Programming for Biology 2014
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
| Sunday, October 12 | |
|---|---|
| 7:00-8:00 | Meet & Greet in the bar
Everyone |
| Monday, October 13 | |
| Welcome & Orientation Simon Prochnik, Sofia Robb, and TAs |
|
| 9:00-10:30 | Intro to Unix - Intro to UNIX Simon |
| 10:30-12:30 | Problem Set - Unix cuffdiff.txt Solutions - Unix TAs |
| lunch | |
| 2:00-4:00 | Perl I - Program structure, statements, variables, and Perl good practices Simon |
| 4:00-5:00 | Problem Set - Perl I Solutions - Perl I TAs |
| dinner | |
| 7:00-8:00 | Perl II - Operators, functions, control structures, and processing the command line Sofia |
| 8:00-10:00 | Problem Set - Perl II Solutions - Perl II TAs |
| Tuesday, October 14 | |
| 9:00-10:30 | Perl III - File I/O Dave |
| 10:30-12:00 | Problem Set - Perl III Perl_III.fasta Perl_III.fastq Perl_III.nobody.txt Solutions - Perl III TAs |
| lunch | |
| 2:00-3:30 | Perl IV - Arrays and lists Sofia |
| 3:30-5:00 | Problem Sets Solutions - Perl IV-Arrays TAs |
| 5:00-6:00 | Run (optional) |
| dinner | |
| 7:00-8:00 | Review Session - perl debugger tutorial |
| 8:00-10:00 | Problem Sets TAs |
| Wednesday, October 15 | |
| 9:00-10:30 | Perl V - Hashes Sofia |
| 10:30-12:00 | Problem Set Solutions - Hashes TAs |
| lunch | |
| 2:00-3:30 | Perl VI -
Regular expressions, split and join Sofia |
| 3:30-5:00 | Problem Sets Solutions - Regular Expressions TAs |
| 5:00-6:00 | Wine and Cheese on Hershey upstairs veranda Everyone |
| dinner | |
| 7:00-8:00 | Review Session (optional) Code from Ken's review session |
| 8:00-10:00 | Problem Sets TAs |
| Thursday, October 16 | |
| 9:00-10:30 | Perl VII - Subroutines, avoiding scope errors + Perl VIII - modules, use FileHandle, Getopts::Long, File::Basename Dave |
| 10:30-12:00 | Subroutines Problem Set Solutions - Subroutines Modules Problem Set Solutions - Modules TAs |
| lunch | |
| 2:00-3:30 | Perl IX - References Simon |
| 3:30-5:00 | Problem Set Solutions - References TAs |
| dinner | |
| 7:00-7:30 | Emacs tutorial Vim tutorial |
| 7:30-9:00 | Review Session (optional) Code from Simon's Review Session |
| 8:00-10:00 | Problem Sets TAs |
| Friday, October 17 | |
| 9:00-10:30 | Perl X - Objects Simon |
| 10:30-12:00 | Problem Set - Perl X Solutions - Objects TAs |
| 12:00 | Class Photo |
| lunch | |
| 2:00-3:30 | Perl XI - BioPerl Sofia |
| 3:30-5:00 | Problem Set - BioPerl Solutions - BioPerl TAs |
| 6:00 | Pizza in Hotchkiss Dining Room in Blackford Hall |
| 7:00-7:30 | Version Control, Git, and Github (optional) Dave |
| 7:30-9:00 | Review Session (optional) Simon passing references code example |
| Saturday, October 18 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Sunday, October 19 | |
| 9:00-10:30 | HTML Ken |
| 10:30-12:00 | Problem Set - HTML Solutions - HTML TAs |
| lunch | |
| 2:00-3:30 | CGI Simon |
| 3:30-5:00 | Problem Set - CGI Solutions - CGI TAs |
| dinner | |
| 7:00-8:30 | Structural Variation Tomas Marques, Pompeu Fabra |
| 9:00-11:00 | Field trip - Carrington's Genomics Research Station, Huntington Everyone |
| Monday, October 20 | |
| 9:00-10:30 | Introduction to Next Gen Sequencing and RNA-Seq Jason Stajich, UCR |
| 10:30-12:00 | Problem Set - RNA-Seq NGS lectures TAs |
| lunch | |
| 2:00-3:30 | VAAST Barry Moore, Univ of Utah |
| 3:30-5:00 | Problem Set VAAST TAs |
| dinner | |
| 7:00-8:30 | Interpreting VAAST Results Barry Moore, Univ of Utah |
| Tuesday, October 21 | |
| 9:00-12:00 | Sequence Similarity - Part 1 Sequence Similarity - Part 2 William Pearson, Univ of Virginia |
| lunch | |
| 2:00-3:30 | Sequence Similarity workshop Pearson sorting code William Pearson, Univ of Virginia |
| 3:30-5:00 | Problem Sets TAs |
| dinner | |
| 7:00-8:30 | Protein Annotation Paul Thomas, USC |
| Wednesday, October 22 | |
| 9:00-10:30 | IGV James Robinson, Broad Institute |
| 10:30-12:00 | Problem Set - IGV ZIP FILE TAs |
| 2:00-3:30 | JBrowse Scott Cain, Ontario Institute for Cancer Research |
| 3:30-5:00 | Jbrowse workshop Scott Cain, Ontario Institute for Cancer Research |
| 6:00 | Pizza in Hotchkiss Dining Room in Blackford Hall...Yay! |
| 7:00-8:30 | Perl XI - Pipelines Simon |
| 10:00 | Final project submissions due |
| 9:00-10:30 | Problem Sets TAs |
| Thursday, October 23 | |
