Escher alternatives?

[Björn Johansson]

Hi all, I am starting to use cobrapy for both my own project ant teaching.

I would very much like to use Escher to visualize the results for my students.

I have invested a full day, but not managing to make it work.

The fact that Escher has not been updated in four years indicate that it is not

a requested feature anymore?

Are there alternatives?

Thanks,

Björn

 

[moritz...@gmail.com]

Hi Björn,

I think that people still like Escher, but it has gone the way of most academic software sadly. Zack King left for an industry position and nobody has picked up the maintenance.

You could try out https://sammipy.readthedocs.io/, but I have no personal experience.

Best,

Moritz

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[Matthias König]

Hi Björn,

you can use cy3sbml with python. I developed the tool some time ago and work for visualization of FBA results and kinetic models.

https://github.com/matthiaskoenig/cy3sbml/

Unfortunately, the documentation is not perfect, but I have to visualize some results next week for another project and would use the opportunity to make a video of the current workflow and a python notebook to demonstrate things.

There are some very old videos around from the early version still in Cytoscape 2, but a lot of things happened in the meanwhile.

https://www.youtube.com/watch?v=BBGiFU_gEAo

I suggest you have a look into Cytoscape 3 and the cy3sbml app and see if this tool could work for you. The flux visualization is basically mapping of the flux distributions on visual properties in the network views.

The biggest issues are always the network layout, i.e. not having some hairballs to visualize on.
So if you have a concrete example, i.e., SBML, Layout mapping on SBML identifiers and some flux distributions (or cobrapy scipts to generate them) I could demonstrate you how to visualize things.

I assume you have some toy example such as e_coli_core where layouts exist.
Best Matthias

[Björn Johansson]

Thank you for your suggestions, I will look into this asap /bjorn