PSC MARC Student Summer Internships in Bioinformatics.

Workshop Dates: June 20 through August 5, 2011.
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15213
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The internship runs for seven weeks, and we accept either graduate students or advanced undergraduate students in the Biological or Chemical Sciences or students in Computer Science or Mathematics. Students are expected to have at least some work in bioinformatics and students majoring in bioinformatics are encouraged to apply. The workshop will begin on Monday, June 20 and run through Friday, August 5, 2011, a period of seven weeks. The Pittsburgh Supercomputing Center (PSC) will pay for participants travel from and back to their home site, as well as room and meals while in Pittsburgh. The rooms will be at the Marriott Residence Inn in Oakland. Participants will be expected to take advantage of the excellent breakfast provided by the Residence Inn, if they desire breakfast. In accordance with NIH policy, no stipend is provided by the PSC.

Students whose background emphasizes Biological and Chemical sciences will generally work on an internship project involving the analysis of a specific gene or enzyme family although other projects are possible. Students whose background emphasizes Mathematical or Computational Sciences will generally work on a specific analysis method or tool. Again, other types of projects are possible. Students should consult with Dr. Hugh Nicholas of the National Resource for Biomedical Supercomputing (NRBSC) and the PSC about their preferences for research projects or a local campus advisor before applying.

The protein family analysis is built around our basic sequence analysis core which focuses on the analysis of a gene and/or protein family through the construction and subsequent mining of a high accuracy multiple sequence alignment. A phylogenetic analysis is conducted, as part of the mining, to help discover gene duplication events and any other anomalies in the history of the family. The subsequent data mining of the high quality MSA yields accurate predictions of the residues conferring specificity to each distinct (defined by a gene duplication) subfamily. This is followed with integrating this analysis with structural insights and structural analysis which culminates in understanding the evolution of new protein mechanisms and activities. Successful projects usually lead to presentations at national or even international bioinformatics conferences.

The second week of the internship coincides with the annual MARC Bioinformatics workshop and students will generally participate in the workshop to insure a sufficiently broad exposure to different techniques and bioinformatics analyses.

In addition to working intensively on their research project the students will be expected to make weekly presentations on their progress. They will also be expected to towards writing a paper summarizing the results of their research project. Thus when they finish the summer the students should be prepared to make a short oral presentation of their research results, have materials that could go in to a poster, and the beginnings of a written presentation of the work.

If you have specific questions about the workshop content please contact Dr. Hugh Nicholas at Nicholas@psc.edu or at (412) 268-5130 with your questions.

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