merge master into Froehlich_CS2018 (#160)

* Added Model bachmann msb2011 (#85)

* Added Bachmann model

Co-authored-by: LoosC <[email protected]>

* Fixed implementation of ActD, CISoe and SOCS3oe

* Fixed wrong headers

Co-authored-by: LoosC <[email protected]>

* Add model names to avoid recompilation. (#90)

* Model zhao quant biol2020 (#95)

Co-authored-by: IvaEwert <[email protected]>

* added model Giordano_Nature2020 (#97)

* added model Giordano_Nature2020

* added simulatedData

* new model bertozzi close #99

* fixed yaml file

* Changed python version (#104)

* added Okuonghae_ChaosSolitonsFractals2020 model (#103)

Co-authored-by: LeonardSchmiester <[email protected]>

* fix parameter scale in Chen - close #21 (#107)

* fix parameter scale in Chen

* fix lin parameters

Co-authored-by: Dilan Pathirana <[email protected]>

* Model lucarelli cell systems2018 (#109)

* Added Lucarelli model

Co-authored-by: LoosC <[email protected]>

* Updated simulated data sheet

* Changed column header

Co-authored-by: LoosC <[email protected]>

* Model Raimundez PCB 2020 - close #55 (#111)

* model Raimundez_PCB2020 added

* add measurement and simulation files

* add measurement and simulation files

* add simulation files

* adapt naming convention

* Model isensee jcb2018 (#112)

* Added Isensee model. Closes #54 

Co-authored-by: JanHasenauer <[email protected]>

* Fixed issues with timepoint specific overrides

* Fixed meas file

Co-authored-by: JanHasenauer <[email protected]>

* Update observables_Fiedler_BMC2016.tsv

correction

* Update measurementData_Fiedler_BMC2016.tsv

correction

* Update parameters_Fiedler_BMC2016.tsv

correction

* Fixed link to PEtab (#116)

* Update measurementData_Fiedler_BMC2016.tsv (#115)

Co-authored-by: LeonardSchmiester <[email protected]>

* simplify observables

* fixup

* fix parameter table

* fix loss of precision in Boehm data

* Rename Bruno_JExpBio to Bruno_JExpBot (#119)

* Run checks on GHA instead of TravisCI (#123)

Closes #105

* Oliveira_NatCommun2021 model (#120)

* Add script to generate problem overview (#122)

Prints some stats for each benchmark problem. Hopefully helpful to select interesting models.

* Model Laske_PLOSComputBiol2019 (Issue #83) (#127)

* Fix Alkan_SciSignal2018 (#129)

* remove extraneous semicolons
* remove null measurements
* update simulated data file
* deduplicate conditions

* Update README stats, refactor stats script (#130)

* add Laske to README
* refactor stats script
* update Alkan in README

* Update parameters_Weber_BMC2015.tsv

* Fix Bachmann_MSB2011 (#136)

* reduce condition table and fix data annotation

* add prior, fixes #135

* remove uninformative priors

* fixup

* Fix Isensee_JCB2018 (#138)

* simplify formulation

* add parameter priors, fixes #137

* fixup conditions

* remove uninformative priors

* reexport conditions/measurements from d2d

* fixup

* fix model

* fixup

* fix empty rows

* remove index from measurement table

* update simulated data

* add priors, fixes #139 (#141)

* Fix lucarelli (#140)

* simplify model/conditions

* fix observables

* remove unused parameter from model

* remove unused columns

* Update simulatedData_Lucarelli_CellSystems2018.tsv

* Simplify Beer, fixes #114 (#134)

* move exp info from model to condition table

* fixup

* fix model

* fix model

* fix model

* fix model

* fix model

* fix model

* Fix priors for Schwen, Bachmann (#143)

* increase accuracy of priors

* fix column names

* Add test data to Fujita_SciSignal2010 (#131)

* New input function to model different experiments involving ramps, pulses and steps.

* Fix Isensee prior (#144)

* fix column name and increase mean accuracy

* remove nan measurements from Blasi

* Overview table: link to respective directory (#148)

* Overview table: link to respective publication (#149)

Add reference links to table based on SBML annotations.

NOTE: Not all current models are properly annotated.


