility_biosimulators.py | 9 +++++---- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/BioModels/test_biomodels_compatibility_biosimulators.py b/BioModels/test_biomodels_compatibility_biosimulators.py index 695c295..ccdf6d0 100644 --- a/BioModels/test_biomodels_compatibility_biosimulators.py +++ b/BioModels/test_biomodels_compatibility_biosimulators.py @@ -180,7 +180,7 @@ def main(): if __name__ == "__main__": - use_original_files = False + use_original_files = False # False allows you to tweak the SED-ML files before running. True overwrites the test files with the original BioModels files. biomodel_id_list = [ "BIOMD0000000001", "BIOMD0000000138", diff --git a/test_suite/process_test_suite.py b/test_suite/process_test_suite.py index 0386e49..f242e0a 100755 --- a/test_suite/process_test_suite.py +++ b/test_suite/process_test_suite.py @@ -634,6 +634,7 @@ def run_test_suite_with_retries(max_retries=10): args.suite_path = os.path.join( os.path.dirname(os.path.realpath(__file__)), "SBML_test_suite", "semantic" ) - args.limit = 0 + if len(sys.argv) == 1: + args.limit = 0 run_test_suite_with_retries() diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py index 6b1919c..3e56522 100644 --- a/test_suite/test_test_suite_compatibility_biosimulators.py +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -186,10 +186,11 @@ def process_cases(args): if __name__ == "__main__": args = parse_arguments() - args.cases = ["00001", "01186"] - args.sbml_level_version = "l3v2" - user_folder = os.path.expanduser("~") + if len(sys.argv) == 1: + # No command line arguments provided, set default values + args.cases = ["00001", "01186"] + args.sbml_level_version = "highest" args.suite_path = os.path.join( - user_folder, "Documents", "compbiolibs", "SBML_test_suite", "semantic" + os.path.dirname(os.path.realpath(__file__)), "SBML_test_suite", "semantic" ) process_cases(args) From 6b6ba7dbc03c324ed3020b320173c25f614661df Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 21 Jan 2025 15:02:37 +0000 Subject: [PATCH 08/10] pre-commit comment for developers --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 1810845..17360b4 100644 --- a/README.md +++ b/README.md @@ -36,13 +36,17 @@ conda activate sbmlshowcase pip install -e . conda activate sbmlshowcase ``` -or for developers +### for for developers ``` conda create -n sbmlshowcase-dev -c conda-forge python=3.10 conda activate sbmlshowcase-dev pip install -e .[dev] conda activate sbmlshowcase-dev ``` +To install the pre-commit hooks +``` +pre-commit install +``` ## Main Folders The repository is organized into several folders each serving a specific purpose. Some of the key folders are: From 4995b9bbc1d0b3310989a76a868ab19b3dec6d4f Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 21 Jan 2025 16:15:45 +0000 Subject: [PATCH 09/10] add back BIOMD models, they are needed in validate all sh --- SBML/BIOMD0000000127_url.xml | 262 +++++++++++++++++++ SBML/BIOMD0000000184.xml | 474 +++++++++++++++++++++++++++++++++++ 2 files changed, 736 insertions(+) create mode 100644 SBML/BIOMD0000000127_url.xml create mode 100644 SBML/BIOMD0000000184.xml diff --git a/SBML/BIOMD0000000127_url.xml b/SBML/BIOMD0000000127_url.xml new file mode 100644 index 0000000..74087bf --- /dev/null +++ b/SBML/BIOMD0000000127_url.xml @@ -0,0 +1,262 @@ + + + + + +

The model is according to the paper Simple Model of Spiking Neurons + In this paper, a simple spiking model is presented that is as biologically plausible as the Hodgkin-Huxley model, yet as computationally efficient as the integrate-and-fire model. Known types of neurons correspond to different values of the parameters a,b,c,d in the model. Figure2RS,IB,CH,FS,LTS have been simulated by MathSBML.

RS: a=0.02, b=0.2, c=-65, d=8.

