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zakandrewking / escher

Build, share, and embed visualizations of metabolic pathways.
https://escher.github.io
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Conversion between xml format and json format #306

Closed hongzhonglu closed 5 years ago

hongzhonglu commented 5 years ago

Hi I have maps in xml format, which can be used for the cellDesigner, are there methods to change it into json format?

zakandrewking commented 5 years ago

You're best bet would be to convert from cell designer to SBML and then SBML to JSON. This has been done before, but I'm not sure how general the approach is. @draeger Do you have any advice?

draeger commented 5 years ago

Indeed. The supplement of the Recon 3D paper describes in detail how to proceed (from page 18), including several post-processing steps. Here is only a short version:

  1. You can use the celldesigner-parser project to convert CellDesigner models to the SBML format with Layout extension.
  2. In the second step, you can load the generated file as input to EscherConverter and export it to Escher's JSON format.

I hope this helps!

hongzhonglu commented 5 years ago

Great thanks for your help! It is very useful for me.