[BioC] Visualization of metabolic network in lpSolve format
Denis Kazakiewicz
d.kazakiewicz at gmail.com
Tue Mar 26 08:40:06 CET 2013
Dear Paul
Thank you very much indeed.
I couldn't come up with (now seems) simple thing that both enzymes and
reactants should be nodes and there should be different kinds of edges.
Also, I was not aware about graphNEL. Looks great.
Thank you again. I was stuck. And this is great relief.
I suspect that links from my previous email didn't go through. If this
was the case.
Here they are.
http://lpsolve.sourceforge.net/5.5/
http://lpsolve.sourceforge.net/5.5/LINDO-format.htm
My next question is not crucial. Just want to make sure.
Indeed, each row represents one reaction.
Do you mean that reactions themselves should be nodes together with
molecules-nodes on the same graph?
With best regards,
Denis
On 25.03.2013 23:16, Paul Shannon wrote:
> Hi Denis,
>
> Taking a quick look at the data.frame you included, I suggest this:
>
> - the Stoichiometry column suggests that each row is a reaction
> - if you parse each reaction into substrates, catalyst and products, you have a graph
> - nodes are the substrates, the reaction, the enzyme/s, the products
> - edges could be "substrateFor", "catalyzes", "produces"
> - all of the rate information, and etc., can be node and edge attributes
> - the graphNEL class can be used to capture all of this information once you parse it out
> - you can use RCytoscape, Rgraphviz and igraph to further manipulate and display the resulting network.
>
> Does this seem promising?
>
> - Paul
>
>
> On Mar 25, 2013, at 10:44 AM, Denis Kazakiewicz wrote:
>
>> Hello
>>
>> Apologize for late response
>>
>> There are 2 R lpSolve packages (lpSolve, lpSolveAPI). There is also a MATLAB package. These should be able read the .ltx format.
>> .ltx is actually a linear programming format. There is some documentation here.
>>
>> The .ltx file was constructed by authors of whole cell Mycoplasma genitalium model (https://simtk.org/home/wholecell) to parametrize metabolic network according to flux balance analysis (FBA) assumptions. Not sure how they did it. Their contacts are on that web page.
>>
>> My initial assumption was that .ltx format would be easy to parse for visualization. I reckon, I was wrong :)
>>
>> Would you please kindly suggest basic steps (or just give some hints) for visualization of metabolic reactions as metabolic map. The example of raw data is attached. It is very easy to reshape them in any required form
>>
>> With best regards
>> Denis
>>
>>
>> On 11.03.2013 18:08, Paul Shannon wrote:
>>> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioconductor mailing list
>>>>>>>
>>>>>>> Bioconductor at r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>
>>>>>>> Search the archives:
>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>> <metabolismPart.ltx>
>>>>
>> <ReactionsExample.RData>
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