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  • minervaminerva
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  • #1111
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Issue created Feb 03, 2020 by Ewa Smula@ewa.smulaDeveloper6 of 10 checklist items completed6/10 checklist items

Export as GPML remarks

  • Colours of pathways/compartments and their fonts are not preserved.
    Names of uncovered pathways/compartments are displayed in the top left corner of canvas instead of the rectangular's inside.
    CellD: https://pg-sandbox.uni.lu/minerva/index.xhtml?id=Metabolism
    GPML: https://pg-sandbox.uni.lu/minerva/index.xhtml?id=modelGPML-01

  • After exporting complex (regular/hypothetical) to GPML, any complex is drawn with dashed line.
    CellD: https://pg-sandbox.uni.lu/minerva/index.xhtml?id=Metabolism&x=4731&y=959&zoom=8&search=complex%20IV&
    GPML: https://pg-sandbox.uni.lu/minerva/index.xhtml?id=modelGPML-01&x=4731&y=953&zoom=8&search=csa42&
    But, empty complex is not light blue colour and not dashed line. It's name is also preserved (see below 3.).
    GPML: https://pg-sandbox.uni.lu/minerva/index.xhtml?id=modelGPML-01&x=7071&y=2317&zoom=8&search=AMPK&

  • Complexes names are changed after export (complex IV -> csa42) and its name is hidden.
    CellD: https://pg-sandbox.uni.lu/minerva/index.xhtml?id=Metabolism&x=4731&y=959&zoom=8&search=complex%20IV&
    GPML: https://pg-sandbox.uni.lu/minerva/index.xhtml?id=modelGPML-01&x=4731&y=953&zoom=8&search=csa42&

  • Known transition omitted and unknown transition are drawn as state transition.

  • All reduced notation reactions are drawn as state transition reactions.

  • Reversed reactions are not drawn.

  • Colours of reactions are not preserved.

  • Arrows are not drawn correctly in reactions protein - RNA.

  • Elements modification sites are not preserved.

  • Activated element - the dashed rectangle is not drawn.
    CellD: https://pg-sandbox.uni.lu/minerva/index.xhtml?id=unknown-rections-check
    GPML: https://pg-sandbox.uni.lu/minerva/index.xhtml?id=unknown-rections-check-model

Edited Apr 02, 2020 by Piotr Gawron
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