Merge pull request #241 from SysBioChalmers/devel

yeast8.4.1
SysBioChalmers · Jul 20, 2020 · 66a7b97 · 66a7b97
2 parents 69ddb00 + a612772
commit 66a7b97
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -163,6 +163,7 @@ Every pull request must be approved by at least one reviewer before it can be me
 This section is meant for the administrator of this repo. The main duties of the administrator are:
 * To make sure conventions and standards in the model are kept.
 * To keep the repository clean and organized, i.e. avoid redundancy in functions and/or data, and keep coherency in naming of files.
+* To manage package dependencies and regularly update them.
 * To help in the reviewing process of external pull requests by assigning reviewers, [labels](https://github.com/SysBioChalmers/yeast-GEM/issues/labels) and [projects](https://github.com/SysBioChalmers/yeast-GEM/projects), if applicable.
 * To keep [issues](https://github.com/SysBioChalmers/yeast-GEM/issues) with the proper labels, and to close them once they are fixed in the `master` branch.
 * In cases of disagreement between contributors, to decide how to resolve the issue.
@@ -175,6 +176,21 @@ The following points should be considered when merging branches to `devel`:
 * Wait at least a day before merging, to allow other developers to inspect the pull request.
 * As soon as the branch is merged, check if `devel` is still possible to merge to `master` (this can be checked [here](https://github.com/SysBioChalmers/yeast-GEM/compare/devel)). If conflicts appear (which should rarely happen and only if the `.xml` file was changed in an unexpected way by a toolbox update), fix the conflict _locally_ as soon as possible in `devel` and then push it (note, **DO NOT** pull any other changes from `master` to `devel`, just the single file that is creating the conflict).
 
+### Managing python dependencies
+
+We use [pip-tools](https://github.com/jazzband/pip-tools) for managing dependencies:
+
+* If a new dependency is needed for users/developers:
+  1. Add the dependency to `/requirements/requirements.in` or `/requirements/dev-requirements.in`, respectively (note that by default any requirement in `requirements.in` will also be in `dev-requirements.in`).
+  2. From `/requirements`, run `pip-compile requirements.in` and/or `pip-compile dev-requirements.in` as needed.
+
+* If dependencies need to be upgraded, from `/requirements` run:
+  ```
+  pip-compile --upgrade requirements.in
+  pip-compile --upgrade dev-requirements.in
+  ```
+  Dependencies should be upgraded regularly, but always first tested in separate branches.
+
 ### Releasing a new version
 
 * A merge of `devel` with `master` invokes a new release.
@@ -196,19 +212,19 @@ yeast-GEM follows [semantic versioning](https://semver.org/), adapted to GEMs:
 
 When releasing, please follow these steps:
   1. Make sure all dependencies in `devel` correspond to the setup from the local computer from which the release will be made. If not, make a single commit in `devel` updating this with a `loadYeastModel`/`saveYeastModel` cycle.
-  2. Create a pull request from `devel` to `master`, indicating all new features/fixes/etc. and referencing every previous pull request included (examples [here](https://github.com/SysBioChalmers/yeast-GEM/releases)). Tip: if any [issue](https://github.com/SysBioChalmers/yeast-GEM/issues) gets solved in the release, write in the pull request description "Fixes #X", where "X" is the issue number. That way the issue will be automatically closed after merge.
+  2. Create a pull request from `devel` to `master`, indicating all new features/fixes/etc. and referencing every previous pull request included (examples [here](https://github.com/SysBioChalmers/yeast-GEM/releases)). Tip: if any [issue](https://github.com/SysBioChalmers/yeast-GEM/issues) gets solved in the release, write in the pull request description "Closes #X", where "X" is the issue number. That way the issue will be automatically closed after merge.
   3. Merge at least a day after (having at least one accepted review).
-  4. Switch locally to `master` and update `history.md`, by putting at the top the same description of the corresponding PR from step 2.
+  4. Switch locally to `master`, pull changes and update `history.md`, by putting at the top the same description of the corresponding PR from step 2.
   5. Bump version with `increaseVersion.m`. **NOTE:** The function will error if unexpected changes are occurring. If this happens, probably step 1 was done incorrectly. To fix it, commit in `devel` any necessary changes and make a new pull request.
-  6. Commit changes from steps 4 and 5 with the message `chore: version X.Y.Z`.
+  6. Commit changes from steps 4 and 5 with the message `chore: version X.Y.Z`, and push to the remote.
   7. Make the new release at GitHub [here](https://github.com/SysBioChalmers/yeast-GEM/releases/new), using the proper tag "vX.Y.Z" and with the same description as the corresponding PR from step 2.
-  8. Pull from `master` to `gh-pages` to update the landing page.
+  8. Merge locally `master` into `gh-pages` and push to update the landing page.
   9. Review the [Zenodo](https://zenodo.org) release: Every new release from Github (step 7) automatically triggers a new release in Zenodo. However, so far it is not possible to fully customize this release, and some manual curation is needed. This includes:
       * Ensuring the title of the release has the format `SysBioChalmers/yeast-GEM: yeast X.Y.Z`.
-      * Correcting author names.
+      * Correcting author names to include all commit authors and PR reviewers that contributed to the release.
       * Ensuring the version of the release has the format `vX.Y.Z`.
       * Setting the language to English.
-      * Adding any Grant IDs (if applicable).
+      * Adding any grant IDs (if applicable).
 
