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sys-bio / sidewinder

A client side web application for building and simulating of biological reactions based on SBML.
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SBML assignments are lost when converted to Network rendering. #16

Closed bartjuw closed 2 years ago

bartjuw commented 2 years ago

Currently no Network rendering support for SBML Assignments. Assignments are read from a SBML file but are discarded once a user visualizes the network. Need to add assignments to Network node or reaction state ( or a new Network persistent state)

bartjuw commented 2 years ago

Currently (Aug 18th, 2022, version alpha 0.49), only Initial Assignments are not saved to SBML file. Assignment rules are preserved.

See attached SBML file for repro.

  1. Load sbml model,
  2. Note:
    • One initial assignment (h = Keq1 +2).
    • Two assignment rules, One for VM1 and one for Keq1.
  3. Now save SBML file.
  4. Open up newly saved SBML file.
  5. Result:
    • No Initial assignment for h is assigned value of 0. Expected h to have an initial assignment of Keq1 +2.
    • The two Assignment rules for VM1 and Keq1 are saved.

feedback_InitialAssign2Assign.xml.txt .

bartjuw commented 2 years ago

Fixed this issue with check in on 8/18/2022. writing Assignment Rules to SBML file is now implemented. User cannot save Initial assignments and assignment rules to network model JSON file as they are a part of the network object and not node or reaction state.