+

IB: a=0.02,b=0.2,c=-55,d=4

+

CH: a=0.02,b=0.2,c=-50,d=2

+

FS:a=0.1b=0.2c=-65,d=2

+

LTS:a=0.02,b=0.25,c=-65,d=2

+

+
+

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication + for more information.

+

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.

+
+

To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691. +

+ + + + + + + + + + + He + Enuo + + enuo@caltech.edu + + BNMC + + + + + + 2007-07-16T09:41:14Z + + + 2014-02-14T11:28:54Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.04 + + + v + 2 + + + + + 5 + v + + 140 + + U + + i + + + + + + + + + + + + + + + + + + + + + a + + + + + b + v + + U + + + + + + + + + + + + + + + + + + + + + + + + + v + Vthresh + + + + + + + c + + + + + + + U + d + + + + + + + + + + + + + + + + + + + + + + + time + 10 + + + + + + + 10 + + + + + + + \ No newline at end of file diff --git a/SBML/BIOMD0000000184.xml b/SBML/BIOMD0000000184.xml new file mode 100644 index 0000000..b217af9 --- /dev/null +++ b/SBML/BIOMD0000000184.xml @@ -0,0 +1,474 @@ + + + + + + + + + +

The model reproduces the time profile of cytoplasmic Calcium as depicted in Fig 3 of the paper. Model successfully reproduced using Jarnac and MathSBML

