Programming for Biology 2012
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
| Sunday, October 14 | |
|---|---|
| 7:00-8:00 | Meet & Greet in the bar
Everyone |
| Monday, October 15 | |
| Welcome & Orientation Simon Prochnik, Sofia Robb, and TAs |
|
| 9:00-10:30 | Intro to Unix - Intro to UNIX Perl I - Program structure, statements, variables, and Perl good practices Simon |
| 10:30-12:30 | Problem Set 1 Problem Set 2 TAs |
| lunch | |
| 2:30-4:00 | Perl II - Operators, functions, control structures, and processing the command line Dave |
| 4:00-5:00 | Problem Set TAs |
| dinner | |
| 7:00-8:00 | Review Session (optional) |
| 8:00-10:00 | Problem Sets TAs |
| Tuesday, October 16 | |
| 9:00-10:30 | Perl III - File I/O Note: these slides are updated with the corrections I made during lecture. Dave |
| 10:30-12:00 | Problem Set Perl_III.fasta Perl_III.fastq Perl_III.txt TAs |
| lunch | |
| 2:00-3:30 | Perl IV - Arrays and lists Sofia |
| 3:30-5:00 | Problem Sets TAs |
| dinner | |
| 7:00-8:00 | Review Session (optional) |
| 8:00-10:00 | Problem Sets TAs |
| Wednesday, October 17 | |
| 9:00-10:30 | Perl V - Hashes Sofia |
| 10:30-12:00 | Problem Set TAs |
| lunch | |
| 2:00-3:30 | Perl VI -
Regular expressions, split and join Sofia |
| 3:30-5:00 | Problem Sets TAs |
| 5:00-6:00 | Wine and Cheese on Hershey upstairs veranda Everyone |
| dinner | |
| 7:00-8:00 | Review Session I) perl debugger notes |
| 8:00-10:00 | Problem Sets TAs |
| Thursday, October 18 | |
| 9:00-10:30 | PerlVII - Subroutines, avoiding scope errors Eric |
| 10:30-12:00 | Problem Set TAs |
| lunch | |
| 2:30-3:30 | Perl VIII - Modules Dave |
| 3:30-5:00 | Problem Set TAs |
| dinner | |
| 7:00-8:00 | Review Session (optional) |
| 8:00-10:00 | Problem Sets TAs |
| Friday, October 19 | |
| 9:00-10:30 | Perl IX - References and multidimensional data Sofia |
| 10:30-12:00 | Problem Sets TAs |
| lunch | |
12:00-1:00 |
Field trip to Dolan Learning Center (optional) Anyone who is interested |
| 2:00-3:30 | Perl X - Objects Simon |
| 3:30-5:00 | Problem Set TAs |
| dinner | |
| 7:00-8:30 | Perl Pipelines Simon |
| 8:30-9:30 | Review Session (optional) |
| Saturday, October 20 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Sunday, October 21 | |
| 9:00-10:30 | Bioperl Sofia |
| 10:30-12:00 | Problem Sets TAs |
| lunch | |
| 2:00-3:30 | MySQL, databases, and DBI Jer-Ming Lecture Notes: PDF | HTML Problem Sets |
| dinner | |
| 7:00-8:00 | HTML Eric |
| 8:00-10:00 | Review Session Dave |
| Monday, October 22 | |
| 9:00-10:30 | Introduction to Next Gen Sequencing Jason Stajich, UCR |
| 10:30-12:00 | Problem Sets TAs |
| lunch | |
| 1:45-2:00 | Class Photograph, on the steps between Bush Auditorium and Blackford Bar Everyone |
| 2:00-3:30 | Haplotypes and Nucleotide Variants Gabor Marth, Boston College |
| 3:30-5:00 | Problem Sets TAs |
| dinner | |
| 7:00-8:30 | Structural Variation Tomas Marques, Pompeu Fabra |
| 9:00-?:00 | Field trip - Carrington's Genomics Research Station, Huntington Everyone |
| Tuesday, October 23 | |
| 9:00-12:00 | Sequence Similarity William Pearson, Univ of Virginia |
| 10:30-12:00 | Workshop William Pearson, Univ of Virginia |
| lunch | |
| 2:00-3:30 | Sequence Similarity workshop William Pearson, Univ of Virginia |
| 3:30-5:00 | Workshop TAs |
| dinner | |
| 7:00-8:30 | Scientific Computing Jim Tisdall, Course Instructor Emeritus |
| 8:30-10:00 | Review Session (optional) TAs |
| Wednesday, October 24 | |
| 9:00-10:30 | CGI Simon |
| 10:30-12:00 | Problem Sets TAs |
| 2:00-3:30 | GBrowse Scott Cain, Ontario Institute for Cancer Research |
| 3:30-5:00 | Gbrowse workshop Scott Cain, Ontario Institute for Cancer Research |
| dinner | |
| 7:00-8:30 | Protein Function Prediction and Annotation Paul Thomas, USC |
| 8:30-10:00 | Final Project Discussion Everyone |
| Thursday, October 25 | |
| 9:00-12:00 | Transcript Assembly Theory Win Hide, Harvard School of Public Health and SANBI |
| lunch | |
| 2:00-3:30 | Trinity, RNA-Seq assembly
More information on some of the topics Brian presented in his lecture: |
| 3:30-4:30 | Trinity assembly workshop part I Brian Haas, Broad Institute |
| dinner | |
