Systems Biology-Building A Metabolic System Network

Question

[vijay]

Please can someone provide me with a exhaustive tutorial on how to model genetic networks using systems biology techniques. Please do recommend some better tools..

Thanks

[Niek De Klein]

better tools than which? which ones did you try out? what was unsatisfactory about them?

[vijay]

Was looking out with cell designer, cytoscape. they tend to involve more manual work.

Answer 1

[Steve Moss]

I'd recommend checking out the Systems Biology Markup Language (SBML) site:

• http://sbml.org/Main_Page

It's always a good idea to do a literature review first on these sorts of things though. Use Google Scholar, or Pubmed etc and get a grip of appropriate search terms for journal articles that might point you in the right direction. I did a search for "genetic network modelling software site:org" on Google and found a few papers and links that might be useful:

• http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010743
• http://onlinelibrary.wiley.com/doi/10.1002/jez.10187/abstract;jsessionid=9EB61FFCEA1314CF9E83E0D9F6F08713.d01t03
• http://bib.oxfordjournals.org/content/10/4/408.full
• http://www.genostar.com/en/genostar-software/gnasim.html
• http://www.infobiotic.org/index.html (http://www.infobiotic.org/tutorial/tutorial_2.html)

It might also be worthwhile checking out this discussion from a few days ago:

• http://www.biostars.org/post/show/44380/database-of-essential-genes/#44629

and a couple of papers I posted about modelling metabolic networks:

• http://bioinformatics.oxfordjournals.org/content/26/4/536.full
• http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020072