+

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92. +

+ + + + + + + + + 2008-08-21T11:36:22Z + + + 2009-09-17T15:58:46Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + vin + + + + + + + + + + + + + + + + + + + + + + + + compartment + kout + X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ER + 4 + vM3 + + + k_CaA + n + + + + + + X + n + + + + + + + + X + n + + + + k_CaA + n + + + + + + + X + n + + + + k_CaI + n + + + + + + + + + Z + m + + + + + + Z + m + + + + kip3 + m + + + + + + Y + X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + vM2 + + + X + 2 + + + + + + + X + 2 + + + + k2 + 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ER + kf + + + Y + X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + compartment + vp + + + X + 2 + + + + + + + X + 2 + + + + kp + 2 + + + + + + + + + + + + + + + compartment + kdeg + Z + + + + + + + From 1442c8b92fc7033b1562711d5842b18b577f3e91 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 29 Jan 2025 09:39:21 +0000 Subject: [PATCH 10/10] add forward slashes in filepaths, fix typos --- README.md | 42 ++++++++++++++++++++---------------------- 1 file changed, 20 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index 17360b4..c1255a2 100644 --- a/README.md +++ b/README.md @@ -6,19 +6,19 @@ This repository contains files and instructions for testing validity of Systems ## Results tables ### SBML -- [LEMS_NML2_Ex9_FN](SBML\tests\results_compatibility_biosimulators.md) +- [LEMS_NML2_Ex9_FN](SBML/tests/results_compatibility_biosimulators.md) ### BioModels -- [BioModels overview table](BioModels\README.md) -- [BIOMD0000000001](BioModels\BIOMD0000000001\tests\results_BIOMD0000000001_url.md) +- [BioModels overview table](BioModels/README.md) +- [BIOMD0000000001](BioModels/BIOMD0000000001/tests/results_BIOMD0000000001_url.md) - [BIOMD0000000138](BioModels/BIOMD0000000138/tests/results_BIOMD0000000138_url.md) -- [BIOMD0000000724](BioModels\BIOMD0000000724\tests\results_Theinmozhi_2018.md) -- [BIOMD0000001077](BioModels\BIOMD0000001077\tests\results_Adlung2021_model_jakstat_pa.md) +- [BIOMD0000000724](BioModels/BIOMD0000000724/tests/results_Theinmozhi_2018.md) +- [BIOMD0000001077](BioModels/BIOMD0000001077/tests/results_Adlung2021_model_jakstat_pa.md) ### Test Suite -- [Test Suite overview table](test_suite\results.md) -- [00001](test_suite\test_00001\tests\results_compatibility_biosimulators.md) -- [01186](test_suite\test_01186\tests\results_compatibility_biosimulators.md) +- [Test Suite overview table](test_suite/results.md) +- [00001](test_suite/test_00001/tests/results_compatibility_biosimulators.md) +- [01186](test_suite/test_01186/tests/results_compatibility_biosimulators.md) ## Clone the Repository To clone this repository to your local machine using the following command: @@ -36,7 +36,7 @@ conda activate sbmlshowcase pip install -e . conda activate sbmlshowcase ``` -### for for developers +### for developers ``` conda create -n sbmlshowcase-dev -c conda-forge python=3.10 conda activate sbmlshowcase-dev @@ -57,10 +57,9 @@ The repository is organized into several folders each serving a specific purpose - [**utils**](utils) containing general functions. ## SBML -[**SBML**](SBML) contains a simple SBML model [`LEMS_NML2_Ex9_FN.sbml`](SBML\LEMS_NML2_Ex9_FN.sbml) and it's simulation file [`LEMS_NML2_Ex9_FN_missing_xmlns. -sedml`](SBML\LEMS_NML2_Ex9_FN_missing_xmlns.sedml). +[**SBML**](SBML) contains a simple SBML model [`LEMS_NML2_Ex9_FN.sbml`](SBML/LEMS_NML2_Ex9_FN.sbml) and it's simulation file [`LEMS_NML2_Ex9_FN_missing_xmlns.sedml`](SBML/LEMS_NML2_Ex9_FN_missing_xmlns.sedml). -[test_compatibility_biosimulators](SBML/tests/test_compatibility_biosimulators.py) adds any missing XML or FBC namespaces to the SED-ML file, wraps up the SBML and SED-ML files into an Open Modeling EXchange format (OMEX) file, submits the OMEX file to different BioSimulator engines either locally via docker (indicated with an `L` for local in the results table), or remotely through the BioSimulators API (indicated with an `R`). The results table created by this script can be found in [here](SBML\tests\results_compatibility_biosimulators.md). +[test_compatibility_biosimulators](SBML/tests/test_compatibility_biosimulators.py) adds any missing XML or FBC namespaces to the SED-ML file, wraps up the SBML and SED-ML files into an Open Modeling EXchange format (OMEX) file, submits the OMEX file to different BioSimulator engines either locally via docker (indicated with an `L` for local in the results table), or remotely through the BioSimulators API (indicated with an `R`). The results table created by this script can be found in [here](SBML/tests/results_compatibility_biosimulators.md). To run the script, change your directory to the SBML folder and run: @@ -68,7 +67,7 @@ To run the script, change your directory to the SBML folder and run: python test_compatibility_biosimulators.py ``` -The following scripts test specific components the process described above and are mainly run as workflows in GitHub Actions. +The following scripts test specific components of the process described above and are mainly run as workflows in GitHub