Visualization of metabolic network in lpSolve format
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@denis-kazakiewicz-5811
Last seen 8.4 years ago
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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Paul Shannon ▴ 750
@paul-shannon-5161
Last seen 8.4 years ago
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
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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
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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@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.inf ormatics.conductor
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@denis-kazakiewicz-5811
Last seen 8.4 years ago
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.in formatics.conductor >
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