Programming for Biology 2011
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Jim Tisdall
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Jim Tisdall
| Sunday, October 16 | |
|---|---|
| 7:00-8:00 | Meet & Greet in the bar
Everyone |
| Monday, October 17 | |
| Welcome & Orientation Simon Prochnik, Jim Tisdall, Sofia Robb, and TAs |
|
| 9:00-10:30 | Using Unix
and Perl I - Program structure, statements, variables, and Perl good practices Simon |
| 10:30-12:30 | Problem Set 1 - Solutions Problem Set 2 - Solutions TAs |
| lunch | |
| 2:30-4:00 | Perl II - Operators, functions, control structures, and processing the command line Dave |
| 4:00-5:00 | Problem Set - Solutions TAs |
| dinner | |
| 7:00-8:00 | Review Session (optional) - Script structure, indentation, commenting your code - Source code |
| 8:00-10:00 | Problem Sets TAs |
| Tuesday, October 18 | |
| 9:00-10:30 | Perl III - File I/O Dave |
| 10:30-12:00 | Problem Set - Solutions TAs |
| lunch | |
| 2:00-3:30 | Perl IV - Arrays and lists Sofia |
| 3:30-5:00 | Problem Sets - Sample FASTA alignment for problem 2 - Solutions TAs |
| dinner | |
| 7:00-8:00 | Review Session (optional) - the Perl debugger and general review - Source code |
| 8:00-10:00 | Problem Sets TAs |
| Wednesday, October 19 | |
| 9:00-10:30 | Perl V - Hashes Sofia |
| 10:30-12:00 | Problem Set - Solutions expression data file TAs |
| lunch | |
| 2:00-3:30 | Perl VI - Regular expressions, split and join Sofia |
| 3:30-5:00 | Problem Sets - Solutions Sample Simple Fasta Parser TAs |
| 5:00-6:00 | Wine and Cheese in Blackford fireplace room (go inside front door and turn right) Everyone |
| dinner | |
| 7:00-8:00 | Review Session (optional) - Source code |
| 8:00-10:00 | Problem Sets TAs |
| Thursday, October 20 | |
| 9:00-10:30 | Perl VII - Subroutines, avoiding scope errors
- Lecture code (including example of returning multiple hashes) Ed |
| 10:30-12:00 | Problem Sets - Solutions TAs |
| lunch | |
| 2:00-2:30 | Class Photo Everyone |
| 2:30-3:30 | Perl VIII - Modules Ashley Shawn |
| 3:30-5:00 | Problem Set - Solutions TAs |
| dinner | |
| 7:00-8:00 | Review Session (optional) - Source code |
| 8:00-10:00 | Problem Sets TAs |
| Friday, October 21 | |
| 9:00-10:30 | Perl IX - References and multidimensional data Simon |
| 10:30-12:00 | Problem Sets - Solutions TAs |
| lunch | |
| 2:00-3:30 | Perl X - Objects Simon |
| 3:30-5:00 | Problem Sets TAs |
| dinner | |
| 7:00-8:30 | Perl Pipelines Simon |
| 9:00-?:00 | Halloween Party! Everyone |
| Saturday, October 22 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Sunday, October 23 | |
| 9:00-10:30 | Bioperl Sofia |
| 10:30-12:00 | Problem Sets Scripts TAs |
| lunch | |
| 2:00-5:00 | GBrowse Scott Cain, Ontario Institute for Cancer Research |
| dinner | |
| 7:00-8:00 | HTML Eric |
| 8:00-10:00 | Review Session - Source code Dave |
| Monday, October 24 | |
| 9:00-10:30 | CGI Simon |
| 10:30-12:00 | Problem Sets TAs |
| lunch | |
| 2:00-3:30 | MySQL, databases, and DBI Jer-Ming |
| 3:30-5:00 | Problem Sets TAs |
| dinner | |
| 6:00-7:00 | Samtools Scott |
| 7:00-8:30 | Scientific Programming Jim |
| 8:30-10:00 | Work on Final Project Proposals Everyone |
| Tuesday, October 25 | |
| 9:00-12:00 | Sequence Similarity William Pearson, Univ of Virginia |
| 10:30-12:00 | Problem Sets William Pearson, Univ of Virginia |
| lunch | |
| 2:00-3:30 | Sequence Similarity workshop William Pearson, Univ of Virginia |
| 3:30-5:00 | Problem Sets TAs |
| dinner | |
| 7:00-10:00 | Free Time or more time for brainstorming and working on project proposals Everyone |
| Wednesday, October 26 | |
| 9:00-10:30 | Next Gen Sequencing I - Introduction Win Hide, Harvard and SANBI |
| 10:30-12:00 | Next Gen Sequencing II part 1 - Theory: Introduction to Galaxy Oliver Hofmann, Harvard |
| lunch | |
| 2:00-5:00 | Next Gen Sequencing II part 2 - Practice: Learn how to use the system, set up accounts, import and manipulate data. Oliver Hofmann, Harvard |
| dinner | |
| 7:00-8:30 | Next Gen Sequencing III - Quality control and alignment Oliver Hofmann, Harvard |
