Question
Tools for analyzing large scale networks
I would like to state the question what kind of tool you would suggest for the analysis of large scale biological networks. The tools i have used so far are of course Cytoscape and Network Workbench. Both have some really nice features but also disadvantages. I would like to discuss with others about this topic and if there are recommendations for specific types of networks making a tool advantageous compared to others.
All Answers (8)
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I am sorry that I am a freshman of systems biology. And recently I have been learning the Cytoscape. I would like to discuss with you when I have some question about cytoscape or network workbench usages. -
Of course! Your are welcome for questions and I hope I can give some suggestions if you have questions! -
Robert I think it depends on the objectives you have in your study
this link is just a brief review on different software solutions
http://www.sysbio.org/dataresources
Cytoscape is really good choice, one of the most integrative approaches,
but once again it should depend on the objectives you have appointed -
Thank you very much, Mamuka! I will have a closer look at the site you suggested. There are interesting tools and resources I did not noticed so far. Especially the Network Biology subsection is very informative.
To be more specific about my fields: I want to model disease networks (not pathways!) and I would like to have the possibility to integrate different datasources like e.g. textbased terms like disease names, target association as well as structural informations or drug-target associations as well as protein-protein interactions. -
You are welcome Robert, its my pleasure to support, you may need customized approach also, have a look on that article, you may find something valuable there, at least in methodological approach
http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0040210#s2
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Hi, I would also advise you Systrip http://tulip.labri.fr/TulipDrupal/?q=systrip for graph analysis. -
Dear Robert, Ecologists have been concerned with large weighted digraphs for almost 70 years now. We have developed a number of quantitative analyses to deal with quantified graphs under the rubric of "ecological network analysis". Packages are available for free download. See <http://www.cbl.umces.edu/~ulan/ntwk/network.html>; (in Fortran IV for DOS) and <http://cran.r-project.org/web/packages/enaR/index.html>; in R. The best, Bob Ulanowicz -
I am also new in Systems Biology. I know Cytoscape. I think Gene Network Analyzer (GNA) developed by Jong and his group can be good choice for gene network.