Co-authored-by: Dilan Pathirana <[email protected]>

* Check SBML metadata, refactor and move scripts (#152)

* add CI check for required sbml metadata
* refactor scripts
* moved scripts to separate dir `scripts/`
* small changes to model info script
* add python pip requirements file
* Fix model IDs, names, and missing references (#153)
    * fix model ids, model names, and references (closes #147 , closes #150 )
    * update overview table

* PR template for new PEtab problems (#154)

* Okuonghae_ChaosSolitonsFractals2020: convert fixed initial assignments to parameter values (#151)

* Add Blasi model selection problem for motif-specific parameters (#157)

* Fix blasi select measurements (#158)

Co-authored-by: LoosC <[email protected]>
Co-authored-by: dilpath <[email protected]>
Co-authored-by: IvaEwert <[email protected]>
Co-authored-by: PaulJonasJost <[email protected]>
Co-authored-by: vanako <[email protected]>
Co-authored-by: Elba Raimúndez Alvarez <[email protected]>
Co-authored-by: JanHasenauer <[email protected]>
Co-authored-by: Jan Hasenauer <[email protected]>
Co-authored-by: Fabian Fröhlich <[email protected]>
Co-authored-by: Daniel Weindl <[email protected]>
Co-authored-by: lorenapohl <[email protected]>
Co-authored-by: C-Peiter <[email protected]>

.github/PULL_REQUEST_TEMPLATE/new_petab_problem.md

@@ -0,0 +1,14 @@
+# Checklist
+- [ ] Information about the model is in the SBML metadata
+    - [ ] Reference to the original publication, and any other relevant references
+    - [ ] A brief model description (one or two sentences)
+    - [ ] A brief description of the data (one or two sentences)
+    - [ ] Any differences between the implementation and the original publication
+- [ ] Information is in the model's GitHub issue
+    - [ ] Any differences between the implementation and the original publication
+    - [ ] Experience of fitting / uncertainty analysis (e.g. optimizer used, hyperparameters, reproducibility of best fit)
+    - [ ] Source of nominal parameters (e.g.: taken from the original publication, or from your own fitting)
+- [ ] PEtab files
+    - [ ] A "simulated data" measurement table is included, using the nominal parameters
+    - [ ] A visualization table is included, that can be used with the simulate data to reproduce figures from the original publication
+- [ ] I am assigned to the GitHub issue

.github/workflows/tests.yml

@@ -0,0 +1,38 @@
+name: Tests
+
+# trigger
+on: [push, workflow_dispatch]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.9]
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v2
+
+    - name: Prepare python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install --upgrade setuptools wheel
+        pip install -r scripts/requirements.txt
+
+    - name: Check with petablint
+      run: ./check_petablint.py
+      working-directory: scripts/
+
+    - name: Show overview
+      run: ./overview.py
+      working-directory: scripts/
+
+    - name: Check SBML metadata
+      run: ./check_sbml_metadata.py
+      working-directory: scripts/

.gitignore

@@ -1,3 +1,4 @@
 .~lock.*
 *.DS_store
 ~$*
+__pycache__

Benchmark-Models/Alkan_SciSignal2018/experimentalCondition_Alkan_SciSignal2018.tsv

