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The Life Scientists:
Noel O'Boyle
Passing on a question from a bioinformatics colleague who needs to put together lectures and practicals on systems biology: "Is there opensource/freely available software that can be used to carry out systems biology analysis?". Any information on existing teaching resources would be welcome...
October 30
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Itachi, Mr. Gunn, Duncan Hull and 3 other people liked this
Try Copasi (http://www.copasi.org/) and JWS Online (http://jjj.biochem.sun.ac.za/).
- Neil Swainston
Thanks - they look useful.
- Noel O'Boyle
That's a tough question to answer. What specifically is he looking at? Pathways? Integrated analysis?
- Deepak Singh
If only it were possible to be specific - pinning down what exactly to cover in a systems biology course is part of the problem. The practicals will probably be limited by what is available and whether case studies or tutorials are provided (or are available on the web).
- Noel O'Boyle
+1 Deepak. Also http://www.sbml.org maintains a list of software compatible with SBML. Most of them are free / open source : http://sbml.org/SBML_So... http://sbml.org/SBML_So...
- Khader Shameer
Thanks Khader - that list looks very useful. Regarding the type of software, really anything from metabolomics analysis, microarray analysis, studying protein-protein interactions graphs would be useful. Again, the focus is on software for use in practicals (so should be easy to use, and free or open source).
- Noel O'Boyle
Bioconductor for microarray analysis, igraph for graph analysis, Cytoscape for visualization, network integration
- Rajarshi Guha
JWS Online (http://jjj.biochem.sun.ac.za/) is quite handy for teaching. The models are of a reasonably small size and it's web-enabled, so no faffing around with installs and what-not.
- Neil Swainston
Noel, you might want to redirect your colleague to http://sciencestack.com with this bioinformatics question.
- Jane Breezler