Check SBML metadata, refactor and move scripts #152
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dweindl
approved these changes
Feb 10, 2022
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| if model_id != petab_problem_id: | ||
| errors.append( | ||
| 'Please change the model ID to match the problem ID.' | ||
| ) |
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This may become a problem once there are problems involving multiple models. Maybe then .startswith()? But okay for now, I think.
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Agreed, but there were some current model(s) that had long IDs prefixed by the problem ID... in the absence of a convention, we could wait until someone shares such a problem with multiple models, and get their opinion.
LeonardSchmiester
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Jun 3, 2022
* 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]>
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Please ignore the missing or incorrect metadata in the test -- this is fixed in #153 . The PRs are mostly separated into changes to scripts and changes to PEtab files.