Visualizing metabolic models
Entering edit mode
7.3 years ago
JJK ▴ 60

I have been working in the field of annotation and modeling for a while now but I never encountered a model viewer that roughly fits my needs and I am amazed that I can't find one.

I see a lot of people creating SBML files and I wanted to view them graphically in a web viewer of some sort to quickly see how it is designed and if there are flaws present.

The following programs I have looked into:

iPath - Nice if you like to stick to KEGG and have nothing new to report yet not flexible

PathwayTools - Nice if you have an annotated genome and want to map it to the MetaCyc database but for me personally the software is a pain to work with.

Escher - I thought this was one I could really use, however when loading a SBML JSON file you need to draw the entire map by hand which is cumbersome (might be able to design something myself but this will probably take a while).

I know there are other software packages available but as far as I can remember these didn't work either but forgot the names.

In short what I was hoping to find in the modeling community a SBML viewer that shows each pathway separately with the corresponding metabolites and reactions using some form of forced layout and that you can manually move them around afterwards.

Did I miss the most promising packages?

web models sbml view • 1.7k views

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