We will develop simple models of germline selection to explain the linkage disequilibrium (correlations) seen in the HapMaP III data. This will involve making simple models and running simulations of these in Matlab.
Week 2: Familiarized myself with MATLAB software and learned specific techniques. Created, prepared, and presented introductory Powerpoint presentation.
Week 3: Attended BioMaPS Institute 3-day workshop/ lecture series on various advances made in the field. Also began creating basic sequences in MATLAB.
Week 4: Continued to create sequences and began "mutating" them so as begin working on new generations of population.
Week 5: Created loop that would initialize population. Worked on allowing loop to produce multiple generations from initial population.
Week 6: Configured loop to produce mutliple generations. Began trying to incorporate mutation rates in offspring.
Week 7: Having difficulty with commands to incorporate mutation rates. Also trying to manipulate reference sequence to reflect changing fitness levels of individuals in population. Finalized model and held back mutations/changing reference sequence to be incorporated in the future. Gave Final Presentation.
Week 8: Working on mutating offspring sequences again.