Special Announcements

Schedule

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
6:00-6:45Open bar - Blackford Bar
6:45-10:00 Course banquet - Hotchkiss Dining room, upstairs Blackford
 
Tuesday, October 25
after breakfast Depart

Everyone

Books Used in the Course

Programming Perl, 4th Edition
Tom Christiansen, Brian d foy, Larry Wall
O'Reilly & Associates

UNIX and PERL to the RESCUE
Keith Brandam, Ian Korf
Cambridge

Mastering Perl for Bioinformatics
James Tisdall
O'Reilly & Associates

Perl Pocket Reference, 5th Edition
Johan Vromans
O'Reilly & Associates

HTML5 Pocket Reference, 5th Edition
Johan Vromans
O'Reilly & Associates


Participants

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 HenryPrinceton Universitylucas.price.henry -- at -- gmail.com
Ken SavilleAlbion Collegeksaville -- at -- albion.edu
Emile Gluck-ThalerThe Ohio State Universitygluckthaler.1 -- at -- osu.edu
Courtney HershbergerCleveland Clinic Foundationhershbc -- at -- ccf.org
Carol AmatoUniversity of Colorado Denver AMCcarol.amato -- at -- ucdenver.edu
Sapan PatelMemorial Sloan Kettering Cancer Centersapanpharmacy -- at -- yahoo.com
Damian Almiron BonninNorris Cotton Cancer Center & Geisel School of MedDamian.Almiron -- at -- dartmouth.edu
Nicolai KroghUniversity of Copenhagennicolai -- at -- sund.ku.dk
Michael DrazerThe University of Chicago Medical Centermdrazer -- at -- medicine.bsd.uchicago.edu
Natasha PachecoUniversity of Alabama at Birminghamnpacheco -- at -- uab.edu
Alexander PocockUniversity of Queenslanduqapococ -- at -- uq.edu.au
Hassan SalemEmory Universityhssalem -- at -- emory.edu
Pedro LowensteinThe University of Michigan, Ann Arborpedrol -- at -- umich.edu
Tam QuachFeinstein Institute of Medical Researchtquach -- at -- nshs.edu
Yi-Jyun LuoOkinawa Institute of Science and Technologylocke.yj -- at -- gmail.com
Kimberly KrautkramerUniversity of Wisconsin-Madisonkkrautkramer -- at -- wisc.edu
Jessica LyonsUniversity of California, Berkeleyjblyons -- at -- berkeley.edu
Shasta WebbUniversity of Calgaryshasta.webb -- at -- ucalgary.ca
Katarzyna LepetaNencki Institute of Experimental Biologyk.lepeta -- at -- nencki.gov.pl
Karthickeyan Chella KrishnanUniversity of California, Los Angeleskchellakrishnan -- at -- mednet.ucla.edu
Masashi YamajiHHMI/The Rockefeller Universitymyamaji -- at -- rockefeller.edu

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