      Make sure to both save & publish your edits. You will find the new release at the top of [all Zenodo releases](https://zenodo.org/search?page=1&size=20&q=conceptrecid:%221494182%22&sort=-publication_date&all_versions=True). Note that it might take some minutes for the Zenodo release to appear after you create the release in Github.
 

diff --git a/ComplementaryData/modelCuration/GapfillingnewRxnProp.tsv b/ComplementaryData/modelCuration/GapfillingnewRxnProp.tsv
@@ -1,29 +1,29 @@
-rxnID	rev	GPR	standard_name	EC	rxnID_kegg	rxnID_MNX	Source;reason
-MNXR94845	1		3-(4-hydroxyphenyl)pyruvate transport			MNXR94845	seed:rxn09802; unknown transporter
-MNXR95431	1		acetate transport			MNXR95431	rhea:27814; unknown transporter
-MNXR95481	1		ADP-ribose transport			MNXR95481	bigg:ADPRIBt; unknown transporter
-MNXR99646	1		farnesyl diphosphate transport			MNXR99646	seed:rxn13290; unknown transporter
-MNXR101858	1		nicotinate transport			MNXR101858	seed:rxn12806; unknown transporter
-MNXR135002	1		O-phosphoethanolamine transport			MNXR135002	seed:rxn05716; unknown transporter
-MNXR102871	1		phosphate transport			MNXR102871	rhea:32823; bigg:PItg; unknown transporter
-MNXR106312	0		propionyl-CoA transport			MNXR106312	bigg:r2499; unknown transporter
-MNXR105076	1		UDP transport			MNXR105076	bigg:UDPtg; unknown transporter
-MNXR105076_2	1		UDP transport			MNXR105076	bigg:UDPtg; unknown transporter
-MNXR105127	1		UMP transport			MNXR105127	rhea:27926; unknown transporter
-MNXR104921	1		TRX1 disulphide transport			MNXR104921	seed:rxn13406; unknown transporter
-MNXR99110	1		oleate transport			MNXR99110	rhea:33655; unknown transporter
-MNXR95426	1		(R)-acetoin transport			MNXR95426	bigg:ACTNt2r; unknown transporter
-MNXR100259	1		L-glutamine transport			MNXR100259	seed:rxn08625; bigg:GLNtm; unknown transporter
-MNXR105127_2	1		UMP transport			MNXR105127	rhea:27926; unknown transporter
-MNXR95809	1		S-adenosyl-L-methionine transport			MNXR95809	seed:rxn09784; bigg:AMETtn; unknown transporter
-MNXR100449	1		glutathione transport			MNXR100449	seed:rxn08677; unknown transporter
-MNXR96123	1		ATP transport	2.7.4.6		MNXR96123	rhea:34999; unknown transporter
-MNXR101385	1		D-mannose 6-phosphate transport			MNXR101385	seed:rxn08880; unknown transporter
-MNXR95416	1		O-acetyl-L-serine transport			MNXR95416	rhea:29659; bigg:ACSERtmi; unknown transporter
-MNXR100494	1		hydrogen sulfide transport			MNXR100494	seed:rxn08689; unknown transporter
-MNXR97002	1		L-cysteinylglycine transport			MNXR97002	seed:rxn05529; unknown transporter
-MNXR96123_2	1		ATP transport	2.7.4.6		MNXR96123	rhea:34999; unknown transporter
-MNXR104966	1		thiosulfate transport			MNXR104966	rhea:32807; unknown transporter
-MNXR104460	1		sulphite transport			MNXR104460	seed:rxn09260; unknown transporter
-MNXR105071	1		UDP-D-glucose transport			MNXR105071	seed:rxn09353; unknown transporter
