Reading Maps in MATLAB Cobra

[Kevin McFarland]

Hi, 

I am trying to run through the core ecoli model tutorial, and want to draw some of the flux maps that are presented in the tutorial. 

I tried to download a .json map from the BIGG database, but the readCbMap function only accepts .txt files. Is there a standard way of converting the json to txt? Or is this method of viewing models no longer used (as the tutorial is from 2010).

Thanks,

Kevin

[Jaime Gonzalez]

Hi Kevin, did you managed to find a solution to this?

[Agustin Maria Pardo]

Hello,

I have the same problem. I want to use "readCbMap" function but I have the ".json" format. Is there a way to convert it to ".txt" format, or use the "readCbMap" with some option parameter?

Regards
Agustin

[Rajiv K]

Hello all, Do we have a solution to this problem? Is there any way we can create our own maps?

Best,
Rajiv K
Department of Biotechnology
Indian Institute of Technology, Madras

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[Trunil Desai]

Hello Rajiv,

I usually create maps using inkscape which is saved in svg format by default. This file can be edited using MATLAB/Python or any programming language to create flux maps.

Regards!

Trunil

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[Ronan M.T. Fleming]

Hi All,

we are looking at ways to interconvert from the cobra toolbox to json
and back...
https://github.com/draeger-lab/EscherConverter/issues/52

Realistically, someone needs to take this up as a project to come up
with a robust solution. What we need is a cobra toolbox map format
that is independent (as much as possible) of the different exchange
formats (SBML, SBGN, json, etc) used to specify map and independent of
the software implementations to generate maps, e.g., cell designer,
escher, newt, etc. By independent, I mean that the map format in the
cobra toolbox should be able to export into each of the major map
formats and be able to accept input from the major software programs
used to generate maps such that we do not have to keep rewriting, and
as a result, continually partially implementing, map support.

Anyone interested?

Regards,

Ronan

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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