Fun with computers

I am proud of my geekiness.  I would rather spend a day building a computer or playing a game than go watch the game at the pub. So it always pleases me when I make my computer do something new, it was kind of the point of going back to school to study computer science.  At the moment I am working on a program that takes an ancestral genetic tree and the mutations in the area of the chromosome and maps the mutations to the different branches of the tree.  I got my first set of results today:

This is selection from the tree built at chromosome 2:13632000 in the HapMap phase II CEU population of 120 phased chromosomes. The first number is the branch number and then the series of SNP mutations that enter the population at that branch:

98, rs16832011
99, rs3769013, rs3769012, rs730005, rs2322813, rs3769008, rs12373779, rs9636213, rs3754689, rs4988201, rs3087343, rs1435577, rs3769001, rs4988163, rs7561565, rs7581814, rs12472293, rs2839740
101, rs11884924, rs16832067, rs3816088, rs2304369, rs4988232, rs4988191, rs4988189, rs4988186, rs4988185, rs4988173, rs4988172

The idea is I can take this information and correlate it to my other program that generates the probability that each branch is a locus of selective pressure and then show which SNPs are probable candidates for causing selection in our species.

The world is messed up

A very good friend of mine is trying to get a job at Target. He is a trustworthy guy and I think he is very nice and is a US Marine Veteran. He is waiting for his third interview for the position.  I was an anomaly having to have a second interview for my fully funded PhD with living stipend with most of my peers having only one interview.

It strikes me as wrong that I could have gotten a higher status job for about equal pay with fewer interviews and much less hassle than my friend.

Teaching and talking about my research

I find it odd that I am writing about how much I am enjoying teaching, given how much I hated school when I was a student. I didn’t enjoy  school until college/university.

Yesterday, I was demonstrating for the evolution day part of the Molecular Genetics and Cell Biology module for the new year of PhD students. It was really nice to feel like I knew what I was talking about given that I took this course last year. It is incredible what a difference a year makes in the DTC programme.  I was able to explain about the different ideas in evolutionary science and offer suggestions of papers and ideas to help the new students understand the topics and it was an incredible feeling knowing that I was able to help people understand.

At the moment I am working on three tasks of my list of TODO items. First I am preparing a talk on my summer projects for Monday’s inter-DTC seminar series. I need to entertain other PhD students for about 20 minutes before I get shot down with intelligent questions.

Second, I am preparing for my first viva on my research proposal.  I need to give a 10 minute talk on what I plan to do for the next 3 years and then have two academics grill me on the proposal. I’m nervous about this but I need to put that to the side and get it done.

Finally, I am working on changing some of the material for next week’s statistics work for the new PhD students. It is nice to be able to have a hand in setting up the practical and assessment work for the module.

After next week, I don’t think I am doing any teaching for a while, so I will be able to focus on my research for a bit.

Finished and submitted my research proposal

So I finished and handed in my research proposal yesterday. I am really proud of myself for getting it done and for getting this far into my post-graduate career. It makes me feel very good to have produced something that other PhD students and some academics feel is a good proposal. It also feels good to know what I am going to be doing for the next while as I get settled into my work.

This is the summary of my research proposal:

This project is a bioinformatics investigation into human evolution using statistical analysis of genomic variation. The project will look at human population variation and discover which mutations were most beneficial to humans. The project will initially focus on a whole-genome approach to discovering signals of selection and subsequently focus on correlating mutations with the signals to determine the causal mutations driving the selection. The project will use and build phylogenetic trees from genomic data gathered by projects such as the 1000 Genomes project or the HapMap project as the basis for a statistical analysis of the coalescent history of our species. A prime focus for the project will be to discover new types of selection and apply detection to multiple species (such as mice and chimpanzees, two important model species). Particular attention will be paid to understanding the roles and relative importance of selective sweeps, standing variation, purifying selection, epistasis, and unknown methods of selection.

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