Human 1.0.0-beta

• Fixes (PR #83):
  • Add script get_ensembl_ID_mapping.py for extracting the most recent information from the Ensembl database and removal of the IDs from non-primary genome assembly
    • Upload ensembl_ID_mapping.tsv with the latest information Ensembl ver: 95 Assembly ver: GRCh38.p12
  • Upload removeNonPrimaryGeneIDs.m script for updating the newly extracted information to humanGEM:
    • 292 Ensemble gene IDs from non-primary genome assembly are removed
    • Update the other gene/protein-related fields: grRules,rxnGeneMat, proteins, prRules, rxnProtMat

human 0.8.3

• Fixes (PR #84):
  • Incorporate manually curated gene-association modifications that are detailed in grRulesCuration_20190206.tsv:
    • 38 reactions have modified gene associations
    • 30 genes are removed
    • 6 new enzyme complexes are incorporated
  • Add function updateGrRules for conducting routine grRules adjustment

human 0.8.2

• Fixes (PR #81):
  • Upload script curateMetFormula4PAPS.m for curating the molecular formulas of the PAPS (m02682) according to #58, this modification affected mass balance status of 100 reactions that include:
    • 28 reactions become fully balanced
    • 63 reactions have improved status and further balanced by function protonBalance4Rxns
    • 9 reactions cannot be balanced and are documented for further checking
    • 2 additional reactions HMR_8824 and HMR_8825 are accidentally balanced by protonBalance4Rxns, even though they have nothing to do with PAPS
    • a total of 93 reactions are fully balanced through this step, and all modifications are saved to curateFormulas4PAPS_rxnChanges.tsv for tracking the changes
  • Add function getNonEmptyList

human 0.8.1

• Features (PR #79):
  • Upload function prettyJson for adding proper indentations and line breaks to raw JSON string
  • Upload applyJSON2RxnAssoc.m script for managing .mat files in subfolder "RxnAssociation”, as discussed in #75
    • ihumanRxns2BiGG.mat and Recon3Rxns2MNX.mat are removed due to repetition
    • ihumanRxns2MNX.mat and Recon3Rxns2HMR.mat are replaced with corresponding JSON format files that have the same content
  • Refine function reformatElements and add function countEmpty to assist cell array manipulation

human 0.8.0

• Fixes/Features (PR #76):
  • Upload curateBiomassReactions.m script for curating biomass reactions
    • 4 biomass reactions are refined by renaming rxn ids, updating subSystems and replacing biomass[x] with biomass[c]
    • biomass_components is kept as functioning biomass reaction while the rest are inactivated as discussed in #63
    • 26 reactions are added and listed in rxns4biomass_20181129.tsv
      • biomass_HepG2 and 7 relevant pool or associated reactions are added
      • 8 transport and 8 exchange reactions are added to enable the export of 8 fatty acid pool metabolites and flux carrying of biomass_components reaction
      • 2 biomass transport and exchange reactions are added
    • subSystems field is converted to nested cell array (#50)
• Style :
  • Remove python subfolder from the repo

human 0.7.0

• Fixes (PR #72):
  • Upload curateExchangeRxns.m script for curating exchange reactions, sink and demand reactions as discussed in #28
    • 7 duplicate pairs are modified by removing redundancy and the curation process is recorded into a plaintext file redundantRxns.JSON, as discussed in #43 and #27
    • 254 sink sink_ and demand DM_ reactions are inactivated (ub=lb=0)
    • 457 irreversible exchange reactions are opened by setting upper and lower bounds to +/-1000, respectively
    • All modifications are saved to curateExchangeRxns_rxnChanges.tsv for tracking the changes

human 0.6.1

• Features/Fixes (PR #69):

  • Upload file metabolicTasks_LeakCheck.xls with a list of numbered metabolic tasks for evaluating the performance of fixing mass/energy leaks in the model
  • Refine script repairModelLeaks.m by referencing specific metabolic task ID number(s) to the corresponding section that supposed to address the issue, as well as including the reaction constraining section. Note that only overall implementation of the changes in this script can achieve those targeted metabolic tasks
    • 41 reactions are modified by adjusting reaction bounds and/or stoichiometry
    • 236 reactions (including 12 that were modified in bounds/stoichiometry adjustment) are constrained in order to achieve the metabolic tasks. These inactivate reactions are archived in inactivationRxns.tsv
    • All modifications are saved to repairModelLeaks_rxnChanges.tsv for tracking the changes
  • feat: Add function loadHumanGEM.m for loading a simulation-ready humanGEM model

• Features (PR #66):

  • Add function getCompNetwork.m for generating metabolic network for a specified compartment
  • Add function getSubNetworksInComp.m that can check graph connectivity for a specified compartment network and output the sub-networks in defined JSON format for map generation purpose
  • Upload a curated list of currency metabolites as currencyMets.tsv

human 0.6.0

• Features/Fixes (PR #62):
  • Upload identifyMassVariableRxns function for identifying mass imbalanced reaction sets, which are archived in variable_mass_rxns_to_constrain.tsv
  • Upload constrainReactions.m script to prepare a defined list of reactions for constraining/removal, as detailed in inactivationRxns.tsv that includes:
    • 162 reactions (from variable_mass_rxns_to_constrain.tsv) involve an identical set of metabolites except for one metabolite pair that lead to imbalanced mass
    • 74 reactions that allow the creation of mass and/or energy, which results in a "leaky" model
  • Upload repairModelLeaks.m script also for fixing reactions leading to mass/energy leaks, by adjusting reaction bounds/direction and changing stoichiometric coefficients and/or metabolites
• Features (PR #59):
  • Adjust README to adapt to renaming the repository from HMR3-GEM to human-GEM

human 0.5.2

• Features/Fixes (PR #56):
  • Upload curateModelSubsystems.m script to update the humanGEM subSystems names, which were manually curated and discussed in #50.
    • Based on similar naming or functions, subSystems names are combined or renamed as detailed in subsystem_name_curated.tsv
    • A total of 7,158 subSystems names in humanGEM are updated

human 0.5.1

• Fixes:
  • Upload fixFormulasWithFULLR.m script (PR #52)
    • A total of 604 humanGEM metabolite formulas, which were found with either strange characters (e.g. "LLLL", "U") #49 or reordered elements that were caused by function alphabetizeMetFormulas.m, are corrected.
    • Three files (Recon3Mets2MNX.mat, metAssocHMR2Recon3.mat, and humanGEM.mat) are updated with correct formulas.
    • The modified formulas in humanGEM are stored in fixFormulasWithFULLR.tsv for tracking the changes.
  • Upload updateGrRulesAndGenes_20181018.m script (PR #51)
    • Correct grRules for HMR_9579 (removing quotes character (")) and HMR_6921 (removing wrongly associated genes ENSG00000198764 and ENSG00000198765).
    • Update the genes and rxnGeneMat fields with the latest grRules field.
    • The proteins, rxnProtMat, and prRules fields are also be updated.