User: Denis Kazakiewicz

Reputation:
70
Status:
New User
Location:
Last seen:
6 years, 8 months ago
Joined:
6 years, 9 months ago
Email:
d************@gmail.com

Posts by Denis Kazakiewicz

<prev • 7 results • page 1 of 1 • next >
0
votes
2
answers
642
views
2
answers
Comment: C: Visualization of metabolic network in lpSolve format
... 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 suspec ...
written 6.7 years ago by Denis Kazakiewicz70
0
votes
2
answers
642
views
2
answers
Comment: C: Visualization of metabolic network in lpSolve format
... 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 ...
written 6.7 years ago by Denis Kazakiewicz70
0
votes
0
answers
385
views
0
answers
Visualize metabolic network using table with reactions
... Hello, I have metabolic reactions in data frame format. Key variables are WholeCellModelID (reaction ID), Enzyme (enzyme ID), Stoichiometry (reaction description in the format like [c]: COA + NAD + PYR <==> ACCOA + CO2 + NADH). So, it is easy to reshape this data if necessary. The question i ...
written 6.7 years ago by Denis Kazakiewicz70
0
votes
2
answers
642
views
2
answers
Answer: A: Visualization of metabolic network in lpSolve format
... 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 t ...
written 6.8 years ago by Denis Kazakiewicz70
0
votes
2
answers
642
views
2
answers
Comment: C: 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] Vi ...
written 6.8 years ago by Denis Kazakiewicz70
0
votes
2
answers
642
views
2
answers
Comment: C: Visualization of metabolic network in lpSolve format
... 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] me ...
written 6.8 years ago by Denis Kazakiewicz70
0
votes
2
answers
642
views
2
answers
Visualization of metabolic network in lpSolve format
... 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 ...
network written 6.8 years ago by Denis Kazakiewicz70

Latest awards to Denis Kazakiewicz

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour