metabolic map coordinate file (CbMap)

[Bushra Saeed Dohai]

Dear COBRA Group,

I want to use readCbMap command to draw the metabolic map, I knew that map coordinate file (e.g ecoli_core_map.txt) should be loaded and exported from BIGG database in order to use readCbMap command. Unfortunately, my organism is not available on BIGG database.

For my model: 

I have xml file that includes reactions and flux values, I am trying to generate the map coordinate files for my organism, I wonder if anyone of you can provide me with an idea on how to do it? is there a function in COBRA or database or software that can generate this? . 

I highly appreciate your kind assistance. Thanks

 Sincerely,

Bushra Dohai Modelling Engineer and Research Technologist   Laboratory of Algal, Systems, and Synthetic Biology Centre for Science and Engineering NYU Abu Dhabi, United Arab Emirates Office Tel: +971 2 628 5144, P.O. Box 129188 http://lasb.abudhabi.nyu.edu

[Ronan M.T. Fleming]

Hi Bushra,
you will have to use some other software to manually layout your metabolic map. This is not contained within the cobra toolbox.
Ronan

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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[robor...@gmail.com]

Hi Bushra,
using maps from Bigg is extremely tedious, but possible. I was able of learn how to modify this maps, but the process is complicated and time consuming. I will try to explain it to as following:
1) download the map from bigg database, as most similar or simple as possible
2) you will get a txt file that you can open in excel
3) you will see 4 different sections.
first one are the mets nodes, with coordinates (x.y) in matlab plus a code that can be whatever number you choose (aka node ID), and coordinates also for the reference that will be shown as the name of the metabolite
second corresponds to the reactions nodes, which is similar to the mets nodes
third correspond to the reactions names, and vectors that will be connecting the different node Ids
the forth one is only text will be added into the map in addition to the names of metabolites.
4) remember this has to be saved as .txt to be opened by matlab. so you can work in excel and save it as txt to be upload to matlab
5) any single mistake in one node id will produce a total collapse of the map. Be careful
6) if you want to modify things from a constructed map, you can do it deleting the rows and adding your own pathways.

Good luck


Roberto Orellana
Lovley Lab
Umass-Amherst

[Ankita Juneja]

Hi Ronan,
I have the same issue. My organism is not present in the BIGG database and I reconstructed the model myself. Is there a way to visualize it using readCbMaps.
I can make my own text file if needed but I have no idea how to assign node numbers and node distance type of things.

Any help would be appreciated.

Ankita.