BOL

Hi Andaleeb,

The "Metabolic network modelling" area is getting more recognition now a dayz. The "omics" era has thrown open gates for innovative approaches in systems biology for BioInformatics Metabolome and metabolomics are gaining more and more attention in order to understand the complexity of the underlying cellular networks in organisms. Moreover, the completion of several genome projects and also ongoing genome sequencing has made the comparison of metabolic pathways possible.

As per my knowledge there are very few know tools and pipeline. I used Pathway Hunter Tool http://pht.tu-bs.de/ (A Comparative Study of Metabolic Networks - An In Silico Systems Biology Tool) in my research. Hope useful for you as well.

In addition, you can create your own pipeline using some of the avaialbe pathway tools, like PTools http://bioinformatics.ai.sri.com/ptools/ , which is a bioinformatics package that assists in the construction of pathway/genome databases such as EcoCyc. Pathway Tools comprises several separate units that work together to generate new pathway/genome databases. An initial fast reconstruction can be developed automatically with it.

Thanks

Hi Andaleeb,

I think following links will be helpful:

http://genomebiology.com/2012/13/11/R111

http://www.thefullwiki.org/Metabolic_network_modelling

http://www.csb.ethz.ch/tools/efmtool/

http://www2.mpi-magdeburg.mpg.de/projects/cna/cna.html/

http://www.ifr.ac.uk/netsci08/Download/Invited/IT14_Schuster.pdf

Thanks

Hi Andaleeb,

The reconstruction of metabolic networks at a genomic scale has been greatly facilitated by the development of sequencing technologies and high throughput “omics” methods. A large number of sophisticated approaches permits the analysis of the structure and dynamics of large sets of biochemical reactions, which are still evolving. Following are the useful links for you.

http://ihcp.jrc.ec.europa.eu/our_labs/predictive_toxicology/doc/EUR_24553_EN.pdf

http://www.mrc-lmb.cam.ac.uk/genomes/madanm/guilhem-wiley.pdf

Book chapter

http://ai.arizona.edu/mis596A/book_chapters/medinfo/Chapter_17.pdf

Metabolic Network Model of a Human Oral Pathogen

http://jb.asm.org/content/191/1/74.full

Pathway processor http://www.ncbi.nlm.nih.gov/pubmed/12097350

MIRAGE http://genomebiology.com/2012/13/11/R111

CardiNet http://www.biomedcentral.com/1752-0509/6/114

Complex networks theory for analyzing metabolic networks

http://arxiv.org/ftp/q-bio/papers/0603/0603015.pdf

Combining Bioinformatics Resources for the Structural Modelling of Eukaryotic Metabolic Networks

http://www.jsbi.org/pdfs/journal1/IBSB05/IBSB05F022.pdf

Thanks