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I need to draw a map of the core metabolism of E.coli. Associated with each reaction in the map I have a number that indicates the flux through this reaction. I want the map to reflect these fluxes through the color of each reaction in the map.

I have tried using tools like Mathematica and Cytoscape, but it is very hard to get a nice layout of the metabolic network. I have seen maps of E.coli metabolism which look very nice on paper. What I need is a map like these, but where I can define the colors of the reactions.

For example, see the image below for an example. Forget about the yellow bounding boxes delimiting compartments. I can spare those.

     enter image description here

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    $\begingroup$ Can you provide a link or two to the type of metabolic map design / layout you prefer? $\endgroup$ – Michael S Taylor Sep 15 '14 at 22:13
  • $\begingroup$ @MikeTaylor Added a picture to the question. $\endgroup$ – becko Sep 16 '14 at 13:07
  • $\begingroup$ Have you looked into papers from systems biology groups which publish these networks reconstructions? They should state there what software was used. $\endgroup$ – Chris Sep 16 '14 at 20:16
  • $\begingroup$ @Chris I haven't found any. There are some tools available, for example, metdraw.com. But when I upload my E.coli SBML model, the plot layout is a disaster. There used to be a web IPython notebook that one could use for some prebuilt models, where you just had to input the reaction fluxes. But now it's gone: nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/… $\endgroup$ – becko Sep 16 '14 at 20:25
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    $\begingroup$ There is a package called igraph in R but I am not sure that will be very convenient. If you don't get a satisfying answer here you may want to try asking on stackOverflow. $\endgroup$ – Remi.b Sep 16 '14 at 20:53
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I'm not sure if they will be useful for your application, but you should look into software used to visualize ecological networks (and maybe also software used for drawing electrical charts). The type of data used there is very similar to what you want to plot, with nodes and links along with metadata for links on e.g. rates or connection strenghts.

I can point you to mangal by ecologist Tim Poisot (blogpost on mangal here), SBGN (Systems Biology Graphical Notation), and there is also the R-package diagram. However, I haven't used them much so I cannot say how useful they will be.

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The basic problem is one of prior knowledge. The information you have about E. coli metabolism is in the form of a simple network, i.e. a list of nodes and the edges (along with their weights) that connect them. From this information alone it's impossible to know, for example, that the reactions in the TCA cycle should be plotted as a perfect circle (that's the circle in the middle of your example graph).

The only source for that information that's likely to be compatible with all of the metabolite/reaction names in your SBML file is the BiGG database. You can download maps that contain, among other things, x-y coordinates for all of the nodes in a metabolic network so that when you plot them they're not arranged in a big sloppy mess. You can then use a tool like COBRA to make the actual plots (look up the documentation for readCbMap and drawFlux).

Even this won't be as pretty as you'd like. The best answer, unfortunately, is a piece of software called Simpheny, which is commercial software that costs about a zillion dollars and is not freely available.

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This is an old question, but Escher is a web app that has been developed that now enables the drawing of these maps using a web tool. Further customization (like reaction colors) could be manually manipulated in the downloadable SVG file.

From the main page linked above, you can load in the E. coli core model and look at (and manipulate) the map:

enter image description here

Escher is described in this publication in PLOS Computational Biology.

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  • $\begingroup$ A very useful contribution to SE Biology. The fact that the question is old is irrelevant, as you have realized. I imagine there will be others like me that were unaware of this. $\endgroup$ – David Dec 18 '18 at 18:36
  • $\begingroup$ @David if you are interested in exploring further, Escher now has add-ons for simulating and visualizing model output overlaid on the map using Escher-FBA described in a very recent publication. You can knock out reactions, change reaction bounds, and all sorts of things (simulates using glpk on the front-end). $\endgroup$ – achilles Dec 19 '18 at 19:13

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