That would be excellent for a GSOC project. On Tue, Mar 8, 2011 at 8:03 AM, Dhruv Kumar <[email protected]> wrote:
> On Tue, Feb 15, 2011 at 10:43 AM, Shannon Quinn <[email protected]> wrote: > > Hi Shannon, > > > > > > > It would be interesting to see how the current implementation can be > > > integrated into your Bioinformatics course work, what extensions you > > > need for this particular domain. > > > > I assume your HMM would be for the purpose of protein/nucleic acid > sequence > > analysis and alignment. HMMs/MDPs are fairly domain-independent, but this > > would definitely be an interesting pursuit; I'm a grad student in comp > bio, > > and I know a lot of folks who would love to use this. > > > > Yes, I'm interested in applying HMMs for protein sequence analysis, and > seeing if they can be applied to predict the side chain conformation of > protein sequences on large data sets using Mahout. The following paper uses > a HMM in form of a Dynamic Bayesian Network for the same purpose: > > http://www.biomedcentral.com/1471-2105/11/306 > > It will be interesting to extend Mahout's existing HMM code so that it > could > be distributed over large clusters. I'm working with a professor here at > UMass on side chain structure prediction as well this semester and he said > that we can craft out a nice, tight proposal for this purpose for GSoC. > > Dhruv > > > > > > > > On the topic of GSoC, I meant to mention: I'm happy to volunteer my > > services as a potential mentor for the summer. > > > > Shannon > > > > Apologies for the brevity, this was sent from my iPhone >
