Programming for Biology 2016
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
| Sunday, October 9 | |
|---|---|
| 7:00-8:00 | Meet & Greet in the bar
Everyone |
| Monday, October 10 | |
| Welcome & Orientation Simon Prochnik, Sofia Robb, and TAs |
|
| 9:00-10:30 | Lecture: Intro to UNIX and Perl1:Program structure and good practices Simon, Sofia |
| 10:30-12:30 | Unix I problem set (cuffdiff.txt file for Unix I, problem 13) Unix I solutions Perl I problem set Perl I solutions TAs |
| lunch | |
| 2:00-3:30 | Perl II: Operators, functions, control structures, and processing the command line Simon, Sofia |
| 3:30-5:00 |
Perl II problem set Perl II solutions TAs |
| dinner | |
| 7:00-9:30 | Review Session: program structure TAs |
| Tuesday, October 11 | |
| 9:00-10:30 | Perl III: File I/O Simon, Sofia |
| 10:30-12:00 | Perl III problem set Perl III solutions TAs |
| lunch | |
| 2:00-3:30 | Perl IV: Arrays and loops Simon, Sofia |
| 3:30-5:00 | Perl IV problem set Perl IV solutions TAs |
| dinner | |
| 7:00-9:30 | Review Session: Perl Debugger Simon, Sofia |
| Wednesday, October 12 | |
| 9:00-10:30 | Perl V: Hashes Sofia |
| 10:30-12:00 | Perl V Problem set Perl V solutions TAs |
| lunch | |
| 2:00-3:30 | Perl VI: Regular expressions, split and join Sofia |
| 3:30-5:00 | Perl VI Problem set Perl VI solutions TAs |
| 5:00-6:00 | Wine and Cheese on Hershey upstairs veranda Everyone |
| dinner | |
| 7:00-9:30 | Review Session Vim tutorial Vim Simple Cheatsheet Vim Cheatsheet emacs tutorial emacs Simple Cheatsheet emacs cheatsheet Deb, Joseph |
| Thursday, October 13 | |
| 9:00-10:30 | Perl VII and Perl VIII: Modules and Subroutines: avoiding scope errors and using FileHandle, Getopts::Long, File::Basename Modules and Subroutines(2015) Perl VIII: Scope Simon |
| 10:30-12:00 | Perl VII problem set Solutions - Subroutines Perl VIII problem set Solutions - Modules TAs |
| lunch | |
| 2:00-3:30 | Perl IX: References Simon |
| 3:30-5:00 | Perl IX problem set Solutions - References TAs |
| dinner | |
| 7:00-9:30 | Review Session Simon, Sofia |
| Friday, October 14 | |
| 9:00-10:30 | Perl X: Objects Simon |
| 10:30-12:00 | Perl X problem set Solutions - Objects TAs |
| lunch | |
| 2:00-3:30 | Lecture: BioPerl Sofia |
| 3:30-5:00 | Bioperl problem set Solutions - BioPerl TAs |
| dinner | |
| 7:00-9:30 | Review: Hashes, FASTA files and other neat stuff original perl script perl script with a comment on every line PostData.pm module Jessen's solution Mike |
| Saturday, October 15 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Sunday, October 16 | |
| 9:00-10:30 | Lecture: HTML Additional HTML help Sofia |
| 10:30-12:00 | HTML Problem Set TAs |
| lunch | |
| 1:30-2:00 | Class photo: meet at back door of Hershey (South side) We'll have our photo taken on the lawn between Hershey and the main road |
| 2:00-3:30 | Lecture: CGI Programming Solutions - CGI Simon |
| 3:30-5:00 | CGI workshop TAs |
| dinner | |
| 7:00-9:30 | Guest Lecture I: Structural Variation Tomas Marques, Universitat Pompeu Fabra |
| 9:30-11:00 | Field trip: Carrington's Genomics Research Station, Huntington Everyone |
| Monday, October 17 | |
| 9:00-10:30 | Lecture: Next Gen Sequencing Eric |
| 10:30-12:00 | NGS problem set TAs |
| lunch | |
| 2:00-3:30 | Guest Lecture II: GMOD and JBrowse Scott Cain, Ontario Institute for Cancer Research |
| 3:30-5:00 | GMOD and JBrowse workshop Scott Cain, Ontario Institute for Cancer Research |
| dinner | |
| 7:00-7:15 |
Project overview |
| 7:15-9:30 |
Perl XI: Pipelines Simon |
| Tuesday, October 18 | |
| 9:00-10:30 | Guest Lecture III: Transcript Assembly I Brian Haas, Broad Institute |
| 10:30-12:00 | Transcript Assembly workshop I Brian Haas, Broad Institute |
| lunch | |
| 2:00-3:30 | Guest Lecture III: Transcript Assembly II Brian Haas, Broad Institute |
| 3:30-5:00 | Transcript Assembly workshop II Brian Haas, Broad Institute |
| dinner | |
| 7:00-9:30 | Review Session Open questions fastq_trimmer.pl fastq_qual_stats.pl Jessen |
| 10:30ish? | Submit project proposals email to Simon and Sofia before midnight Simon, Sofia |
| Wednesday, October 19 | |
| 9:00-10:30 | Guest Lecture IV: Metagenomics I Brandi Cantarel, UTSW |
| 10:30-12:00 | Metagenomics workshop Brandi Cantarel, UTSW |
| lunch | |