| Thursday, October 27 | |
| 9:00-12:00 | Next Gen Sequencing IV - Reviewing alignments and examining variants Oliver Hofmann, Harvard |
| lunch | |
| 2:00-3:30 | Next Gen Sequencing V - More on variants, annotating SNPs, identifying novel SNPs Oliver Hofmann, Harvard |
| dinner | |
| 7:00-8:30 | Fun with Next Gen Sequencing Richard McCombie, Cold Spring Harbor Laboratory |
| Friday, October 28 | |
| 9:00-9:30 | Final Project Assignment Announcement Instructors |
| 9:30-12:00 | Projects TAs |
| lunch | |
| 2:00-5:00 | Projects TAs |
| dinner | |
| 7:00-10:00 | Projects TAs |
| Saturday, October 29 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Sunday, October 30 | |
| 9:00-12:00 | Projects TAs |
| lunch | |
| 2:00-5:00 | Projects TAs |
| dinner | |
| 7:00-10:00 | Projects TAs |
| Monday, October 31 | |
| 9:00-12:00 | Projects TAs |
| lunch | |
| 2:00-5:00 | Projects TAs |
| 6:00-6:45 | Open bar |
| 6:45-8:00 | Course banquet |
| Tuesday, November 1 | |
| 9:00-12:00 | Final Project Presentations Everyone |
| lunch | |
| after lunch | Depart Everyone |
| Instructors | ||
|---|---|---|
| Simon Prochnik | DOE - Joint Genome Institute, Walnut Creek, CA | prochnik -- at -- gmail.com |
| Jim Tisdall | tisdall -- at -- tisdall.net | |
| Sofia Robb | University of California, Riverside | sofia.robb -- at -- ucr.edu |
| Tutors | ||
| Jer-Ming Chia | Cold Spring Harbor Laboratory | chia -- at -- cshl.edu |
| Ed Lee | University of California, Berkeley | elee -- at -- berkeleybop.org |
| Dave Messina | Stockholm University | david.messina -- at -- sbc.su.se |
| Eric Ross | Stowers Institute | ejr -- at -- stowers.org |
| Shawn Rynearson | University of Utah | shawn.rynearson -- at -- gmail.com |
| Ashley Wolf | Harvard University | arwolf -- at -- chgr.mgh.harvard.edu |
| Guest Lecturers | ||
| Scott Cain | Ontario Institute for Cancer Research | scott -- at -- scottcain.net |
| Winston Hide | Harvard School of Public Health, South African National Bioinformatics Institute | whide -- at -- hsph.harvard.edu |
| Oliver Hofmann | Harvard School of Public Health | ohofmann -- at -- hsph.harvard.edu |
| Richard McCombie | Cold Spring Harbor Laboratory | mccombie -- at -- cshl.edu |
| William Pearson | University of Virginia | wrp -- at -- virginia.edu |
| Students | ||
| Methode Bacanamwo | Morehouse School of Medicine | mbacanamwo -- at -- msm.edu |
| Carrie Buchanan | Vanderbilt University | carriecb -- at -- gmail.com |
| David Ciarlariello | The Ohio State University | ciarlariello.1 -- at -- osu.edu |
| Laurel Cooper | Oregon State University | cooperl -- at -- science.oregonstate.edu |
| Julia Yue Cui | University of Kansas Medical Center | ycui -- at -- kumc.edu |
| Frida Danielsson | Royal Institute of Technology - KTH | frida.danielsson -- at -- scilifelab.se |
| Julie Dutil | Ponce School of Medicine | jdutil -- at -- psm.edu |
| Kurt Hetrick | Johns Hopkins University | khetric1 -- at -- jhmi.edu |
| Siva Jetty | The University of Arizona | jettyr -- at -- ag.arizona.edu |
| Vijai Joseph | Memorial Sloan-Kettering Cancer Center | josephv -- at -- mskcc.org |
| Sarah Kocher | Harvard University | skocher -- at -- gmail.com |
| Jonathan (Alex) Pasternak | University of Alberta - EmbryoGENE | Jap -- at -- ualberta.ca |
| Sophie Plouviez | Duke University Marine Laboratory | sophie.plouviez -- at -- duke.edu |
| Davida Smyth | NYU | davida.smyth -- at -- med.nyu.edu |
| Shawn Thatcher | University of Delaware | shawnrt -- at -- udel.edu |
| Luz Rosalina Tincopa Marca | Leipzig University | rosalina -- at -- bioinf.uni-leipzig.de |
| Deborah Triant | University of Virginia | dtriant -- at -- virginia.edu |
| Patrick Tschopp | Harvard Medical School | tschopp -- at -- genetics.med.harvard.edu |
| Helen Wright | University of Liverpool | hlwright -- at -- liv.ac.uk |
| Bin Zhang | Cold Spring Harbor Laboratory | bzhang -- at -- cshl.edu |
| Zhao Zhang | University of Massachusetts Medical School | zhao.zhang -- at -- umassmed.edu |