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Human 1.1.0
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@haowang-bioinfo haowang-bioinfo released this 13 Jun 14:22
v1.1.0
2c3eb56
  • 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
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