Global metabolism visualization of FBA results advice

[MB]

Dear All,

I am a PhD student new to FBA who has inherited a genome scale metabolic model (Written in SBML Level 1 Version 2) for a facultative anaerobe. This appears to still need gap filling as it still behaves aerobically under anaerobic conditions. The model contains 1K+ reactions/3K+ nodes and I am trying to visualize the complete FBA output vectors (generated using COBRA in MATLAB) on a full global KEGG view cellular metabolic map as I have only been able to glean limited information from looking solely at reaction flux value changes over different oxygen import upper bound reductions.

Following the suggestions on the COBRA I have attempted to use Paint4Net and ReconMap (though have not yet attempted the CellDesigner option). Paint4Net could not handle the number of nodes of the model and I have not wanted to restrict the number. ReconMap is the concept of what I am looking for. I followed the instructions and while I get the  'Overlay was sucessfully sent to ReconMap!' message and a named overlay tab I can tick on/off on Minerva, ticking the overlay on does not put any overlap on the provided map (as the example they provide does).

I have also attempted Cytoscape, MetDraw and FBASimVis within VANTED 2.6.5. In all of these cases, my model can load correctly, but I cannot find a way to organise/give the model a global KEGG view of metabolism I am familiar with. In FBASimVis I am able to download all of the smaller KEGG pathway models/layouts, but the global form does not.

As ReconMap is in theory exactly what I'm looking for, can anyone suggest a fix to my issue? Alternatively, does anyone know of ways of inputting the complete metabolic model layout for models in Cytoscape/FBASimVis within VANTED? Or do any veterans have suggestions for other strategies that they use to the same effect?

Thanks,

MB

[Ronan M.T. Fleming]

Hi MB,

when calling 

function [serverResponse] = buildFluxDistLayout( minerva, model, solution, identifier, hexColour, thickness)

make sure that solution.v has non-zero entries and that those entries are not too small. Test this using

solution.v(solution.v~=0)=1;

If that does not work, play around with line 40 of

https://github.com/opencobra/cobratoolbox/blob/2c5855c6187b3bc3b414088fec29041ac3c8a28c/src/visualization/maps/ReconMap/buildFluxDistLayout.m

normalizedFluxes = normalizeFluxes(abs(solution.v), thickness);

to see if you need to normalise a different way to get the overlay to show.

Regards,

Ronan 

--

---
You received this message because you are subscribed to the Google Groups "COBRA Toolbox" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cobra-toolbox+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

--
Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
----------------------------------------------------------------------------
Division of Systems Biomedicine and Pharmacology,

Leiden Academic Centre for Drug Research,

Faculty of Science,

Leiden University.

http://analyticalbiosciences.leidenuniv.nl

&

H2020 Project Coordinator

Systems Medicine of Mitochondrial Parkinson’s Disease

http://sysmedpd.eu

----------------------------------------------------------------------------
Mobile:  +352 621 175 112
Skype: ronan.fleming
----------------------------------------------------------------------------
(This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)