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new format for Chen #21

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elbaraim opened this issue Nov 21, 2018 · 33 comments · Fixed by #107
Closed

new format for Chen #21

elbaraim opened this issue Nov 21, 2018 · 33 comments · Fixed by #107
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@elbaraim elbaraim self-assigned this Nov 21, 2018
@LoosC LoosC reopened this Nov 22, 2018
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LoosC commented Nov 22, 2018

simulatedData sheet not filled

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dweindl commented Dec 5, 2018 

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_CD274mRNA' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_IL13_cell' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_RecSurf' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_SOCS3' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_SOCS3mRNA' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_pIL4Ra' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_pJAK2' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'sigma_pSTAT5' should have a constant value of 'false'.

@dweindl dweindl reopened this Dec 5, 2018
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elbaraim commented Dec 5, 2018

this is not the correct model
Chen model does not have these species

@elbaraim elbaraim closed this as completed Dec 5, 2018
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dweindl commented Dec 5, 2018

Sorry, Raia_CancerResearch2011

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Corrected in Raia

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dweindl commented Dec 5, 2018

Those were supposed to go here:

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'c515' should have a constant value of 'false'.

libSBML Error (SBML component consistency): Any <compartment>, <species>, <parameter>, or (in Level 3) <speciesReference> whose identifier is the value of a 'variable' attribute in an <assignmentRule>, must have a value of 'false' for 'constant'.
Reference: L2V4 Section 4.11.3
 The parameter with id 'c285' should have a constant value of 'false'.

SBML Document failed to load (see error messages above)

@dweindl dweindl reopened this Dec 5, 2018
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dweindl commented Dec 6, 2018 

libSBML Error (MathML consistency): Outside of a <functionDefinition>, if a <ci> element is not the first element within a MathML <apply>, then the <ci>'s value can only be chosen from the set of identifiers of (in L2V1) <species>, <compartment>, or <parameter> objects; (in L2V2-L2V5), <species>, <compartment>, <parameter> or <reaction> objects; (in L3V1) <species>, <compartment>, <parameter>, <reaction> or <speciesReference> objects and (in L3V2) <species>, <compartment>, <parameter>, <reaction>, <speciesReference> objects or L3 package objects with defined mathematical meaning. 
Reference: L2V4 Section 3.4.3
 The formula 'Step0' in the math element of the <kineticLaw> uses 'Step0' that is not the id of a species/compartment/parameter/reaction.

libSBML Error (MathML consistency): Outside of a <functionDefinition>, if a <ci> element is not the first element within a MathML <apply>, then the <ci>'s value can only be chosen from the set of identifiers of (in L2V1) <species>, <compartment>, or <parameter> objects; (in L2V2-L2V5), <species>, <compartment>, <parameter> or <reaction> objects; (in L3V1) <species>, <compartment>, <parameter>, <reaction> or <speciesReference> objects and (in L3V2) <species>, <compartment>, <parameter>, <reaction>, <speciesReference> objects or L3 package objects with defined mathematical meaning. 
Reference: L2V4 Section 3.4.3
 The formula 'Step0' in the math element of the <kineticLaw> uses 'Step0' that is not the id of a species/compartment/parameter/reaction.

libSBML Error (MathML consistency): Outside of a <functionDefinition>, if a <ci> element is not the first element within a MathML <apply>, then the <ci>'s value can only be chosen from the set of identifiers of (in L2V1) <species>, <compartment>, or <parameter> objects; (in L2V2-L2V5), <species>, <compartment>, <parameter> or <reaction> objects; (in L3V1) <species>, <compartment>, <parameter>, <reaction> or <speciesReference> objects and (in L3V2) <species>, <compartment>, <parameter>, <reaction>, <speciesReference> objects or L3 package objects with defined mathematical meaning. 
Reference: L2V4 Section 3.4.3
 The formula 'Step0' in the math element of the <kineticLaw> uses 'Step0' that is not the id of a species/compartment/parameter/reaction.

@dweindl dweindl reopened this Dec 6, 2018
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dweindl commented Mar 11, 2019

Model parameter 'Step0' neither present in condition table nor in parameter table.

@dweindl dweindl reopened this Mar 11, 2019
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it is defined as a constant set to 0
<parameter id="Step0" value="0" constant="true"/> line 719

@elbaraim
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none of the steps are defined in the experimental data nor condition file

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dweindl commented Mar 19, 2019

Okay, will check what's wrong there with the validator

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dweindl commented Mar 19, 2019

Yeah, was an error there.

@dweindl dweindl closed this as completed Mar 19, 2019
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working now on the visualization specification file

@erikadudki erikadudki reopened this Aug 20, 2019
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@elbaraim : could you check the simulation values
in the simulation.tsv the simulation data is in the range of [0,4], in the measurement.tsv, the data is in the range of [0,90]...

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@elbaraim : could you check: in the measurement file for simulation conditions model1_data3 and model1_data4, the data seems to be the same? should not be the case, for different conditions?

@elbaraim
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I will look into this, thanks for posting!

@LeonardSchmiester
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Need to update data!

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@elbaraim ! 😡

@LeonardSchmiester LeonardSchmiester transferred this issue from LeonardSchmiester/Benchmark-Models Feb 26, 2020
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@elbaraim Any updates here?