-MNXR105021	1		UDP-N-acetyl-alpha-D-glucosamine transport			MNXR105021	seed:rxn09342; unknown transporter
+rxnID	rev	GPR	standard_name	EC	rxnID_kegg	rxnID_MNX	bigg	Source;reason
+MNXR94845	1		3-(4-hydroxyphenyl)pyruvate transport			MNXR94845		seed:rxn09802; unknown transporter
+MNXR95431	1		acetate transport			MNXR95431		rhea:27814; unknown transporter
+MNXR95481	1		ADP-ribose transport			MNXR95481	ADPRIBt	unknown transporter
+MNXR99646	1		farnesyl diphosphate transport			MNXR99646		seed:rxn13290; unknown transporter
+MNXR101858	1		nicotinate transport			MNXR101858		seed:rxn12806; unknown transporter
+MNXR135002	1		O-phosphoethanolamine transport			MNXR135002		seed:rxn05716; unknown transporter
+MNXR102871	1		phosphate transport			MNXR102871	PItg	rhea:32823; unknown transporter
+MNXR106312	0		propionyl-CoA transport			MNXR106312	r2499	unknown transporter
+MNXR105076	1		UDP transport			MNXR105076	UDPtg	unknown transporter
+MNXR105076_2	1		UDP transport			MNXR105076	UDPtg	unknown transporter
+MNXR105127	1		UMP transport			MNXR105127		rhea:27926; unknown transporter
+MNXR104921	1		TRX1 disulphide transport			MNXR104921		seed:rxn13406; unknown transporter
+MNXR99110	1		oleate transport			MNXR99110		rhea:33655; unknown transporter
+MNXR95426	1		(R)-acetoin transport			MNXR95426	ACTNt2r	unknown transporter
+MNXR100259	1		L-glutamine transport			MNXR100259	GLNtm	seed:rxn08625; unknown transporter
+MNXR105127_2	1		UMP transport			MNXR105127		rhea:27926; unknown transporter
+MNXR95809	1		S-adenosyl-L-methionine transport			MNXR95809	AMETtn	seed:rxn09784;unknown transporter
+MNXR100449	1		glutathione transport			MNXR100449		seed:rxn08677; unknown transporter
+MNXR96123	1		ATP transport	2.7.4.6		MNXR96123		rhea:34999; unknown transporter
+MNXR101385	1		D-mannose 6-phosphate transport			MNXR101385		seed:rxn08880; unknown transporter
+MNXR95416	1		O-acetyl-L-serine transport			MNXR95416	ACSERtmi	rhea:29659;unknown transporter
+MNXR100494	1		hydrogen sulfide transport			MNXR100494		seed:rxn08689; unknown transporter
+MNXR97002	1		L-cysteinylglycine transport			MNXR97002		seed:rxn05529; unknown transporter
+MNXR96123_2	1		ATP transport	2.7.4.6		MNXR96123		rhea:34999; unknown transporter
+MNXR104966	1		thiosulfate transport			MNXR104966		rhea:32807; unknown transporter
+MNXR104460	1		sulphite transport			MNXR104460		seed:rxn09260; unknown transporter
+MNXR105071	1		UDP-D-glucose transport			MNXR105071		seed:rxn09353; unknown transporter
+MNXR105021	1		UDP-N-acetyl-alpha-D-glucosamine transport			MNXR105021		seed:rxn09342; unknown transporter
diff --git a/ComplementaryScripts/deprecated/modelCuration/addiSce926changes.m b/ComplementaryScripts/deprecated/modelCuration/addiSce926changes.m
@@ -4,8 +4,6 @@
 % iSce926 source: http://www.maranasgroup.com/submission_models/iSce926.htm
 %
 % NOTE: changeGeneAssociation.m is a function from cobra
-% 
-% Hongzhong Lu & Benjamín Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %Load model:

