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Bug: Fix compatibility running ecFSEOF with GECKO3 models #301

Merged
merged 13 commits into from
May 11, 2023
Merged

Bug: Fix compatibility running ecFSEOF with GECKO3 models #301

merged 13 commits into from
May 11, 2023

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ae-tafur
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@ae-tafur ae-tafur commented Apr 5, 2023

Main improvements in this PR:

  • Fix compatibility in ecFSEOF to GECKO3 models
  • Change name function simulateGrowth to follow chore: consistent names and terminology #229
  • Model adapter class was added to use userData/model/output as default folder to store results

I hereby confirm that I have:

  • Selected develop as a target branch (top left drop-down menu)

@ae-tafur ae-tafur added the bug label Apr 5, 2023
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github-actions bot commented Apr 5, 2023 •
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This PR has been automatically tested with GH Actions. Here is the output of the tests:

 
Running geckoCoreFunctionTests
Model-specific DLKcat input stored at /home/m/actions-runner/_work/GECKO/GECKO/test/unit_tests/ecTestGEM/data/DLKcat_input_test.tsv
Limit has been reached. Protein P5 seems to be problematic. Consider changing the kcat.
Done geckoCoreFunctionTests
__________

Note: In the case of multiple test runs, this post will be edited.

@edkerk edkerk merged commit 189e7fa into develop May 11, 2023
@edkerk edkerk deleted the fix/ecFSEOF branch May 11, 2023 23:32
@edkerk edkerk linked an issue May 12, 2023 that may be closed by this pull request
bug: refactor ecFSEOF for GECKO3 model format #300
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edkerk added a commit that referenced this pull request Jul 3, 2023
@edkerk @ae-tafur @mihai-sysbio
GECKO 3.1.0 (#333)
9148132 
* fix: getStandardKcat with multiple subSystems

* Bug: Fix compatibility running ecFSEOF with GECKO3 models (#301)

* reverse: simulateGrowth for ecFSEOF

* fix: consistency in terminology

* refactor: fluxes for a target

* refactor: compatibility to GECKO3 ecFlux_scanning

* refactor: add compatibility to GECKO3

* fix: typo

* fix: save file type file

* fix: filter tolerance

* fix: if not carbon uptake have been defined

* fix: add toleracne to protein pool

* refactor: spaces instead of tabs

* fix: function input description

* Update src/geckomat/utilities/ecFSEOF/run_ecFSEOF.m

---------

Co-authored-by: edkerk <[email protected]>

* feat: user defined proteins to ignore in tunning kcats (#306)

* fix: applyCustomKcats with customKcats structure input (#304)

* fix: applyCustomKcats should allow struct as input

* fix: applyCustomKcats correct parse default param

* fix: applyCustomKcats

* applyCustomKcats doc and tests

* refactor: reduce command window output testss

* Apply suggestions from code review

Co-authored-by: Albert Tafur Rangel <[email protected]>

---------

Co-authored-by: Albert Tafur Rangel <[email protected]>

* doc: updateProtPool and flexibilizeProtConcs (#297)

* fix: updateProtPool avoid correctinf for f twice

* doc: flexibilizeProtConcs explain overconstraining

* fix: loadProtData measuredProt if NaN exist

* doc: protocol.m describe updateProtPool input

* fix: updateProtPool simplified new pool calculation

* chore: update protocol for updateProtPool

---------

Co-authored-by: Mihail Anton <[email protected]>

* feat: a function that creates a the project structure an adapter class (#312)

* feat: create structure project

* feat: include empty .keep files

---------

Co-authored-by: edkerk <[email protected]>

* feat: currencyMets and pseudoreactions handling (#313)

* fix: writeDLKcatInput currencyMets handling

* fix: filter out pseudoreactions makeEcModel

* fix: makeEcModel find pseudoreactions

* chore: restructure tutorials (#310)

* chore: rename userData to tutorials

* chore: move protocol and adapters

* chore: keep original in full under blankExample

* chore: compact adapters for human and yeast

* chore: cleanup protocol for yeast

* feat: add a model adapter under blankExample

* chore: rename adapter

* feat: copy protocol from yeast to human

* fix: typo

* fix: new folder names in adapters

* fix: update paths to tutorials

* refactor: model adapter expects full adapter path and extension

* fix: file paths for yeast-GEM tutorial

* style: protocol in tutorial prints step

* chore: rm doc

* feat: compress outputs about downloading complexes

* fix: full path to adapter in test

* fix: full paths for adapters in tests

* fix: undo bad path change

* chore: remove blankExample, use startGECKOproject

* chore: restore yeast-GEM protocol.m content

* chore: run through yeast-GEM protocol

* feat: simplify ModelAdapterManager commands

* fix: allow to set empty default adapter

* fix: tests refer to test adapter

---------

Co-authored-by: edkerk <[email protected]>

* feat: add manually-generated doc for online use

* feat: updateGECKOdoc function

* chore: update documentation

by running updateGECKOdoc()

* fix: getStandardKcat and applyKcatConstraints (#320)

* fix: getStandardKcat light model standard enzyme

In light ecModels, even if standard enzyme is not a pseudo-substrate (it will always use prot_pool instesad), standard enzyme should still be in ecModel.ec.enzyme (and .rxnEnzMat etc.), to calculate MW/kcat.

