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Fix model IDs, names, and missing references #153

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merged 6 commits into from
Feb 21, 2022
Merged

Fix model IDs, names, and missing references #153

merged 6 commits into from
Feb 21, 2022

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dilpath
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@dilpath dilpath commented Feb 10, 2022

closes #147
closes #150

@dilpath dilpath mentioned this pull request Feb 10, 2022
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dweindl
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👍

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elbaraim commented Feb 15, 2022 •
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some models have some arFramework3 annotations from d2d that have been added in this PR, e.g. Okuonghae_ChaosSolitonsFractals2020, @dilpath do you know why?

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dilpath commented Feb 15, 2022

some models have some arFramework3 annotations from d2d that have been added in this PR, e.g. Okuonghae_ChaosSolitonsFractals2020, @dilpath do you know why?

Thanks, was copied from another model, now renamed to #benchmark_models_petab.

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@dilpath some models have metaid but for some was removed, could you check this to make it consistent?

some models have some arFramework3 annotations from d2d that have been added in this PR, e.g. Okuonghae_ChaosSolitonsFractals2020, @dilpath do you know why?

Thanks, was copied from another model, now renamed to #benchmark_models_petab.

Thanks! SalazarCavazos_MBoC2020 model still contains arFramework3 as annotation :)

Additionally, I found that some models contain metaid while some others not, and for example for Oliveira it was removed

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dilpath commented Feb 15, 2022

@dilpath some models have metaid but for some was removed, could you check this to make it consistent?

some models have some arFramework3 annotations from d2d that have been added in this PR, e.g. Okuonghae_ChaosSolitonsFractals2020, @dilpath do you know why?

Thanks, was copied from another model, now renamed to #benchmark_models_petab.

Thanks! SalazarCavazos_MBoC2020 model still contains arFramework3 as annotation :)

Additionally, I found that some models contain metaid while some others not, and for example for Oliveira it was removed

Now restored to the original metaid, with rdf:about set to its appropriate (the same) value. Also opened #155 to address this.

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👍🏼

@dilpath dilpath merged commit 8b80b02 into refactor_scripts Feb 21, 2022
@dilpath dilpath deleted the fix_ids_names_refs branch February 21, 2022 15:32
dilpath added a commit that referenced this pull request Feb 21, 2022
@dilpath
Check SBML metadata, refactor and move scripts (#152)
d7c52f9 
* 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
LeonardSchmiester added a commit that referenced this pull request Jun 3, 2022
@LeonardSchmiester @LoosC
@dilpath @iewert @PaulJonasJost @vanako @elbaraim @JanHasenauer @FFroehlich @dweindl @lorenapohl @C-Peiter
merge master into Froehlich_CS2018 (#160)
a6159de 
* 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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@dweindl dweindl dweindl approved these changes

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@dilpath @elbaraim @dweindl