[BioC] Visualization of metabolic network in lpSolve format
d.kazakiewicz at gmail.com
Fri Mar 8 01:35:49 CET 2013
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
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:
>> 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
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor