Merge pull request #7 from paulflang/pl/sbmlopt

Pl/sbmlopt

.gitignore

@@ -3,11 +3,16 @@
 .venv
 .wenv
 .wenv1
+.vscode
 *.our_rcp_workspace
 
 *.diff
 *.project
 *trash*
+*poster*
+*presentation*
+*_manu.pdf
+*_manu.svg
 
 # More specific
 versions/test_cBNGL/

README.md

@@ -2,7 +2,7 @@
 
 [![DOI](https://zenodo.org/badge/426996673.svg)](https://zenodo.org/badge/latestdoi/426996673)
 
-`cell_cycle_petab` is a repository that stores several cell cycle model versions and their corresponding PEtab problems. The data in the measurement tables stems from snapshot measurements by [Stallaert et al. (2021)](https://github.com/paulflang/cell_cycle_time_course/blob/main/4i_stallaert/raw.md). Pseudo-time courses were reconstructed with [reCAT](https://github.com/tinglab/reCAT). Visualisations of these time courses can be found in the [cell_cycle_time_course](https://github.com/paulflang/cell_cycle_time_course) repository. The model generation process is documented in the [cell_cycle_model](https://github.com/paulflang/cell_cycle_model) repository. For further details, please refer to [Paul Lang's dissertation](https://ora.ox.ac.uk/objects/uuid:888439ad-99ac-4e89-9473-cc4864cf1e94).
+`cell_cycle_petab` is a repository that stores several cell cycle model versions and their corresponding PEtab problems. The data in the measurement tables stems from snapshot measurements by [Stallaert et al. (2021)](https://github.com/paulflang/cell_cycle_time_course/blob/main/4i_stallaert/raw.md) in RPE1 cells. Pseudo-time courses were reconstructed with [reCAT](https://github.com/tinglab/reCAT). Visualisations of these time courses can be found in the [cell_cycle_time_course](https://github.com/paulflang/cell_cycle_time_course) repository. The model generation process is documented in the [cell_cycle_model](https://github.com/paulflang/cell_cycle_model) repository. For further details, please refer to [Paul Lang's dissertation](https://ora.ox.ac.uk/objects/uuid:888439ad-99ac-4e89-9473-cc4864cf1e94).
 
 ## Models
 
@@ -34,3 +34,12 @@ Figures for the manuscript *Reusable rule-based cell cycle model explains compar
     - [`/versions/v3.2.0/results_20220421/plot_sacess_320_manu.py`](/versions/v3.2.0/results_20220421/plot_sacess_320_manu.py)
 - [Figure 9](/versions/v4.0.0/results_20230120/v4.0.0_manu.png):
     - [`/versions/v4.0.0/results_20230120/plot_sacess_400_manu.py`](/versions/v4.0.0/results_20230120/plot_sacess_400_manu.py)
+- [Figure 10](/versions/v4.0.0/results_20230307/v4.0.0_manu.png):
+    - [`/versions/v4.0.0/results_20230307/plot_sacess_400_manu.py`](/versions/v4.0.0/results_20230307/plot_sacess_400_manu.py)
+
+## Barebones SBML models fitted to RPE1 data
+
+Barebones SBML files with parameters optimized to fit the time courses of RPE1 cells can be found for the following model versions:
+- [v3.0.1](/versions/v3.0.1/results_20220421/v3.0.1_optimized.sbml)
+- [v3.2.0](/versions/v3.2.0/results_20220421/v3.2.0_optimized.sbml)
+- [v4.0.0](/versions/v4.0.0/results_20230307/v4.0.0_optimized.sbml)

versions/substitute_sbml_pars.py

@@ -0,0 +1,22 @@
+import os
+import petab
+from libsbml import writeSBMLToFile
+base_dir = os.path.dirname(os.path.abspath(__file__))
+
+# Options
+fig2yaml = {
+    "Figure 9": os.path.join(base_dir, "v4.0.0", "results_20230307", "v4.0.0_plot.yaml"),
+    "Figure S10": os.path.join(base_dir, "v3.0.1", "results_20220421", "v3.0.1_plot.yaml"),
+    "Figure S11": os.path.join(base_dir, "v3.2.0", "results_20220421", "v3.2.0_plot.yaml")
+    }
+
+for yaml in fig2yaml.values():
+    # Load PEtab problem
+    petab_problem = petab.Problem.from_yaml(yaml)
+    doc = petab.sbml.get_model_for_condition(petab_problem, "wt")[0]
+    doc.setLevelAndVersion(3, 1)
+    model = doc.getModel()
+    for s in model.getListOfSpecies():
+        s.setHasOnlySubstanceUnits(True)
+    fn = os.path.splitext(yaml)[0].rstrip("plot") + "optimized.sbml"
+    writeSBMLToFile(doc, fn)