Human 1.2.1

• Features (PR #144):
  • add function for removing InChI entries that are out of sync with metFormulas
• Fixes (PR #139):
  • adjust getINITModel2 to avoid removing metabolic task-associated metabolites
• Features (PR #138):
  • add new generic biomass reaction
    • add a new biomass reaction biomass_human that was formuated based on literature, databases, and previous modeling resources, and set as default for general use
    • 4 new pool rxns/pool mets (tRNAs, lipids, amino acids, cofactors and vitamins) associated to new biomass rxn are added
    • remove the cell-line specific biomass_HepG2 reaction
    • 7 pool rxns/pool mets associated to biomass_HepG2 are also removed
    • modified model changes are updated to the humanGEMRxn/MetAssoc.JSON and newHumanBiomassRxn_modelChanges_mets/rxns.tsv files

Human 1.2.0

• Features (PR #147):
  • Add annotation info back to model prior to exporting SBML
• Features (PR #131):
  • Major mass-rebalance of HumanGEM
    • 11 rxns are fixed for incorrect reversibility info (introduced by #113)
    • 4 met names are changed by replacing space with hyphen
    • 6 new mets are added
    • 21 new transport/exchange rxns are added through expanding 20 mets from existing comps to new ones
    • 465 unique mets are updated with new formula/charge
    • 729 rxn equations are updated
    • 203 duplicated rxns are removed
    • 196 rxns are blocked due to misuse of R group or pool mets
    • 10 previously inactivated reactions are reopened
    • 34 duplicated mets are merged
    • 27 unique mets are modified with updated external identifiers
    • 16 rxns are modified with updated external identifiers
    • 38 grRules are retrieved from their duplicated and removed counterparts
    • Modified annotation info and model changes are updated to the humanGEMRxn/MetAssoc.JSON and rebalance_modelChanges_mets/rxns.tsv files

Human 1.1.3

• Features (PR #142):
  • Promote community input by having Gitter chat room and Contribution guidelines
• Features (PR #141):
  • Update/reformat metabolic-task files from current and previous modeling work
• Fixes (PR #130):
  • Resolve stoichiometric inconsistencies caused by lipid pool reactions and metabolites
    • 16 new pool metabolites (4 unique) are added
    • 6 new pool reactions (fatty acid, 1-acylglycerol-3P, and acyl-CoA) with averagely weighted components are added
    • original imbalanced cholesterol-ester pool reactions (HMR_3537 and HMR_3622) are renamed to plasma type after replacing with new pool reactions
    • 2 transport reactions are added for fatty acid and acyl-CoA pool
    • 23 unique pool metabolites are replaced with corresponding new ones among 27 lipid pool reactions
    • 12 unique pool metabolites (a total of 23) become unused and removed
    • the old pool metabolites that are still in use are renamed to liver tissue type
    • 3 protein-associated fields (proteins, prRules, rxnProtMat) are removed

Human 1.1.2

• Features (PR #132):
  • New function importHumanYaml and modified writeHumanYaml for enabling lossless conversion between mat and yml model files
• Fixes (PR #125):
  • Systematically correct invalid BiGG rxn/met ids in humanGEMMetAssoc.JSON and humanGEMRxnAssoc.JSON, as detailed in #124

Human 1.1.1

• Features (PR #122):
  • New function annotateModel for adding reaction, metabolite, and/or gene annotation information
• Fixes (PR #123):
  • Add and modify metabolites for adjusting exchange reactions, as addressed in #117
• Style (PR #133):
  • Capitalize model filenames

Human 1.1.0

• Fixes/Features (PR #113):
  • Adjust electron transport chain reactions, to address issues #98, #99, #100, #101, #102
    • A number of changes are conducted to the electron transport chain reactions for refining ATP metabolism according to above issues, which are further formulated into metabolicTasks_VerifyModel.xls as new metabolic tasks that can be used for routine model evaluation
    • Duplicated reactions (HMR_7638 and Htmi) are resolved
    • The rxnRecon3DID field is removed from the model
    • All modifications are saved to curateATPmetabolism_rxnChanges.tsv for tracking changes
• Features (PR #116):
  • Associate mitochondrial amino acid importer, as discussed in issue #109
    • 2 newly identified transporters are added to HMR_5113 and HMR_5114
    • The corresponding reference and confidence scores are updated, together with the fields associated with gene and protein
• Features (PR #120):
  • Provide Human1 stoichiometric matrix with comprehensive external association and annotation, as detailed in issue #107
    • Add getHuman1RxnAssoc and getHuman1MetAssoc scripts for refining/retrieving previously prepared association/annotation to reactions and metabolites, respectively.
    • The curated external identifiers are now stored in HumanGEMRxnAssoc and HumanGEMMetAssoc, both are organized in JSON format (#75)
    • 7 identifiers from different databases or human GEMs were assigned to reactions, and 10 identifiers for metabolites

Human 1.0.3

• Style (PR #110, #111):
  • Update README and capitalize repo name
• Features (PR #108):
  • Incorporate functions, scripts, and other changes to facilitate model applications:
    • Update of the tINIT algorithm
    • Task-essential gene analysis
    • Visualization of results
    • Re-organization of repo functions

Human 1.0.2

• Fixes (PR #103):
  • Modify subSystem by script mergeGlutamateSubsystem , according to #87
• Features (PR #105):
  • Enhance automatic update of readme file while releasing model
  • Adjust exportHumanGEM to allow switching off dependencies.txt generation

Human 1.0.1

• Features/Fixes:
  • Add metadata and conduct miscellaneous fixes (#95), as discussed in #71
    • Append metadata to Yaml format file by new function writeHumanYaml
    • Implement inclusion of metadata and other fixes by script miscModelCurationScript_20190323 
  • Enable automatic model release (#96)
    • Add function exportHumanGEM and adjust increaseHumanGEMVersion allowing for automatic model release

Human 1.0.0

• Fixes (PR #90):
  • Add script removeSinkDMRxns.m for removing Sink and Demand reactions, as discussed in #28
    • 254 Sink/DM reactions are removed
    • 52 unused metabolites are also removed
    • all modifications are saved to removedSinkDMrxns.tsv for tracking the changes
• Features:
  • Additional model file formats (xml, txt and yml) are included in humanGEM
• Style (PR #91):
  • Rename and reformat function increaseModelVersion to ensure uniqueness