[BioC] Visualization of metabolic network in lpSolve format

[Paul Shannon]

Hi Denis,

I have looked at the sample input file you included -- thanks for sending that.  

Two questions:  how is that input file created?  How is it read?

If there are identifiable functions that do either of these things -- especially the latter, a reader -- then they could provide a jumpstart on the job of parsing this into a graph object, for further computation or visualization.   We don't want to replicate that parser if we don't need to.   I notice that yacc and lex are used in the the lpSolve CRAN package you mention.

I have googled around a bit on the topic of "lpsolve format" but have not been able to associate your example with anything I find.  This approach could also lead to the discovery of an already-written parser.  Or perhaps a translator to a more standard format.

To summarize:  can you point me to already-existing, supported code that writes or reads files in the format you sent?

Sorry I cannot (yet, at least) provide a ready-made answer to your question.

 - Paul


On Mar 8, 2013, at 11:14 AM, Denis Kazakiewicz wrote:

> Hello
> 
> I am afraid, previously email with attachments could not get to the mailing list. Sorry if this was the case
> 
> The file attached is the example of input file for lpSolve package
> http://cran.r-project.org/web/packages/lpSolve/index.html
> 
> And tacking the opportunity to correct the question for the last time.
> The aim is to visualize data as a graph either directed or undirected. It should not be too pretty picture. Just suitable for farther analysis
> 
> Would you please kindly point out which approaches could be used.
> 
> With best regards
> Denis
> 
> 
> 
> 
> 
> 
> 
> On 08.03.2013 17:42, Yi, Ming (NIH/NCI) [C] wrote:
>> Hi, Denis:
>> 
>> Thanks for your info. I am a bit confused although very interested about it. Which R package you talked about and also I did not see the attachement? Is it possible to let me have it as well.
>> 
>> Thanks and best
>> 
>> Ming Yi
>> 
>> ABCC/ISP
>> Frederick National Lab of Cancer Research (formerly NCI-Frederick)
>> Frederick, MD 21702
>> 
>> -----Original Message-----
>> From: Denis Kazakiewicz [mailto:d.kazakiewicz at gmail.com]
>> Sent: Thursday, March 07, 2013 7:41 PM
>> To: bioconductor at r-project.org
>> Subject: [BioC] Fwd: Re: Visualization of metabolic network in lpSolve format
>> 
>> 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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>> 
> 
> <metabolismPart.ltx>