@@ -1,91 +1,74 @@
-conditionId	Dox_level	Gem_level	SN38_level
-model1_data1	0	0	0
-model1_data2	0	0.0003	0
-model1_data3	0	0.002	0
-model1_data4	0	0.01	0
-model1_data5	0	0.04	0
-model1_data6	0	6e-05	0
-model1_data7	0	0	0
-model1_data8	0.0016	0	0
-model1_data9	0.008	0	0
-model1_data10	0.04	0	0
-model1_data11	0.2	0	0
-model1_data12	1	0	0
-model1_data13	0	0	0
-model1_data14	0	0	0.0003
-model1_data15	0	0	0.002
-model1_data16	0	0	0.01
-model1_data17	0	0	0.04
-model1_data18	0	0	6e-05
-model1_data19	0	0	0
-model1_data20	0.01	0	0
-model1_data21	0.05	0	0
-model1_data22	0.1	0	0
-model1_data23	0	0	0
-model1_data24	0	0	0.01
-model1_data25	0	0	0.05
-model1_data26	0	0	0.1
-model1_data27	0	0	0
-model1_data28	0	0.01	0
-model1_data29	0	0.05	0
-model1_data30	0	0.1	0
-model1_data31	0	0	0
-model1_data32	0.00078125	0	0
-model1_data33	0.0012346	0	0
-model1_data34	0.0015625	0	0
-model1_data35	0.003125	0	0
-model1_data36	0.0037037	0	0
-model1_data37	0.00625	0	0
-model1_data38	0.011111	0	0
-model1_data39	0.0125	0	0
-model1_data40	0.025	0	0
-model1_data41	0.033333	0	0
-model1_data42	0.05	0	0
-model1_data43	0.1	0	0
-model1_data44	0.3	0	0
-model1_data45	0	0	0
-model1_data46	0	0	0.00078125
-model1_data47	0	0	0.0012346
-model1_data48	0	0	0.0015625
-model1_data49	0	0	0.003125
-model1_data50	0	0	0.0037037
-model1_data51	0	0	0.00625
-model1_data52	0	0	0.011111
-model1_data53	0	0	0.0125
-model1_data54	0	0	0.025
-model1_data55	0	0	0.033333
-model1_data56	0	0	0.05
-model1_data57	0	0	0.1
-model1_data58	0	0	0.3
-model1_data59	0	0	0
-model1_data60	0	0.00078125	0
-model1_data61	0	0.0012346	0
-model1_data62	0	0.0015625	0
-model1_data63	0	0.003125	0
-model1_data64	0	0.0037037	0
-model1_data65	0	0.00625	0
-model1_data66	0	0.011111	0
-model1_data67	0	0.0125	0
-model1_data68	0	0.025	0
-model1_data69	0	0.033333	0
-model1_data70	0	0.05	0
-model1_data71	0	0.1	0
-model1_data72	0	0.3	0
-model1_data73	0	0.001	0
-model1_data74	0	0.004	0
-model1_data75	0	0.012	0
-model1_data76	0	0.037	0
-model1_data77	0	0.111	0
-model1_data78	0	0.333	0
-model1_data79	0.004	0	0
-model1_data80	0.012	0	0
-model1_data81	0.037	0	0
-model1_data82	0.111	0	0
-model1_data83	0.333	0	0
-model1_data84	1	0	0
-model1_data85	0	0	0.004
-model1_data86	0	0	0.012
-model1_data87	0	0	0.037
-model1_data88	0	0	0.111
-model1_data89	0	0	0.333
-model1_data90	0	0	1
+conditionId	Dox_level	Gem_level	SN38_level
+model1_data1	0.0	0.0	0.0
+model1_data2	0.0	0.0003	0.0
+model1_data3	0.0	0.002	0.0
+model1_data4	0.0	0.01	0.0
+model1_data5	0.0	0.04	0.0
+model1_data6	0.0	6e-05	0.0
+model1_data8	0.0016	0.0	0.0
+model1_data9	0.008	0.0	0.0
+model1_data10	0.04	0.0	0.0
+model1_data11	0.2	0.0	0.0
+model1_data12	1.0	0.0	0.0
+model1_data14	0.0	0.0	0.0003
+model1_data15	0.0	0.0	0.002
+model1_data16	0.0	0.0	0.01
+model1_data17	0.0	0.0	0.04
+model1_data18	0.0	0.0	6e-05
+model1_data20	0.01	0.0	0.0
+model1_data21	0.05	0.0	0.0
+model1_data22	0.1	0.0	0.0
+model1_data25	0.0	0.0	0.05
+model1_data26	0.0	0.0	0.1
+model1_data29	0.0	0.05	0.0
+model1_data30	0.0	0.1	0.0
+model1_data32	0.00078125	0.0	0.0
+model1_data33	0.0012346	0.0	0.0
+model1_data34	0.0015625	0.0	0.0
+model1_data35	0.003125	0.0	0.0
+model1_data36	0.0037037	0.0	0.0
+model1_data37	0.00625	0.0	0.0
+model1_data38	0.011111	0.0	0.0
+model1_data39	0.0125	0.0	0.0
+model1_data40	0.025	0.0	0.0
+model1_data41	0.033333	0.0	0.0
+model1_data44	0.3	0.0	0.0
+model1_data46	0.0	0.0	0.00078125
+model1_data47	0.0	0.0	0.0012346
+model1_data48	0.0	0.0	0.0015625
+model1_data49	0.0	0.0	0.003125
+model1_data50	0.0	0.0	0.0037037
+model1_data51	0.0	0.0	0.00625
+model1_data52	0.0	0.0	0.011111
+model1_data53	0.0	0.0	0.0125
+model1_data54	0.0	0.0	0.025
+model1_data55	0.0	0.0	0.033333
+model1_data58	0.0	0.0	0.3
+model1_data60	0.0	0.00078125	0.0
+model1_data61	0.0	0.0012346	0.0
+model1_data62	0.0	0.0015625	0.0
+model1_data63	0.0	0.003125	0.0
+model1_data64	0.0	0.0037037	0.0
+model1_data65	0.0	0.00625	0.0
+model1_data66	0.0	0.011111	0.0
+model1_data67	0.0	0.0125	0.0
+model1_data68	0.0	0.025	0.0
+model1_data69	0.0	0.033333	0.0
+model1_data72	0.0	0.3	0.0
+model1_data73	0.0	0.001	0.0
+model1_data74	0.0	0.004	0.0
+model1_data75	0.0	0.012	0.0
+model1_data76	0.0	0.037	0.0
+model1_data77	0.0	0.111	0.0
+model1_data78	0.0	0.333	0.0
+model1_data79	0.004	0.0	0.0
+model1_data80	0.012	0.0	0.0
+model1_data81	0.037	0.0	0.0
+model1_data82	0.111	0.0	0.0
+model1_data83	0.333	0.0	0.0
+model1_data85	0.0	0.0	0.004
+model1_data86	0.0	0.0	0.012
+model1_data87	0.0	0.0	0.037
+model1_data88	0.0	0.0	0.111
+model1_data89	0.0	0.0	0.333
+model1_data90	0.0	0.0	1.0