diff --git a/ComplementaryScripts/deprecated/modelCuration/fixBiomassComp.m b/ComplementaryScripts/deprecated/modelCuration/fixBiomassComp.m
@@ -10,8 +10,6 @@
 %    growth rates (Van Hoek et al. 1988)
 %
 % Function adapted from SLIMEr: https://github.com/SysBioChalmers/SLIMEr
-%
-% Benjamin Sanchez. Last update: 2018-09-07
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function fixBiomassComp

diff --git a/ComplementaryScripts/deprecated/modelCuration/makeFormulasCompliant.m b/ComplementaryScripts/deprecated/modelCuration/makeFormulasCompliant.m
@@ -1,8 +1,6 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % makeFormulasCompliant.m
 % Corrects SBML-incompatible metabolite formulas.
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %aa codes:

diff --git a/ComplementaryScripts/deprecated/modelCuration/modelCorrections.m b/ComplementaryScripts/deprecated/modelCuration/modelCorrections.m
@@ -1,8 +1,6 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % modelCorrections.m
 % Corrects various issues in yeast7
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %Correct glucan coefficients in biomass reaction

diff --git a/ComplementaryScripts/deprecated/modelCuration/takeOutFromFormula.m b/ComplementaryScripts/deprecated/modelCuration/takeOutFromFormula.m
@@ -1,8 +1,6 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % formula = takeOutFromFormula(formula,elements)
 % Takes away from formula each of the elements specified.
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function formula = takeOutFromFormula(formula,elements)

diff --git a/ComplementaryScripts/deprecated/modelCuration/updateMetaboliteFormula.m b/ComplementaryScripts/deprecated/modelCuration/updateMetaboliteFormula.m
@@ -2,9 +2,6 @@
 % model = updateMetaboliteFormula(model)
 %
 % Reads the data file and updates the metabolite formula information in the model
-%
-% William T. Scott, Jr.
-% Last Update: 2018-08-23
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % Load model

diff --git a/ComplementaryScripts/deprecated/otherChanges/addSLIMErxns.m b/ComplementaryScripts/deprecated/otherChanges/addSLIMErxns.m
@@ -1,7 +1,5 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % addSLIMErxns
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %Start COBRA & load model:

diff --git a/ComplementaryScripts/deprecated/otherChanges/clusterBiomass.m b/ComplementaryScripts/deprecated/otherChanges/clusterBiomass.m
@@ -1,7 +1,5 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % model = clusterBiomass(model)
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function model = clusterBiomass(model)

diff --git a/ComplementaryScripts/deprecated/otherChanges/convertYmn2FBC2.m b/ComplementaryScripts/deprecated/otherChanges/convertYmn2FBC2.m
@@ -9,8 +9,6 @@
 % We also had to remove "-" characters from gene names to "_", since
 % otherwise gene-reaction association information is lost for several
 % reactions in FBC v2 file.
-%
-% Simonas Marcišauskas
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % Firstly loading an old COBRA version, i.e. the latest commit before

diff --git a/ComplementaryScripts/increaseVersion.m b/ComplementaryScripts/increaseVersion.m
@@ -12,8 +12,6 @@ function increaseVersion(bumpType)
 %
 %   Usage: increaseVersion(bumpType)
 %
-%   Benjamin Sanchez, 2018-09-25
-%
 
