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Overview table: link to respective publication #149

Merged
merged 3 commits into from
Feb 7, 2022
Merged

Overview table: link to respective publication #149

merged 3 commits into from
Feb 7, 2022

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dweindl
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@dweindl dweindl commented Feb 7, 2022

Add reference links to table based on SBML annotations.

NOTE: Not all current models are properly annotated.

@dweindl
Overview table: link to respective publication
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Add reference links to table based on SBML annotations.

NOTE: Not all current models are properly annotated.
@dweindl dweindl requested a review from dilpath February 7, 2022 10:59
dilpath
dilpath approved these changes Feb 7, 2022
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👍

Small preference for e.g. get_reference_uris() and markdown_columns["reference_uris"], but fine as is

Benchmark-Models/model_info.py Outdated Show resolved Hide resolved
@dweindl dweindl merged commit f423b0d into master Feb 7, 2022
@dweindl dweindl deleted the table_ref branch February 7, 2022 11:25
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 @dilpath