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Did you have a chance to look into this @elbaraim ? Should be just exchanging the data and simulating to see if the results fit, right?

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dweindl commented Mar 16, 2020

ping @elbaraim

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Apparently there is a bug in the visualization file, @erikadudki could you have a look?

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fixed it 👍

@elbaraim
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reopened: see #106

@elbaraim elbaraim reopened this Jan 26, 2021
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When looking at the issue #106

I also found that in the original Benchmark collection some parameters "got lost" during the initial SBML export. Therefore, also missing in the PEtab implementation.

These are: KD_iressa_mt, KD_iressa_wt, k98, k99 and k100.

This is weird, since these parameters appear in the d2d model file, e.g., KD_iressa_wt (already checked for the others).

I will keep on looking and post an update ASAP.

@elbaraim elbaraim mentioned this issue Jan 27, 2021
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Additionally these parameters from the original paper
k10, Kinh2, Kinh3, Kinh4, Ks, k13, k14, k22b, k28b, k16b, k34b, k3, KD_ATP, KD, k121, kd_v853
do not appear in the current implementation.

However I checked all of them and they do not have any role in the original model (publication). They only appear in the list of parameters.

So I think it is fine that they do not appear,
any contrary thoughts on this? @LeonardSchmiester

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Additionally these parameters from the original paper
k10, Kinh2, Kinh3, Kinh4, Ks, k13, k14, k22b, k28b, k16b, k34b, k3, KD_ATP, KD, k121, kd_v853
do not appear in the current implementation.

However I checked all of them and they do not have any role in the original model (publication). They only appear in the list of parameters.

So I think it is fine that they do not appear,
any contrary thoughts on this? @LeonardSchmiester

So they are defined as parameters in the original SBML model but don't occur in any reactions etc.?! If they are not used in any context I guess it should be fine to not have them in the model

@elbaraim
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Additionally these parameters from the original paper
k10, Kinh2, Kinh3, Kinh4, Ks, k13, k14, k22b, k28b, k16b, k34b, k3, KD_ATP, KD, k121, kd_v853
do not appear in the current implementation.
However I checked all of them and they do not have any role in the original model (publication). They only appear in the list of parameters.
So I think it is fine that they do not appear,
any contrary thoughts on this? @LeonardSchmiester

So they are defined as parameters in the original SBML model but don't occur in any reactions etc.?! If they are not used in any context I guess it should be fine to not have them in the model

Exactly. They only appear in the list of parameters.

@LeonardSchmiester
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When looking at the issue #106

I also found that in the original Benchmark collection some parameters "got lost" during the initial SBML export. Therefore, also missing in the PEtab implementation.

These are: KD_iressa_mt, KD_iressa_wt, k98, k99 and k100.

This is weird, since these parameters appear in the d2d model file, e.g., KD_iressa_wt (already checked for the others).

I will keep on looking and post an update ASAP.

Where these parameters also in the original model from the publication? Could it be, that they are somehow replaced with other expressions in D2D?

@elbaraim
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When looking at the issue #106
I also found that in the original Benchmark collection some parameters "got lost" during the initial SBML export. Therefore, also missing in the PEtab implementation.
These are: KD_iressa_mt, KD_iressa_wt, k98, k99 and k100.
This is weird, since these parameters appear in the d2d model file, e.g., KD_iressa_wt (already checked for the others).
I will keep on looking and post an update ASAP.

Where these parameters also in the original model from the publication? Could it be, that they are somehow replaced with other expressions in D2D?

These parameters indeed appear in the original model from the publication. Regarding the replacement thing, this is what I am trying to check atm :)

@elbaraim
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When looking at the issue #106
I also found that in the original Benchmark collection some parameters "got lost" during the initial SBML export. Therefore, also missing in the PEtab implementation.
These are: KD_iressa_mt, KD_iressa_wt, k98, k99 and k100.
This is weird, since these parameters appear in the d2d model file, e.g., KD_iressa_wt (already checked for the others).
I will keep on looking and post an update ASAP.

Where these parameters also in the original model from the publication? Could it be, that they are somehow replaced with other expressions in D2D?

These parameters indeed appear in the original model from the publication. Regarding the replacement thing, this is what I am trying to check atm :)

So I have checked the model compilation and these parameters are removed in the symbolic expressions, then I guess the replacement that you mentioned is taking place (as I said, they appear in the model definition file). Seems fine then.

I will continue then with the issue regarding the parameter scales. Do you agree @LeonardSchmiester ?

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I will continue then with the issue regarding the parameter scales. Do you agree @LeonardSchmiester ?

Yes, sounds good.

@FFroehlich
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Whats the status here?

@elbaraim elbaraim mentioned this issue Feb 5, 2021
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elbaraim added a commit that referenced this issue Mar 3, 2021
@elbaraim @dilpath
fix parameter scale in Chen - close #21 (#107)
ba91cdc 
* fix parameter scale in Chen

* fix lin parameters

Co-authored-by: Dilan Pathirana <[email protected]>
LeonardSchmiester added a commit that referenced this issue 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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fix parameter scale in Chen - close #21 Benchmarking-Initiative/Benchmark-Models-PEtab
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@elbaraim @FFroehlich @LoosC @dweindl @LeonardSchmiester @erikadudki