 %Check if in master:
 currentBranch = git('rev-parse --abbrev-ref HEAD');

diff --git a/ComplementaryScripts/loadYeastModel.m b/ComplementaryScripts/loadYeastModel.m
@@ -1,8 +1,6 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % model = loadYeastModel
 % Loads model and adds the rxnGeneMatrix to the structure
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function model = loadYeastModel

diff --git a/ComplementaryScripts/missingFields/GetMNXID.m b/ComplementaryScripts/missingFields/GetMNXID.m
@@ -13,8 +13,6 @@
 %
 %   Usage: model = GetMNXID(model,type,level)
 %
-%   Feiran Li, 2018-09-18
-%
 
 if nargin<3
     level = 1;

diff --git a/ComplementaryScripts/missingFields/addBiGGidentifiers.m b/ComplementaryScripts/missingFields/addBiGGidentifiers.m
@@ -3,9 +3,6 @@
 %   Loads the model, adds all BiGG identifiers for both metabolites and
 %   reactions, and saves the model back.
 %
-%   Sebastian N. Mendoza, 2019-03-15
-%   Benjamin J. Sanchez, 2020-05-05
-%
 
 % Load model:
 cd ..

diff --git a/ComplementaryScripts/missingFields/addConfidenceScores.m b/ComplementaryScripts/missingFields/addConfidenceScores.m
@@ -6,8 +6,6 @@
 % Reactions without gene but need for modelling: 1
 % Reactions without gene: 0
 % Exchange reactions: NaN
-%
-% Hongzhong Lu & Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function model = addConfidenceScores(model)

diff --git a/ComplementaryScripts/missingFields/addGeneNames.m b/ComplementaryScripts/missingFields/addGeneNames.m
@@ -1,7 +1,5 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % model = addGeneNames(model)
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function model = addGeneNames(model)

diff --git a/ComplementaryScripts/missingFields/addSBOterms.m b/ComplementaryScripts/missingFields/addSBOterms.m
@@ -1,7 +1,5 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % model = addSBOterms(model)
-%
-% Benjamin J. Sanchez. Last update: 2018-11-26
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function model = addSBOterms(model)

diff --git a/ComplementaryScripts/missingFields/changeRules.m b/ComplementaryScripts/missingFields/changeRules.m
@@ -1,7 +1,5 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % model = changeRules(model)
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function model = changeRules(model)

diff --git a/ComplementaryScripts/missingFields/deleteRepeated.m b/ComplementaryScripts/missingFields/deleteRepeated.m
@@ -4,8 +4,6 @@
 % only non repeated elements, and also the list of the positions deleted.
 %
 % NOTE: Must be a string or cell array
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function [list,deleted] = deleteRepeated(list)

diff --git a/ComplementaryScripts/missingFields/findInDB.m b/ComplementaryScripts/missingFields/findInDB.m
@@ -1,8 +1,6 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % [uni,EC] = findInDB(rxn_pos,model,DB)
 % Matches the uniprot and EC number for a given rxn into a given database.
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function [uni,EC] = findInDB(rxn_pos,model,DB)

diff --git a/ComplementaryScripts/missingFields/findSubSystem.m b/ComplementaryScripts/missingFields/findSubSystem.m
@@ -1,7 +1,5 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % subSystem = findSubSystem(uniprot,kegg)
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function subSystem = findSubSystem(uniprot,kegg)

diff --git a/ComplementaryScripts/missingFields/getAllPath.m b/ComplementaryScripts/missingFields/getAllPath.m
@@ -11,8 +11,6 @@
 % OUTPUTS:
 % FinalGenesets     All gene sets with only "ANDs" (cell array)
 % FinalReactions    New reaction IDs (cell array)
-%
-% Cheng Zhang
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function [FinalGenesets, FinalReactions] = getAllPath(model,reaction)

diff --git a/ComplementaryScripts/missingFields/getMissingFields.m b/ComplementaryScripts/missingFields/getMissingFields.m
@@ -1,7 +1,5 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % model = getMissingFields(model)
-%
-% Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function model = getMissingFields(model)

diff --git a/ComplementaryScripts/missingFields/mapIDsViaMNXref.m b/ComplementaryScripts/missingFields/mapIDsViaMNXref.m
@@ -18,8 +18,6 @@
 %
 %   Usage: targetList=mapIDsViaMNXref(type,queryList,fromDB,toDB)
 %
-%   Hao Wang, 2018-05-23
-%
 
 targetList={};
 

