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I have before visualised reactions on VMH Recon Map (with the help of Cobra toolbox tutorial). I would now also like to color metabolites, but I found no appropriate tutorial.
I have tried to use metabolite names/ids in different available columns (see below), but could not make it work (it worked only with KEGG, but mapping from Bigg to KEGG is not ideal).
Can you let me know how I can color metabolites by bigg id, (e.g. cit or cit_m for citrate).

This are the fields I belie are available for coloring, I tried the bold ones, but did not work. I got the fields list from error report on VMH Recon Map.
name, gene_name, model_name, value, compartment, type, color, identifier, elementIdentifier, reactionIdentifier, lineWidth, description, reverseReaction, brenda, taxonomy, kegg reaction, chembl, gene ontology, mirbase sequence database, pubmed, digital object identifier, hgnc symbol, panther family, kegg orthology, drugbank, mirbase mature sequence database, wikipedia (english), reactome, biomodels database, consensus cds, toxicogenomic chemical, mouse genome database, vmh reaction, mirtarbase mature sequence database, refseq, bigg reaction, interpro, protein family database, cazy, drugbank target v4, chembl target, chemical abstracts service, clinicaltrials.gov, uniprot, chebi, hgnc, string, bigg metabolite, tair locus, kegg pathway, unknown, entrez gene, bigg compartment, ensembl, wormbase, protein data bank, enzyme nomenclature, chemspider, online mendelian inheritance in man, uniprot isoform, pubchem-substance, mesh, stitch, unigene, rhea, saccharomyces genome database, pubchem-compound, pharmgkb pathways, kegg compound, wikipathways, hmdb, vmh metabolite, kegg genes, clusters of orthologous groups, ensembl plants, wikidata, ontology for biomedical investigations,

Hi, I have followed the steps as per the tutorial to create iMAT reconstruction of the ecoli_core_model.mat. The output is very different from what is provided in the documentation.

I have rechecked with the latest version of the toolbox. I am consistently getting different output with different solvers too. I have attached the output what I am getting.

Do have a look at this. Do run the tutorial once again. There were some changes made to the iMAT after the last update of this tutorial. The final optimal solution after solving the MILP is different from the output in the tutorial.

The output I got here.

Thanks.

Dear all,
I want to find some interventions applied to a strain by using optforce.The model I used is iJO1366 of E.coli,and the objective is trptophan.It is successful.But when I change the objective to lysine,it shows some errors when I run '[mustLSet, pos_mustL] = findMustL(model, minFluxesW, maxFluxesW, 'constrOpt', constrOpt, 'runID', runID, 'outputFolder', 'OutputsFindMustL', 'outputFileName', 'MustL' , 'printExcel', 1, 'printText', 1, 'printReport', 1, 'keepInputs', 1, 'printLevel', 3)'.

The error is:

Operands to the || and && operators must be convertible to logical scalar values.

Error in changeObjective (line 39)
if (isempty(rxnID) || rxnID == 0)

Error in findMustL (line 297)
model2 = changeObjective(model, model.rxns(pos_actives));
I wonder what cause it?
Thanks!

I've been trying to run the tutorial_mgPipe.m, but after the pan-models are created, I get the following error:

Error using addMultipleReactions (line 162)
Subscripted assignment dimension mismatch.

Error in addMicrobeCommunityBiomass (line 42)
dummy = addMultipleReactions(dummy,rxns,mets,S,'lb',lb,'ub',ub);

Error in createPersonalizedModel (line 73)

I believe all of my cobratoolbox files are up to date. Is there something I might be missing?

Sincerely,

Matt

Hi
there is not any readCbMap function in may cobra toolbox. Is there any problem in installation or any alternative command?
Samira

Hi!

I tried to run the tutorial_atomicallyResolveReconstruction.mlx tutorial on MATLAB online and I got the following error:

Error using readtable (line 498)
Unable to open file '/MATLAB Drive/COBRA/fork-cobratoolbox/tutorials/analysis/atomicallyResolveReconstruction/metaboliteIds.xlsx as a workbook. Check that file exists, read access is available, and the file is a valid spreadsheet file. 

Error in addMetInfoInCBmodel (line 31)
   dbData = readtable(inputData);

Then I cheched for the file COBRA.tutorials/analysis/atomicallyResolveReconstruction/metaboliteIds.xlsx and I realised that is an empty one.

Should that be this way?

Apologies if I missed something on the way.

Regards,
Haris

Hi,

I have been running the DEMETER pipeline using the tutorial provided in cobratoolbox. However, I recently encountered this error when running line 9 of the tutorial.

[infoFilePath,inputDataFolder] = prepareInputData(infoFilePath,'spreadsheetFolder',spreadsheetFolder);

Unable to perform an assignment with 0 elements on the right-hand side.

Error in prepareInputData (line 137)
                infoFile{i,gramCol}=agoraInfoFile{taxRow,agoraGramCol};

I think some changes have been made in the core code of prepareInputData that now give this error.

I'm using Matlab 2020a and ibm_cplex as solver.