Actions. - [test_biosimulators_api](SBML/tests/test_biosimulators_api.py) - [test_biosimulators_docker](SBML/tests/test_biosimulators_docker.py) - [test_biosimulators_local](SBML/tests/test_biosimulators_local.py) @@ -79,7 +78,7 @@ The following scripts test specific components the process described above and a ## BioModels ### Overview with all curated BioModels -[parse_biomodels](BioModels\parse_biomodels.py) creates an overview table in [`BioModels/README.md`](BioModels\README.md), testing curated [BioModels](https://www.ebi.ac.uk/biomodels/). +[parse_biomodels](BioModels/parse_biomodels.py) creates an overview table in [`BioModels/README.md`](BioModels/README.md), testing curated [BioModels](https://www.ebi.ac.uk/biomodels/). To run the script, change your directory to the BioModels folder and run: @@ -87,16 +86,16 @@ To run the script, change your directory to the BioModels folder and run: python parse_biomodels.py ``` ### Test specific BioModels -[test_biomodels_compatibility_biosimulators](BioModels\test_biomodels_compatibility_biosimulators.py) +[test_biomodels_compatibility_biosimulators](BioModels/test_biomodels_compatibility_biosimulators.py) tests engine compatibility of BioModels listed in `biomodel_id_list` ([BIOMD0000000001](https://www.ebi.ac.uk/biomodels/BIOMD0000000001), [BIOMD0000000138](https://www.ebi.ac.uk/biomodels/BIOMD0000000138), [BIOMD0000000724](https://www.ebi.ac.uk/biomodels/BIOMD0000000724), [BIOMD0000001077](https://www.ebi.ac.uk/biomodels/BIOMD0000001077)) and creates subfolders containing the results. Results can be found in `BioModels/BIOMOD_id/tests/results_BioModel_name.md`. -For example for BioModel [BIOMD0000000001](https://www.ebi.ac.uk/biomodels/BIOMD0000000001), results can be found [here](BioModels\BIOMD0000000001\tests\results_BIOMD0000000001_url.md). +For example for BioModel [BIOMD0000000001](https://www.ebi.ac.uk/biomodels/BIOMD0000000001), results can be found [here](BioModels/BIOMD0000000001/tests/results_BIOMD0000000001_url.md). ## test_suite ### Overview with semantic test suite cases Processes the [semantic](https://github.com/sbmlteam/sbml-test-suite/tree/release/cases/semantic) [SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite?tab=readme-ov-file) test cases which should all be valid SBML models with deterministic simulation results. -[process_test_suite](test_suite\process_test_suite.py) creates an overview table summarising whether the SBML files, SBML units, and SED-ML files are valid. In addition to that it shows whether the XML SBML namespaces (`xmlns-sbml`) are missing, and whether the models can be run (`pass` / `FAIL`) in tellurium natively, or remotely through the BioSimulators API. The table can be found [here](test_suite\results.md). +[process_test_suite](test_suite/process_test_suite.py) creates an overview table summarising whether the SBML files, SBML units, and SED-ML files are valid. In addition to that it shows whether the XML SBML namespaces (`xmlns-sbml`) are missing, and whether the models can be run (`pass` / `FAIL`) in tellurium natively, or remotely through the BioSimulators API. The table can be found [here](test_suite/results.md). To run the script, change your directory to the test_suite folder and run: @@ -104,20 +103,20 @@ To run the script, change your directory to the test_suite folder and run: python process_test_suite.py ``` -There are several command line options for testing a limited amount of cases or specific test suite cases, see the [test_suite README](test_suite\README.md) for more information. +There are several command line options for testing a limited amount of cases or specific test suite cases, see the [test_suite README](test_suite/README.md) for more information. ### Testing specific test suite cases -[test_test_suite_compatibility_biosimulators](test_suite\test_test_suite_compatibility_biosimulators.py) tests engine compatibility of specific semantic test suite cases (00001, 01186) Results can be found in `test_suite/test_case_id/tests/results_compatibility_biosimulators.md`. +[test_test_suite_compatibility_biosimulators](test_suite/test_test_suite_compatibility_biosimulators.py) tests engine compatibility of specific semantic test suite cases (00001, 01186) Results can be found in `test_suite/test_case_id/tests/results_compatibility_biosimulators.md`. -For example for for semantic test case [00001](https://www.ebi.ac.uk/biomodels/BIOMD0000000001), results can be found [here](test_suite\test_00001\tests\results_compatibility_biosimulators.md). +For example for for semantic test case [00001](https://www.ebi.ac.uk/biomodels/BIOMD0000000001), results can be found [here](test_suite/test_00001/tests/results_compatibility_biosimulators.md). To run the script, change your directory to the test_suite folder and run: ``` python test_test_suite_compatibility_biosimulators.py ``` -There are several command line options in the [test_suite README](test_suite\README.md). +There are several command line options in the [test_suite README](test_suite/README.md). # Converting NeuroML2/LEMS to & from SBML @@ -142,4 +141,3 @@ Note these features can be accessed easily with the [pyNeuroML](https://docs.neu pynml -sbml-import SBMLFile.sbml duration dt See also https://github.com/ModECI/modelspec/blob/main/examples/COMBINE.md. -