diff --git a/ComplementaryScripts/modelCuration/CheckBalanceforSce.m b/ComplementaryScripts/modelCuration/CheckBalanceforSce.m
@@ -2,8 +2,6 @@
 % the input is model and new reaction ID lists
 % output is a result with pass or error
 % NOTE: getElementalBalance.m is a function from raven
-%
-% Feiran Li
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function [MassChargeresults] = CheckBalanceforSce(model,rxn,MassChargeresults)

diff --git a/ComplementaryScripts/modelCuration/CheckEnergyProduction.m b/ComplementaryScripts/modelCuration/CheckEnergyProduction.m
@@ -2,8 +2,6 @@
 % ATP and NADH production
 % the input is model and new reaction ID lists
 % output is a result with pass or error
-%
-% Feiran Li
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function [energyResults,redoxResults] = CheckEnergyProduction(model,rxn,energyResults,redoxResults)
@@ -21,9 +19,9 @@
                              mets,coefs,false,0,1000);
     model_test = changeObjective(model_test,'GenerateATP', 1);
     sol = optimizeCbModel(model_test);
-    if sol.obj <= 360 && sol.obj > 0 %later can be changed to the experimental value
+    if sol.f <= 360 && sol.f > 0 %later can be changed to the experimental value
         energyResults = [energyResults; model.rxns(rxnID),'pass',num2str(sol.obj)];
-    elseif sol.obj > 360
+    elseif sol.f > 360
         energyResults = [energyResults; model.rxns(rxnID),'Fail',num2str(sol.obj)];
     else
         energyResults = [energyResults; model.rxns(rxnID),'error','error'];
@@ -39,7 +37,7 @@
                              mets,coefs,false,0,1000);
     model_test = changeObjective(model_test, model_test.rxns(end), 1);
     sol = optimizeCbModel(model_test);
-    if sol.obj <= 120 && sol.obj > 0 %later can be changed to the experimental value
+    if sol.f <= 120 && sol.f > 0 %later can be changed to the experimental value
         redoxResults = [redoxResults; model.rxns(rxnID),'pass',num2str(sol.obj)];
     elseif sol.obj > 120
         redoxResults = [redoxResults; model.rxns(rxnID),'Fail',num2str(sol.obj)];

diff --git a/ComplementaryScripts/modelCuration/MissingTransDeadEnd.m b/ComplementaryScripts/modelCuration/MissingTransDeadEnd.m
@@ -6,8 +6,6 @@
 %         DEM_reason is a combined list with possible reasons for all
 %         deadend mets.
 %         output format for canbesolved: deadentMetsName MNXID deadendMetsInanotherComps Possible solution
-% Feiran Li 2019-02-01
-% Feiran Li 2019-07-22 update some field name in case of casuing confusion
 
 model_org = model;
 changeCobraSolver('gurobi', 'LP');

diff --git a/ComplementaryScripts/modelCuration/SubstrateUsage.m b/ComplementaryScripts/modelCuration/SubstrateUsage.m
@@ -6,8 +6,6 @@
 % it can be used as a "solo" substrate.
 %
 % NOTE: requires COBRA
-% 
-% Feiran Li     2018-08-25
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % Load model:

diff --git a/ComplementaryScripts/modelCuration/UpdateDBnewRxn.m b/ComplementaryScripts/modelCuration/UpdateDBnewRxn.m
@@ -7,8 +7,6 @@
 %       Before run the codes below, the file should be manually editted.
 %       COBRA required.
 %       New reaction should be in .tsv format.
-%
-% Feiran Li & Hongzhong Lu
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % Load model

diff --git a/ComplementaryScripts/modelCuration/addBiologRxnToGEM.m b/ComplementaryScripts/modelCuration/addBiologRxnToGEM.m
@@ -6,8 +6,6 @@
 %        Biolog_newRxnMet.tsv.
 %
 % NOTE: changeGeneAssociation.m is a function from COBRA
-%
-% Feiran Li     2018-08-25
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % Load model:
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,8 +18,6 @@ @@
     %
     %   Usage: targetList=mapIDsViaMNXref(type,queryList,fromDB,toDB)
     %
-    %   Hao Wang, 2018-05-23
-    %
     targetList={};
@@ Expand Down @@