| 9:00-12:00 | Genome Sequencing and Assembly Genome assembly workshop Mike Schatz, CSHL |
| lunch | |
| 2:00-3:30 | Trinity, RNA-Seq assembly More information on some of the topics Definition of SAM file format document samtools software suite Brian Haas, Broad Institute |
| 3:30-5:00 | Trinity assembly workshop part I VirtulBox setup Brian Haas, Broad Institute |
| dinner | |
| 7:00-8:30 | Trinity assembly workshop part II Trinity_programming_exercises Solutions - Trinity_programming_exercises Brian Haas, Broad Institute |
| Friday, October 24 | |
| All day | Free Time Relax, have some fun!! Everyone |
| 9:00-?:00 | Halloween Party! Everyone |
| Saturday, October 25 | |
| 9:00-9:30 | Final Project Signup Everyone |
| 9:30-12:00 | Projects TAs |
| lunch | |
| 2:00-5:00 | Projects TAs |
| dinner | |
| 7:00-10:00 | Projects TAs |
| Sunday, October 26 | |
| 9:00-12:00 | Projects TAs |
| lunch | |
| 2:00-5:00 | Projects TAs |
| dinner | |
| 7:00-10:00 | Projects TAs |
| Monday, October 27 | |
| 9:00-12:00 | Projects TAs |
| lunch | |
| 4:00-6:00 | Final Project Presentations - Hershey West Everyone |
| 6:00-6:45 | Open bar - Blackford Bar |
| 6:45-10:00 | Course banquet - Hotchkiss Dining room, upstairs Blackford |
| Tuesday, October 28 | |
| 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 | ||
| Steven Ahrendt | University of California, Riverside | sahrendt0 -- at -- gmail.com |
| Dave Messina | Cofactor Genomics | david_messina -- at -- cofactorgenomics.com |
| Shawn Rynearson | University of Utah | shawn.rynearson --- at -- gmail.com |
| Deborah Triant | University of Virginia | dtriant -- at -- virginia.edu |
| Ken Youens-Clark | University of Arizona | kyclark -- at -- gmail.com |
| Guest Lecturers | ||
| Scott Cain | Ontario Institute for Cancer Research | scott -- at -- scottcain.net |
| 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 |
| Tomas Marques | Universitat Pompeu Fabra | tomas.marques -- at -- upf.edu |
| Barry Moore | University of Utah | barry.moore -- at -- genetics dot utah dot edu |
| William Pearson | University of Virginia | wrp -- at -- virginia.edu |
| James Robinson | Broad Institute | jrobinso -- at -- broadinstitute.org |
| Michael Schatz | CSHL | mschatz -- at -- cshl.edu |
| Jason Stajich | University of California, Riverside | jason.stajich -- at -- ucr.edu |
| Paul Thomas | University of Southern California | pdthomas -- at -- usc.edu |
| Students | ||
| Mr. Oluwafemi Alaba | Institute of Tropical Agricultural Bioscience | o.alaba -- at -- cgiar.org |
| Dr. Jean-Denis Beaudoin | Yale University | Jean-Denis.Beaudoin -- at -- yale.edu |
| Dr. Javier del Campo | Institut de Ciències del Mar - CSIC | fonamental -- at -- gmail.com |
| Dr. Tenzin Gayden | McGill University | tenzin.gayden -- at -- mail.mcgill.ca |
| Mr. Tasos Gogakos | Rockefeller University | tasos.gogakos -- at -- gmail.com |
| Dr. Andrii Gryganskyi | Lambert Spawn Co. | Andrii.Gryganskyi -- at -- gmail.com |
| Dr. Markus Hafner | National Institutes of Health / NIAMS | markus.hafner -- at -- nih.gov |
| Dr. Elisabeth Hehenberger | University of British Columbia | helisabe -- at -- mail.ubc.ca |
| Mr. Matthew Hernandez | Icahn School of Medicine at Mount Sinai | matthew.hernandez -- at -- mssm.edu |
| Dr. Iker Irisarri | University of Konstanz | iker.irisarri -- at -- uni-konstanz.de |
| Dr. Scott Jackson | U.S. FDA | scott.jackson -- at -- nist.gov |
| Dr. Ryan Kepler | United States Department of Agriculture-ARS | rmkepler -- at -- gmail.com |
| Dr. Gulum Kosova | Massachusetts General Hospital | gkosova -- at -- mgh.harvard.edu |
| Mr. Patrick McLaughlin | Drexel University | patrickjmcl -- at -- gmail.com |
| Dr. Kevin Monahan | Columbia University | kevingmonahan -- at -- gmail.com |
| Mr. Joseph Orkin | Washington University in St. Louis | orkin -- at -- wustl.edu |
| Dr. Benjamin Schwessinger | UC Davis | bschwessinger -- at -- ucdavis.edu |
| Dr. Lesley Ann Sutton | Uppsala University | lesley.sutton -- at -- igp.uu.se |
| Dr. Luz Tavera-Mendoza | Dana-Farber Cancer Institute/Harvard Medical School | LuzE_Tavera -- at -- dfci.harvard.edu |
| Dr. Min Yue | University of Pennsylvania | yuemin -- at -- vet.upenn.edu |
| Mr. Buyun Zhao | University of Cambridge | bzhao -- at -- mrc-lmb.cam.ac.uk |
