[BioC] Fwd: Re: Visualization of metabolic network in lpSolve format

[Denis Kazakiewicz]

Sorry. Correction
Instead of 'The aim is to convert data to simple undirected graph. From 
the example above vertices AC_c and ACTP should be connected via edge AckA.'
Should be 'The aim is to convert data to simple undirected graph.'


-------- Original Message --------
Subject: 	Re: [BioC] Visualization of metabolic network in lpSolve format
Date: 	Fri, 08 Mar 2013 01:35:49 +0100
From: 	Denis Kazakiewicz <d.kazakiewicz at gmail.com>
To: 	bioconductor at r-project.org <bioconductor at r-project.org>



Hello Paul

Sure.
Example of file format  is in the attachments

For example, acetate in cytosole appears as a result of two reactions 
with IDs AckA and TX_ACUP
The stoichiometries of these reactions are
ACTP + ADP ? AC + ATP
AC[e] + H[e] ? AC[c] + H[c]
where [e] means extracellular space and [c] means cytosole

The corresponding line in the attached file is
  AC_c) 1 AckA 1 TX_ACUP = 0 ! acetate

ACTP is consumed in one reaction above (AckA). Therefore stoichiometric 
coefficient for this reaction will be -1.
ACTP is produced with stoichiometric coefficient 1 by reaction with ID Pta
ACCOA + PI ? ACTP + COA
So, corresponding line will be
ACTP) -1 AckA 1 Pta = 0 ! Acetyl phosphate

The aim is to convert data to simple undirected graph. From the example 
above vertices AC_c and ACTP should be connected via edge AckA.

With bets regards
Denis






On 08.03.2013 00:22, Paul Shannon wrote:
> Hi Denis,
>
> Can you provide a very small example?   I would then be glad to see what might be available within Bioconductor for visualization.
>
>   - Paul
>
>
> On Mar 7, 2013, at 2:54 PM, Denis Kazakiewicz wrote:
>
>> Hello,
>>
>> There is a metabolic network in lpSolve format. Objective function for flux balance analysis is included.
>>
>> Is there a way to visualize network topology?
>>
>> With best regards
>> Denis Kazakiewicz
>> Bioinformatics Master student
>> Wroclaw
>> Poland
>>
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