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manual-fixes.md

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Description of changes that went into the manual-fixes directory:

  • Many SBML files had accidentally exposed the layout annotation as if it was normal layout, which it can only be in SBML L3. The incorrect namespaces for layout were removed, and the listOfLayouts moved back inside the annotation. [LPS]
  • For BIOMD0000000872, the _url and _urn versions of the layout annotation had invalid reaction lists, so I replaced them with the reation list from the valid one. [LPS]
  • Removed BIOMD0000000883/MAP3K8_Thyroid_Spheres_V3.4.cps.xml, since it was just a straight copy of the COPASI file (i.e. same name without .xml appended). [LPS]
  • Removed avogadro units from BIOMD0000000965, since avogadro was added for SBML L3, but this was an L2 model. [LPS]
  • Changed globalRenderInformation to renderInformation in two models. [LPS]
  • Removed consecutive .'s from filenames [JRK]
    • BIOMD0000000927/Baker2017_Fig14..xml
    • BIOMD0000000928/Baker2017_Fig14..xml
  • Corrected rdf:resource="urn:miriam:unknown: in multiple files [JRK]
    • BIOMD0000000498/BIOMD0000000498.cps
    • BIOMD0000000498/BIOMD0000000498_url.xml
    • BIOMD0000000498/MitchellMedesIronFigures567.cps
    • BIOMD0000000661/BIOMD0000000661_url.xml
    • BIOMD0000000661/MODEL1006230046.cps
    • BIOMD0000000724/Theinmozhi_2018.cps
    • BIOMD0000000724/Theinmozhi_2018.xml
    • BIOMD0000000734/BIOMD0000000734.xml
    • BIOMD0000000734/Parmar2017_Deficient_Rich_tracer.cps
    • BIOMD0000000735/Parmar2017_Adequate_tracer.cps
    • BIOMD0000000735/Parmar2017_Adequate_tracer.xml
    • BIOMD0000000736/Parmar2017_Adequate_diet_Anemia_NoTracer.cps
    • BIOMD0000000736/Parmar2017_Adequate_diet_Anemia_NoTracer.xml
    • BIOMD0000000736/Parmar2017_Deficient_NoTracer.xml
    • BIOMD0000000737/Parmar2017_Deficient_NoTracer.xml
    • BIOMD0000000738/Parmar2017_Rich_NoTracer.cps
    • BIOMD0000000738/Parmar2017_Rich_NoTracer.xml
    • BIOMD0000000872/MODEL1605030001_url.xml
    • BIOMD0000000923/BIOMD0000000923.xml
    • BIOMD0000000923/Liò2012_Modelling osteomyelitis_Control Model.cps
    • BIOMD0000000923/Liò2012_Modelling osteomyelitis_Control Model.xml
    • BIOMD0000000927/Baker2017_Fig14.cps
    • BIOMD0000000927/Baker2017_Fig14.xml
    • BIOMD0000000928/Baker2017_Fig14.cps
    • BIOMD0000000928/Baker2017_Fig14.xml
    • BIOMD0000000932/Garde2020.cps
    • BIOMD0000000932/Garde2020.xml
    • BIOMD0000000933/Kosiuk2015.cps
    • BIOMD0000000933/Kosiuk2015.xml
    • BIOMD0000000944/Goldbeter2013.cps
    • BIOMD0000000944/Goldbeter2013.xml
    • BIOMD0000000952/Rodenfels2019_V1.cps
    • BIOMD0000000952/Rodenfels2019_V1.xml
  • Corrected <CopasiMT:unknown rdf:resource=""/> in multiple files [JRK]
    • BIOMD0000000930/Liu2017.cps
    • BIOMD0000000930/Liu2017.xml