Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fujita_SciSignal2010 test data #131

Merged
merged 3 commits into from
Oct 22, 2021
Merged

Fujita_SciSignal2010 test data #131

merged 3 commits into from
Oct 22, 2021

Conversation

dilpath
Copy link
Collaborator

@dilpath dilpath commented Sep 30, 2021

Previously only the "step" data was included (for training).

Added a piecewise to the model equivalent to

if time <= EGF_end:
    EGF = EGF_rate*[time] + EGF_0
else:
    EGF = 0

This is to model the step, pulse, and ramp inputs (see conditions file).

elbaraim
elbaraim approved these changes Oct 22, 2021
View reviewed changes
Copy link
Collaborator

@elbaraim elbaraim left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

👍🏼

@dilpath dilpath merged commit cae9254 into master Oct 22, 2021
@dilpath dilpath deleted the fujita_test_data branch October 22, 2021 14:16
dweindl added a commit to AMICI-dev/AMICI that referenced this pull request Oct 25, 2021
@dweindl
Update expected llh for Fujita_SciSignal2010
4da0133 
Expected llh changed due to incresead precision of measurements in Benchmarking-Initiative/Benchmark-Models-PEtab#131
@dweindl dweindl mentioned this pull request Oct 25, 2021
Merged
dweindl added a commit to AMICI-dev/AMICI that referenced this pull request Oct 25, 2021
@dweindl
Update expected llh for Fujita_SciSignal2010 (#1577)
46d18a6 
Expected llh changed due to incresead precision of measurements in Benchmarking-Initiative/Benchmark-Models-PEtab#131
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]>
@dilpath dilpath mentioned this pull request Jun 17, 2022
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@elbaraim elbaraim elbaraim approved these changes

Assignees

@dilpath dilpath

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@dilpath @elbaraim