| 7:00-8:30 | Trinity assembly workshop part II Brian Haas, Broad Institute |
| 8:30-9:00 | Final Project Assignment Announcement Instructors |
| Friday, October 26 | |
| All day | Free Time Relax, have some fun!! Everyone |
| 9:00-?:00 | Halloween Party! Everyone |
| Saturday, October 27 | |
| 9:00-12:00 | Projects TAs |
| lunch | |
| 2:00-5:00 | Projects TAs |
| dinner | |
| 7:00-10:00 | Projects TAs |
| Sunday, October 28 | |
| 9:00-12:00 | Projects TAs |
| lunch | |
| 2:00-5:00 | Projects TAs |
| dinner | |
| 7:00-10:00 | Projects TAs |
| Monday, October 29 | |
| 9:00-12:00 | Projects TAs |
| lunch | |
| 2:00-4:00 | Final Project Presentations Everyone |
| 6:00-6:45 | Open bar |
| 6:45-10:00 | Course banquet |
| Tuesday, October 30 | |
| after breakfast | Depart Everyone |
| Instructors | ||
|---|---|---|
| Simon Prochnik | DOE - Joint Genome Institute, Walnut Creek, CA | prochnik -- at --- gmail.com |
| Sofia Robb | University of California, Riverside | sofia.robb -- at --- ucr.edu |
| Tutors | ||
| Jessen Bredeson | University of California, Berkeley | jessenbredeson -- at --- berkeley.edu |
| Sarah Kocher | Harvard University | skocher -- at --- fas.harvard.edu |
| Dave Messina | Cofactor Genomics | david_messina -- at -- cofactorgenomics.com |
| Raghuraman Ramamurthy | University of California, Riverside | raghuramu6 -- at --- gmail.com |
| Shawn Rynearson | University of Utah | shawn.rynearson --- at -- gmail.com |
| Eric Ross | Stowers Institute | ejr -- at --- stowers.org |
| Deborah Triant | University of Virginia | dtriant -- at -- virginia.edu |
| Guest Lecturers | ||
| Scott Cain | Ontario Institute for Cancer Research | scott -- at -- scottcain.net |
| Jer-Ming Chia | Cold Spring Harbor Laboratory | chia -- at -- cshl.edu |
| Brian Haas | Broad Institute | bhaas -- at -- broad.mit.edu |
| Winston Hide | Harvard School of Public Health, South African National Bioinformatics Institute | whide -- at -- hsph.harvard.edu |
| Gabor Marth | Boston College | marth -- at -- bc.edu |
| Tomas Marques | Universitat Pompeu Fabra | tomas.marques -- at -- upf.edu |
| Richard McCombie | Cold Spring Harbor Laboratory | mccombie -- at -- cshl.edu |
| William Pearson | University of Virginia | wrp -- at -- virginia.edu |
| Jason Stajich | University of California, Riverside | jason.stajich -- at -- ucr.edu |
| Paul Thomas | University of Southern California | pdthomas -- at -- usc.edu |
| Jim Tisdall | support -- at -- jimtisdall.com | |
| Students | ||
| Gladys Andino | Purdue University | gandino -- at -- purdue.edu |
| Dr. Ariel Bazzini | Yale University | ariel.bazzini -- at -- yale.edu |
| Dr. Hossein Borhan | AAFC | hossein.borhan -- at -- agr.gc.ca |
| Dr. Keith Boundy | University of Massachusetts Medical School | keith.boundy -- at -- umassmed.edu |
| Dr. Brad Cavinder | University of California | bradc -- at -- ucr.edu |
| Ms. Molly Hall | The Pennsylvania State University | mah546 -- at -- psu.edu |
| Dr. Ryan Hartmaier | University of Pittsburgh | hartmaierr -- at -- upmc.edu |
| Ms. Mei-Yee Law | University of Utah | meiyee -- at -- neuro.utah.edu |
| Mr. Marco Leung | UT MD Anderson Cancer Center | mleung -- at -- mdanderson.org |
| Dr. Leslie Low | Malaysian Palm Oil Board | lowengti -- at -- mpob.gov.my |
| Laetitia Martin | Cornell University | lbm63 -- at -- cornell.edu |
| Phillip Murray | Yale University | phillip.murray -- at -- yale.edu |
| Mr. Mtakai Ngara | International Institute of Tropical Agriculture | m.ngara -- at -- cgiar.org |
| Dr. Gabrielle Nickel | Case Western Reserve University | gabrielle.nickel -- at -- case.edu |
| Mr. Matthew Oetjens | Vanderbilt University | matthew.t.oetjens -- at -- vanderbilt.edu |
| Mr. Kaushik Panda | The Ohio State University | panda.10 -- at -- osu.edu |
| Dr. Jasmine Seda Miro | Pontifical Catholic University of Puerto Rico | jasmine_seda -- at -- pucpr.edu |
| Dr. Sohela Shah | Memorial Sloan Kettering Cancer Center | shahs -- at -- mskcc.org |
| Ms. Ozge Tasdemir-Yilmaz | University of Massachusetts Medical School | ozge.tasdemir -- at -- umassmed.edu |
| Ms. Anna Zinovyeva | Umass Medical School | anna.zinovyeva -- at -- umassmed.edu |