| 2:00-3:30 | Guest Lecture IV: Metagenomics II Brandi Cantarel, UTSW |
| 3:30-5:00 | Metagenomics workshop Brandi Cantarel, UTSW |
| dinner | |
| 7:00-8:00 | Guest Lecture V: Ethics and Reproducibility in research Jan Witkowski, Executive Director Banbury Centre, Cold Spring Harbor Laboratory |
| 8:00-10:00 | Problem sets Review Session |
| Thursday, October 20 | |
| 9:00-10:30 | Guest Lecture VII: BLAST Ian Korf, UC Davis |
| 10:30-12:00 | BLAST workshop Ian Korf, UC Davis |
| lunch | |
| 2:00-3:30 | Guest Lecture VII: BLAST Ian Korf, UC Davis |
| 3:30-5:00 | Programming task Programming task in mark down Ian Korf, UC Davis |
| dinner | |
| 7:00-9:30 | Review Session: Open questions TAs |
| Friday, October 21 | |
| All day | Free Time Relax, have some fun!! Everyone |
| 9:00-?:00 | Halloween Party!(Clarkston Dinning room) Everyone |
| Saturday, October 22 | |
| 9:00-9:30 | Signup for Final Project groups Everyone |
| All day | Group Projects Everyone |
| Sunday, October 23 | |
| All day | Group Projects Everyone |
| Monday, October 24 | |
| 9:00-12:00 | Group Projects Everyone |
| lunch | |
| 2:00-4:00 | Final Project wrap up Everyone |
| 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 25 | |
| after breakfast | Depart Everyone |
| Instructors | ||
|---|---|---|
| Simon Prochnik | DOE - Joint Genome Institute, Walnut Creek, CA | prochnik -- at -- gmail.com |
| Sofia Robb | Stowers Institute for Medical Research, Kansas City, MO | sofia2341 -- at -- gmail.com |
| Teaching Assistants | ||
| Jessen Bredeson | University of California, Berkeley | jessenbredeson -- at -- berkeley.edu |
| Michael Campbell | CSHL | mcampbel -- at -- cshl.edu |
| Wendy Ingram | University of California, Berkeley | wendy.m.ingram -- at -- gmail.com |
| Joseph Orkin | University of Calgary | joseph.orkin -- at -- ucalgary.ca |
| Eric Ross | Stowers Institute for Medical Research (HHMI), Kansas City, MO | ejr -- at -- stowers.org |
| Deborah Triant | University of Florida | dtriant -- at -- virginia.edu |
| Guest Lecturers | ||
| Scott Cain | Ontario Institute for Cancer Research, Medina, OH | scott -- at -- scottcain.net |
| Brandi Cantarel | UTSW, Dallas, TX | brandi.cantarel -- at -- baylorhealth.edu |
| Brian Haas | Broad Institute, Cambridge, MA | bhaas -- at -- broadinstitute.org |
| Ian Korf | University of California, Davis, CA | ifkorf -- at -- ucdavis.edu |
| Tomas Marques-Bonet | Universitat Pompeu Fabra, Barcelona, Spain | tomas.marques -- at -- upf.edu |
| Students | ||
| Luke Henry | Princeton University | lucas.price.henry -- at -- gmail.com |
| Ken Saville | Albion College | ksaville -- at -- albion.edu |
| Emile Gluck-Thaler | The Ohio State University | gluckthaler.1 -- at -- osu.edu |
| Courtney Hershberger | Cleveland Clinic Foundation | hershbc -- at -- ccf.org |
| Carol Amato | University of Colorado Denver AMC | carol.amato -- at -- ucdenver.edu |
| Sapan Patel | Memorial Sloan Kettering Cancer Center | sapanpharmacy -- at -- yahoo.com |
| Damian Almiron Bonnin | Norris Cotton Cancer Center & Geisel School of Med | Damian.Almiron -- at -- dartmouth.edu |
| Nicolai Krogh | University of Copenhagen | nicolai -- at -- sund.ku.dk |
| Michael Drazer | The University of Chicago Medical Center | mdrazer -- at -- medicine.bsd.uchicago.edu |
| Natasha Pacheco | University of Alabama at Birmingham | npacheco -- at -- uab.edu |
| Alexander Pocock | University of Queensland | uqapococ -- at -- uq.edu.au |
| Hassan Salem | Emory University | hssalem -- at -- emory.edu |
| Pedro Lowenstein | The University of Michigan, Ann Arbor | pedrol -- at -- umich.edu |
| Tam Quach | Feinstein Institute of Medical Research | tquach -- at -- nshs.edu |
| Yi-Jyun Luo | Okinawa Institute of Science and Technology | locke.yj -- at -- gmail.com |
| Kimberly Krautkramer | University of Wisconsin-Madison | kkrautkramer -- at -- wisc.edu |
| Jessica Lyons | University of California, Berkeley | jblyons -- at -- berkeley.edu |
| Shasta Webb | University of Calgary | shasta.webb -- at -- ucalgary.ca |
| Katarzyna Lepeta | Nencki Institute of Experimental Biology | k.lepeta -- at -- nencki.gov.pl |
| Karthickeyan Chella Krishnan | University of California, Los Angeles | kchellakrishnan -- at -- mednet.ucla.edu |
| Masashi Yamaji | HHMI/The Rockefeller University | myamaji -- at -- rockefeller.edu |