Comments (2)
tomlue
commented on June 2, 2024
I should be able to iterate on this this weekend. Would you like to meet up on it next week?
from ontox-phymdos.
DanielRoodzant
commented on June 2, 2024
I should be able to iterate on this this weekend. Would you like to meet up on it next week?
Yes I would like that.
I think I know a way to get the converter so that including the Celldesigner extension won't be needed.
By adding SBO-terms to the data Celldesigner can understand which icon to give a compound or reaction.
See:
https://minerva.pages.uni.lu/doc/user_manual/v15.0/SBML-SBOTerms/
And the highlighted section on:
https://minerva.pages.uni.lu/doc/examples/v14.0/02-sbml-modify/#:~:text=Applying%20SBOTerms%20to,type%20is%20provided.
The idea would be to have a user select a type such as Gene, Protein or Simple molecule and then code in the corresponding SBO-term to the sbml.
from ontox-phymdos.
Related Issues (20)
- pmdep - clear table upon button click
- pmdep - Create definitions file containing minimal amount of tables and columns
- pmdep - Get familiar with Celldesigner SBML and raw SBML formats.
- pmdep - Get familiar with the python code from the SBtab - SBML converters.
- pmdep - Write R functions for converting SBtab to SBML.
- pmdep - Write R functions for converting SBML to SBtab.
- Create minimal example workflow article-data -> celldesinger HOT 1
- pmdep - test Cytoscape SBGN visualization on node.js HOT 1
- pmdep - look into a way to externally launch Cytoscape visualization HOT 3
- pmdep - integrate SBOterms for SBtab -> sbml and for sysrev -> sbml HOT 1
- pmdep - Polish app dashboard
- pmdep - Create validator for SBtab files
- pmdep - Integrate RSysrev in app
- PMDEP - Add status bar for MINERVA
- pmdep - Add small example graph in dashboard
- pmdep - Add error handlers to the app to prevent crashing
- pmdep - Write R functions to upgrade the SBtab - SBML converter to the Celldesigner formatting
- Python error in RsConnect publishing HOT 1
- Add phymdos as SRVC flow
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