* refactor: applyKcatConstraints simplify light

* refactor: getStandardKcat

* fix: applyKcatConstraints zero-kcats light ecModel

* feat: copyECtoGEM function

* fix: minor bugs identified (#316)

* fix: use logical vector to construct equations

* fix: increase default tolerance

* style: typo

* style: use standard input names

* fix: adaptar default method name

* fix: set values under solver tol to zero

* feat: run_ecFSEOF check alphaLims parameter

---------

Co-authored-by: Eduard Kerkhoven <[email protected]>

* feat: updates related to tutorials (#319)

* feat: new/updated functions around enzyme usage

* feat: install and adapter manager

* feat: Crabtree plot and data

* feat: updated protocol and model file

* refactor: rename tutorials full_ and light_ecModel

* feat: loadConventionalGEM can load YAML

* feat: use progressbar to give time estimates

* fix: ecFVA correct number of simulations

* feat: sensitivityTuning reports eccodes

* feat: fillProtConcs select column from protData

* feat: flexibilizeProtConcs sort by highest ratio

* feat: plotCrabtree plus graphs

* feat: plot light vs full ecModel analysis

* feat: GECKOInstaller checks RAVEN version

* feat: update of full_ecModel protocol

moved progressbar to RAVEN 2.8.2

* fix: getStandardKcat light model standard enzyme

In light ecModels, even if standard enzyme is not a pseudo-substrate (it will always use prot_pool instesad), standard enzyme should still be in ecModel.ec.enzyme (and .rxnEnzMat etc.), to calculate MW/kcat.

* refactor: applyKcatConstraints simplify light

* refactor: getStandardKcat

* feat: light_ecModel tutorial overhaul

* fix: plot light vs full

* fix: applyKcatConstraints zero-kcats light ecModel

* feat: copyECtoGEM function

* chore: updateDocumentation

* fix: full_ecModel/protocol.m step 13

* full_ecModel misc small fixes

* fix: full_ecModel/protocol.m step 15

* fix: full_ecModel/protocol.m install instructions

* fix: findMetSmiles report success and handle prot_

* fix: full_ecModel customKcat non-funct. protein

* fix: plotCrabtree avoid flux minimalization

* fix: full_ecModel various minor changes

* fix: GECKOInstaller RAVEN dep version bump

* fix: full_ecModel and light_ecModel from review

* fix: remove unused functions

* feat: rerun light_ecModel pipeline

* refactor: change vanHoek1998.csv to .tsv

* fix: full_ecModel tutorial ecFVA (#321)

* fix: remake ecFVA plot with generic plot function

* fix: GECKOInstaller ignore doc subfolder

* chore: updateGECKOdoc

* fix: remove old ecFVA.tsv

no purpose to write this file

* refactor: speedup fuzzyKcatMatching & getECfromGEM

* feat: saveEcModel more logical input

* refactor: swap TIFF for PDF

* refactor: applyComplexData (#323)

* refactor: speed increase applyComplexData

* feat: applyComplexData progressbar + code comments

* feat: light_ecModel tutorial getSubsetEcModel (#322)

* fix: remake ecFVA plot with generic plot function

* fix: GECKOInstaller ignore doc subfolder

* chore: updateGECKOdoc

* fix: remove old ecFVA.tsv

no purpose to write this file

* fix: getStandardKcat no standard gene in light-ec

* fix: light_ecModel until step 29

* feat: getSubsetEcModel + tutorial

* feat: parameters format, phylDist.mat file and yeast-GEM.yml (#325)

* refactor: rename KEGG params to param.kegg.

to param.kegg.geneID

* refactor: rename Complex params to param.complex

* refactor: rename UniProt params to param.uniprot.

* fix: remove unused obj.params entries

remnants of GECKO2

* refactor: add _id to uniprot taxonomy

* refactor: use taxonomicID from complex portal

easier to find than precise species name

* feat: use RAVEN's phylDist.mat

from RAVEN 2.8.3 includes species names

* feat: tutorial yeast-GEM as yaml

* feat: yeast-GEM file is for tutorial only

* fix: remove unused manualModifications

* fix: small fixes

* docs: add link to tutorials in README

* docs: skip mentioning the required RAVEN version, since it is checked at installation

* feat: compare light vs full ecModel (#328)

* chore: rerun full_ecModel tutorial

* feat: light vs full ecModel comparison

* doc: swap step 29 and 30

* chore: rerun light_ecModel tutorial (#331)

* chore: rerun full_ecModel tutorial

* feat: light vs full ecModel comparison

* doc: swap step 29 and 30

* chore: rerun light_ecModel tutorial

* refactor: consistent use of isozyme

In agreement with manuscript

* chore: updateDocumentation

* doc: format of warning messages

* fix: plotlightVSfull.m handle use of alt solvers

* fix: consistent cutoff for low fluxes

---------

Co-authored-by: Albert Tafur Rangel <[email protected]>
Co-authored-by: Mihail Anton <[email protected]>
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@edkerk edkerk edkerk approved these changes

@IVANDOMENZAIN IVANDOMENZAIN Awaiting requested review from IVANDOMENZAIN

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bug: refactor ecFSEOF for GECKO3 model format
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