Other than where specified, these are my notes from the IB07 Conference, and are in no way
expressions of opinion, and any errors are probably just due to my own
There are a large number of concepts and methods. Need to integrate different networks and additional information networks.
CABiNet (COmprehensive Analysis of Biological Networks). It is a generic network analysis suite with a semi-automatic network processing pipeline and methods for the exploration of a protein's functional network. The work was driven by the need to ID the substructures of the network (via clustering, network topologies, and known communities), and the knowledge that networks are incomplete (superposition of networks). Problems with the former include the fact that different algorithms may lead to different results. Created with component-oriented architecture. The architecture slides were very clear, but necessarily hard to reproduce in these notes. Uses Hibernate, Spring, and EJBs, among others. The "n-tier" architecture they used is called Genre. There is an asynchronous invocation of processing pipeline based on Message Driven Beans.
Via their integration tier they have acces to SIMAP, which is used in the detection of orthologs. It contains millions of proteins and FASTA hits, and they can do real-time orthology searches. There is web-service and ejb access.
One example pipeline would be functional classification based on multiple biological networks. Another would be the identification of functional modules from gene expression data (you can upload microarray data). They also showed a real example of a protein interaction network from a nucleosomal complex, and then added more and more data sources until the network grew quite complex.
Here comes my opinion: The clearest talk of the afternoon, dealing with an externally-available application that allows the user to create pipelines to perform network analysis. This one did have good architecture slides: perhaps a few too many 😉 . Their architecture makes me wonder if they use AndroMDA or some other MDA, as such plugins to maven can build Hibernate/Spring/EJB/web services layers. They should have mentioned other similar projects, and how they are different, as I wouldn't know. However, that's a small beef. Finally, how do they know how good each data source is? Do they have a rating of each data source, for instance against a gold standard?