Tuesday, November 08, 2005

Summer courses in digital biology

For the past three years, Dr. Linnea Fletcher and I have been teaching summer courses through the Chautauqua program funded by the National Science Foundation. These courses are organized on a national basis by the University of Pittsburgh and the Council of Chautauqua Field Centers, and supported by the National Science Foundation Division of Undergraduate Education.

Some of the courses offer the chance to learn about fascinating topics in exotic places, like one course on Galileo that was offered in Italy. But if you can't go to Italy, you might like to come to Texas, where you can learn about digital biology and hear good music in the city limits of Austin. Since our courses are in June and it's too hot to go outside, it's a great time of year to work indoors during the day in an air-conditioned computer lab, and venture out to hear music at night.

It's a bit early, but I'm posting the course descriptions, now, to make more people aware of the courses and gather topic requests. We make changes every year to incorporate new resources and tackle cool papers that we've read. So if you have a topic request, or you attended past courses and want to post rave reviews, please add your note in the comments at the end of the post.

Registration information will be available soon at: http://www.chautauqua.pitt.edu

A Hands-On Tour Through the World of Bioinformatics
LINNEA FLETCHER, Austin Community College and SANDRA G. PORTER, Geospiza, Inc.
Date: June 8th-10th in Austin, TX

High-throughput data collection, web-based bioinformatics tools, and molecular databases have changed the nature of biological research. This course places a strong emphasis on hands-on practice with bioinformatics resources to explore current topics in biological research. Activities and topics in this course are updated yearly in order to incorporate new tools, developments and ideas in fields of genomics, proteomics, and structural informatics. Example topics are: Genotyping, DNA sequence analysis, sequence assembly and alignments, identifying SNPs and other types of sequence variation, genotyping, designing PCR assays, BLAST, making the most of a database search, molecular modeling tools (Cn3D), genetic databases, OMIM, and interpreting experimental results. Lastly, participants discuss how bioinformatics can be applied in their courses.

For college teachers of: bioscience-based courses such as microbiology, genetics, biology, pharmacology, allied health, biotechnology and molecular biology. Prerequisites: none.


Studying Evolution with Bioinformatics
LINNEA FLETCHER, Austin Community College SANDRA G. PORTER, Geospiza, Inc.
Date: June 12-14th in Austin, TX

Students in this course will learn how bioinformatics resources can be applied to the study of evolution on a molecular level. This course includes a significant hands-on component, with new topics introduced every year. Example topics include: genome browsers and tools for comparative genomics, evolution in HIV, evidence for a common ancestor, and looking at genetic codes. Participants learn how to use the UCSC genome browser, prepare a data set, generate multiple sequence alignments, and prepare phylogenetic trees, and use free tools for viewing three-dimensional structures from related proteins. Discussion topics include: choosing sequences for phylogenetic studies, along with different methods for creating phylogenetic trees (neighbor joining, parsimony, maximum likelihood). Topics such as orthology, paralogy, homology, homoplasy, and comparative genomics will also be covered. Case studies where phylogenetic trees have been tested experimentally will also be discussed. Lastly, participants discuss and explore how bioinformatics resources can be used in their courses.

For college teachers of: bioscience-based courses including biology, microbiology, organismal biology, molecular biology, genetics, evolutionary biology, and biotechnology.
Prerequisites: the introductory course, June 8-10th, is recommended.

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