human 0.5.0

• Features (PR #42):
  • Upload curateMitochMembraneComp.m for curating reactions related to the inner mitochondrial membrane compartment [i]
    • 4 duplicated reactions related to the electron transport chain were removed
    • 2 unused reactions (r1330 and r1331) were constrained (ub=lb=0)
    • 15 electrogenic proton-transporting rxns were constrained by preventing protons from mitochondria to cytosol compartments
    • reaction LPAMtm was reversed in reaction direction
    • 58 electrogenic reactions involving proton transport between mitochondria and cytosol compartments were modified through replacing H+[c] with H+[i]
    • All modifications were saved to curateMitochMembraneComp_rxnChanges.tsv for tracking the changes
• Chore:
  • Update rxnAssoc.mat array structure by adding the 4 electron transport chain related reaction pairs

human 0.4.2

• Fixes (PR #39):
  • Upload miscModelCurationScript_20181012.m script
    • Restore reactions HMR_1572 and HMGCOAtx that were removed previously by script miscModelCurationScript_20180921.m
    • Remove five non-standard fields (e.g. rxnKEGGID) from humanGEM to comply with RAVEN model structure
• Style :
  • Organize subfolder for python scripts and clean up outdated scripts

human 0.4.1

• Features (PR #32):
  • Add function addCuratedComplexRulesToModel that incorporates new manually verified complex-subunit information derived from the CORUM database (curated_CORUM_grRules_20180924.txt) into 61 humanGEM grRules.
• Fixes (PR #35):
  • Upload miscModelCurationScript_20181005.m script that detects humanGEM v0.4.0 for additional duplicate reaction pairs among which the Recon3D versions are then removed
  • Update metFrom field by filling 49 blank entries derived from adding boundary metabolites to sink/DM reactions (PR #30)
• Chore:
  • Update rxnAssoc.mat array structure with 91 additional reaction associations

human 0.4.0

• Features (PR #30):
  • Upload protonBalance4Rxns.m function that can detect and rebalance the reactions that are solely caused by mismatch of protons
  • Upload balanceProtonsInRxns.m script for updating humanGEM.mat
    • Add 49 boundary metabolites to 253 demand and sink type reactions to comply with RAVEN format
    • A total of 1,419 proton-related reactions are rebalanced

human 0.3.1

• Features (PR #23):
  • Conduct extensive metabolite curations for providing curated formulas and charges with script updateMetChargesFormulas.m
  • Unify MetaNetX ids for humanGEM metabolites based on HMR2 and Recon3D association
  • Add function addMetCompsField.m
• Fixes (PR #24):
  • Miscellaneous curations in reactions, genes and related fields that are detailed in miscModelCurationScript_20180921.m
    • Update EC number to HMR_4365
    • 8 reaction grRules are modified
    • Reverse reaction direction for HMR_4964
    • reactions HMR_1572 and HMGCOAtx are removed
  • Add function removeReactionsFull.m
• Chore:
  • Update compartment-free array structure metAssocHMR2Recon3.mat with comprehensive external associations (e.g. KEGG, BiGG, HMDB, ChEBI)

human 0.3.0

• Fixes (PR #19):
  • Through screening exchange reaction originated from Recon3D, a total of 1198 boundary version metabolites were added to 1639 exchange reactions using addBoundaryMets.m, to comply with RAVEN model structure
  • Continue on checking duplicate reactions between HMR and Recon3D in humanGEM
    • There were 9 duplicate pairs detected among exchange reactions after adding above boundary version metabolites
    • A total of 976 additional duplicate pairs were identified by detecting reactions that are the reverse of one another (e.g. A+B -> C+D versus C+D -> A+B)
    • Re-structure rxnAssoc.mat array by adding reaction bounds information, and update the content by adding above newly detected duplicate pairs
  • Remove duplicate reactions from humanGEM based on the updated information in rxnAssoc.mat
  • Update GPR rules and associated fields in humanGEM by combining grRules information from iHsa and Recon3D
  • Curate metFrom and rxnFrom fields for correctly reflecting the sources of metabolites and reactions
• Features (PR #20):
  • Add increaseVersion function for managing new releases

human 0.2.0

• Features (PR #17):
  • Conduct systematic model integration of Recon3D into humanGEM
  • Curate two cell arrays (metAssoc and rxnAssoc) of comprehensive metabolite/reaction associations between Recon3D and humanGEM for model integration
  • Update grRules and relevant fields by integrating curated information from iHsa and Recon3D models
  • Provide proteins fields with Uniprot SwissProt IDs
  • Add prRules and rxnProtMat fields to enable protein-based simulation analysis

human 0.1.0

• Comprehensive rxn/met associations to external databases/GEMs
• Update gene curation results including: removal of pseudogenes, updated Ensemble IDs and other gene-related fields (grRules, rxnGeneMat, geneComps)
• Start to implement new model name humanGEM