Workshop Program
Saturday, July 19
- 8:00-9:00 AM
- Breakfast in Mission Park Dining Hall for participants who arrive Friday night
- 9:00-10:00 AM
- Registration (Bagels, coffee, and juice available)
Science Atrium, Integrated Science Center (Thompson Labs) - 10:00 AM-Noon
- "Making sense of DNA and protein sequence analysis tools"
Tools: BLAST, sequence alignment, exon prediction, ScanProSite
Leader: Dave Baumler, University of Wisconsin
- Powerpoint Presentation (PowerPoint 2.3MB Jul21 08)
- NCBI MiniCourses #2
- Noon-1:30 PM
- Lunch (Mission Park Dining Hall)
- 1:30-3:30 PM
- "Identification of Disease Genes Using NCBI Resources"
Tools: OMIM, COG's, SNP's, MapViewer, gene expression databases
Leaders: Susan Singer (Carleton College) and Jodi Schwarz (Vassar College)
- link to Model of NCBI Entrez Databases
- link to NCBI Minicourses
- Intro to NCBI MapViewer (Microsoft Word 171kB Jul18 08)
- Intro to NCBI Entrez SNP (Microsoft Word 207kB Jul18 08)
- Intro to NBCI OMIM (Microsoft Word 176kB Jul18 08)
- Intro to NCBI COGs (Microsoft Word 643kB Jul18 08)
- Intro to NCBI Entrez GEO (Microsoft Word 921kB Jul18 08)
- 3:30-4:15 PM
- Break
- 4:15-5:45 PM
- Independent work with tools
- 6:00 PM
- Dinner (Mission Park Dining Hall)
Sunday, July 20
- 8:00-9:00 AM
- Breakfast in Spencer Living Room
- 9:00-10:30 AM
- "Microbial genome analysis and comparisons"
Tools: Microbial Genome Resource (NCBI), MAUVE, Enteropathogen Resource Integration Center
Leader: Dave Baumler
- Presentation (PowerPoint 7.7MB Jul21 08)
- NCBI MiniCourses #12
- Baumler modules and associated materials
- MAUVE users guide (Acrobat (PDF) 315kB Jul21 08)
- Understanding phage, the viruses that infect microorganisms, via genome alignments (PowerPoint 9.3MB Jul21 08)
- 10:30-11:00 AM
- Break
- 11:00-Noon
- "Microbial genome analysis and comparisons" continued
- Noon-1:30 PM
- Lunch in Mission Park Dining Hall
- 1:30-3:30 PM
- "Structural Analysis" tools
Tools: Conserved domain database search, others
Leader: Ranyee Chiang, University of California San Francisco
- Powerpoint presentation (PowerPoint 7.9MB Jul20 08)
- Hemoglobin Structural Analysis Activity (Microsoft Word 65kB Jul20 08)
- ModBase Activity (Microsoft Word 29kB Jul20 08)
- Meng list of sequence alignments
- http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/menutut.html
- 3:30-4:00 PM
- Break
- 4:00-5:30 PM
- "Structural analysis", continued and Independent work with tools
- 6:00 PM
- Barbeque in Science Quad
Monday, July 21
- 8:00-9:00 AM
- Breakfast in Mission Park Dining Hall
- 9:00-10:30 AM
- "Phylogenetic tree estimation"
Tools: MEGA
Leaders: Erica Crespi, Vassar College
Presentation (PowerPoint 8.2MB Jul22 08)
- 10:30-11:00 AM
- Break
- 11:00 AM-Noon
- Independent work with MEGA
- Noon-1:30 PM
- Lunch in Mission Park Dining Hall
- 1:30-3:30 PM
- Independent I3U development/Consultations with Assessment Consultant
Resource people: Ross Nehm (Ohio State University), Norm Bell (Williams College, wet-lab development), Workshop leaders - 3:30-4:00 PM
- Break
- 4:00-5:00 PM
- Independent I3U development/consultations, continued
- 5:00-6:00 PM
- "Open source community development of bioinformatics tools for genome analysis in an undergraduate setting"
Leaders: Gane Ka-Shu Wong and Paul Lu, University of Alberta
Crowdsourcing and Bioinformatics (Acrobat (PDF) 82kB Jul30 08) - 6:00 PM
- Banquet (Location TBA)
Keynote presentation: Panda genome project-From DNA sequence data to population dynamics and conservation
Gane Ka-Shu Wong
Keynote for 2008 Genomics Workshop (PowerPoint 5.9MB Jul21 08)
Tuesday, July 22
- 8:00-9:00 AM
- Breakfast in Mission Park Dining Hall
- 9:00-10:30 AM
- Independent I3U development/consultations, continued
- Assessment Resources
Pedagogy and Assessment Resources from SERC
- 10:30-11:00 AM
- Break
- 11:00 AM-Noon
- Independent I3U development/consultations, continued
- Noon-1:30 PM
- Lunch at Spice Root (Indian Buffet)
- August 20 - Activity sheet with title, author, summary, goals, context, and draft assessments in dev site
- Prior to teaching your i3U- Add description and activity files to your activity sheet
- Within 3 weeks of teaching your i3U - complete faculty reflection, complete teaching notes
- Prior to June workshop - finalize shareable version and request that activity sheet be made live
- June workshop to discuss experiences, provide input to white paper and overarching paper, writing time for group papers
- 1:30-2:30 PM
- Round table discussion on open source bioinformatics tool development
- 2:30-3:30 PM
- Independent I3U development/consultations, continued
- 3:30-4:00 PM
- Break
- 4:00-5:30 PM
- PERL: Uses in the classroom for DNA exploration
Leader: Mark LeBlanc, Wheaton College
presentation (PowerPoint 243kB Jul23 08)
collection of course materials (Zip Archive 437kB Jul23 08)
- 6:00 PM
- Dinner in Mission Park Dining Hall
Wednesday, July 23
- 8:00-9:00 AM
- Breakfast in Mission Park Dining Hall
- 9:00-10:00 AM
- Departure for participants not staying for PERL discussion
- 10:00 AM-Noon
- Discussion of effective strategies for teaching PERL
- Noon-1:00 PM
- Lunch at Thai Garden
- 1:00-3:30 PM
- Discussion of bioinformatics tool development for annotation
- 4:00 PM
- Departure