It seems as if the Latest commit
9bc1b6b
on 2 Apr was incompletely merged, or something to that effect...

contribute('opencobra/COBRA.tutorials')

   ~~~ COBRA.tutorials ~~~


  (You can abort any process using CTRL+C)

  [1] Start a new branch.
  [2] Select an existing branch to work on.
  [3] Publish a branch.
  [4] Delete a branch.
  [5] Update the fork.

-> Please select what you want to do (enter the number): 1
-> Please enter a name of the new branch that you want to work on (example: add-constraints): courseLeiden19
dev> Your Github username is: rmtfleming. (Success)
dev> Your Github email is: [email protected]. (Success)
dev> -> Please define the location of your fork
current: /Users/rfleming/work/sbgCloud/code/MATLAB.devTools
Enter the path(press ENTER to use the current path): /Users/rfleming/work/sbgCloud/code/
dev> Your fork directory has been set to: /Users/rfleming/work/sbgCloud/code/fork-COBRA.tutorials. (Success)
dev> [cloneFork] Cloning the fork https://github.com/rmtfleming/COBRA.tutorials.git (might take some time)
dev> -- Configuration --------
dev> GitHub username: rmtfleming
dev> GitHub email: [email protected]
dev> Local directory : /Users/rfleming/work/sbgCloud/code/fork-COBRA.tutorials
dev> Remote fork URL: https://github.com/rmtfleming/COBRA.tutorials.git
dev> Remote repository URL: https://github.com/opencobra/COBRA.tutorials.git
From github.com:rmtfleming/COBRA.tutorials

• branch develop -> FETCH_HEAD
  error: Terminal is dumb, but EDITOR unset
  Not committing merge; use 'git commit' to complete the merge.
  [resetDevTools] The development tools have been reset (soft reset).
  Error using updateFork (line 120)
  dev> [updateFork] Impossible to pull changes from the branch of the
  fork. (Error)
  Error in checkoutBranch (line 55)
  updateFork(true);
  Error in initContribution (line 69)
  checkoutBranch(branchName);
  Error in contribute (line 156)
  initContribution(strtrim(reply));

At the system command line:

mp0015:fork-COBRA.tutorials rfleming$ git status
On branch develop
All conflicts fixed but you are still merging.
(use "git commit" to conclude merge)

Changes to be committed:

modified:   analysis/browseNetwork/tutorial_browseNetwork.m
modified:   analysis/browseNetwork/tutorial_browseNetwork.mlx
modified:   reconstruction/ecoliCoreModel/part1/tutorial_ecoliCoreModel_part1.m
modified:   reconstruction/ecoliCoreModel/part1/tutorial_ecoliCoreModel_part1.mlx
modified:   reconstruction/ecoliCoreModel/part2/tutorial_ecoliCoreModel_part2.m
modified:   reconstruction/ecoliCoreModel/part2/tutorial_ecoliCoreModel_part2.mlx

Seemed to be fixed using:
mp0015:fork-COBRA.tutorials rfleming$ git commit -am 'changes in cloned repo'
[develop a94ec81] changes in cloned repo
mp0015:fork-COBRA.tutorials rfleming$ git status
On branch develop
nothing to commit, working tree clean

Good morning,
I am trying to work with the latest upload of the cobratoolbox (downloaded from gitbash using: git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox), and, when executing the initCobraToolbox line in Matlab R2019b, the following message appears:

initCobraToolbox

  _____   _____   _____   _____     _____     |
 /  ___| /  _  \ |  _  \ |  _  \   / ___ \    |   COnstraint-Based Reconstruction and Analysis
 | |     | | | | | |_| | | |_| |  | |___| |   |   The COBRA Toolbox - 2021
 | |     | | | | |  _  { |  _  /  |  ___  |   |
 | |___  | |_| | | |_| | | | \ \  | |   | |   |   Documentation:
 \_____| \_____/ |_____/ |_|  \_\ |_|   |_|   |   http://opencobra.github.io/cobratoolbox
                                              | 

Checking if git is installed ... Done (version: 2.33.1).
Checking if the repository is tracked using git ... Done.
Checking if curl is installed ... Done.
Checking if remote can be reached ... Done.
Initializing and updating submodules (this may take a while)...Entering 'binary'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/analysis/CnaCobraInterface'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/analysis/GeoCalcLib'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/analysis/PolytopeSamplerMatlab'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/analysis/Volume-and-Sampling'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/analysis/gaimc'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/analysis/octave-networks-toolbox'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/base/samplers/looplessFluxSampler'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/base/solvers/lusol'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/base/solvers/pdco'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/base/utilities/Smith-Decomposition'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'external/base/utilities/condalab'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'papers'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'test/models'
Your branch is up to date with 'origin/master'.
Already on 'master'
Entering 'tutorials'
error: invalid path 'dataIntegration/metaboAnnotator/data/ctf-main\mets\molFiles/10zhepta.mol'
error: invalid path 'dataIntegration/metaboAnnotator/data/ctf-main\mets\molFiles/_apine.mol'
error: invalid path 'dataIntegration/metaboAnnotator/data/ctf-main\mets\molFiles/dopa.mol'
fatal: run_command returned non-zero status for tutorials
.
Error using initCobraToolbox (line 233)
The submodules could not be initialized.

I have been looking into it, and I suspect it could be the latest upload done into tutorials/dataIntegration/metaboAnnotator/data is not properly defined, because when I enter in the github, the folder named: "ctf-main\mets\molFiles" is the one that is giving me problems.

edit: formatting

Hi all, when I run the optforce, I meet the followed error. Could you help me find the reason?
The code and error is as followed:

constrOpt = struct('rxnList', {{'r_1714', 'r_2111', 'new5'}}, 'values', [-1.634, 0, 1.9]');
[mustLSet, pos_mustL] = findMustL(model1, minFluxesW, maxFluxesW, 'constrOpt', constrOpt, ...
'runID', runID, 'outputFolder', 'OutputsFindMustL', ...
'outputFileName', 'MustL' , 'printExcel', 1, 'printText', 1, ...
'printReport', 1, 'keepInputs', 1, 'verbose', 0);
No constructor 'org.apache.poi.xssf.usermodel.XSSFWorkbook' with matching signature found.

Error in xlwrite (line 150)
xlsWorkbook = XSSFWorkbook();

Error in findMustL (line 333)
xlwrite([outputFileName '_Info'], Info);