Programming for Biology
Suzi Lewis
Simon Prochnik
Jim Tisdall
Suzi Lewis
Simon Prochnik
Jim Tisdall
| Monday, October 11 | |
|---|---|
| Welcome & Orientation Suzi Lewis, Simon Prochnik, Jim Tisdall and TAs |
|
| 9:00-10:30 | Using Unix Simon |
| 10:30-12:00 | Problem Sets - files for problem sets TAs |
| lunch | |
| 2:00-3:30 | Perl I - Program structure, statements, variables Jim |
| 4:00-5:30 | Problem Sets TAs |
| dinner | |
| 7:00-8:00 | Meet & Greet in the bar |
| 8:00-9:00 | Review Session (optional) |
| 9:00-10:00 | Problem Sets TAs |
| Tuesday, October 12 | |
| 9:00-10:30 | Perl II - Conditionals, logical operators, loops and filehandles Suzi |
| 10:30-12:00 | Problem Set - file for problem #12 TAs |
| lunch | |
| 2:00-3:30 | Perl III - Arrays and Hashes Suzi |
| 4:00-5:30 | Problem Sets TAs |
| dinner | |
| 7:00-8:00 | Review Session (optional) - Review session source code - Problem set #1 source code |
| 8:00-10:00 | Problem Sets TAs |
| Wednesday, October 13 | |
| 9:00-10:30 | Perl IV - References Dave |
| 10:30-12:00 | Problem Sets TAs |
| lunch | |
| 2:00-4:30 | Perl V - Regular Expressions Jim |
| 5:00-6:00 | Wine and Cheese Everyone |
| dinner | |
| 7:00-8:00 | Review Session (optional) - Review session source code - Problem set #2 source code |
| 8:00-10:00 | Problem Sets TAs |
| Thursday, October 14 | |
| 9:00-10:30 | Perl VI - Subroutines and Modules Dave |
| 10:30-12:00 | Problem Sets TAs |
| lunch | |
| 2:00-3:30 | Perl VII - Object-oriented Perl Simon |
| dinner | |
| 7:00-8:00 | Scientific Programming Jim |
| 8:00-9:00 | Review Session (optional) - Problem set #3 source code |
| 8:30-10:00 | Problem Sets TAs |
| Friday, October 15 | |
| 9:00-10:30 | Bioperl I Sofia |
| 10:30-12:00 | Problem Sets TAs |
| lunch | |
| 2:00-3:30 | Bioperl II Sofia |
| 3:30-5:00 | Problem Sets TAs |
| dinner | |
| 7:00-8:00 | Review Session (optional) - Problem set #4 source code |
| 8:00-10:00 | Problem Sets TAs |
| Saturday, October 16 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Sunday, October 17 | |
| 9:00-11:00 |
DB Design and SQL Sheldon McKay, University of Arizona |
| 11:00-12:00 | Problem Sets TAs |
| lunch | |
| 2:00-3:30 | DBI Sheldon McKay, University of Arizona |
| 4:00-5:30 | Problem Sets TAs |
| dinner | |
| 7:00-8:30 | Perl Pipelines Simon |
| 8:30-18:00 | Review Session (optional) - Problem set #5 source code |
| 9:00-?:00 | Field trip - Carrington's Genomics Research Station, Huntington Everyone |
| Monday, October 18 | |
| 9:00-12:00 | HTML Jeremy |
| lunch | |
| 2:00-3:30 | CGI Sheldon McKay, CSHL |
| 3:30-5:00 | Problem Sets TAs |
| dinner | |
| 7:00-8:30 | SNP, new seq tech, Solexa I Stephane Deschamps, Dupont |
| 8:30-10:00 | Review Session (optional) - Problem set #6 source code TAs |
| Tuesday, October 19 | |
| 9:00-12:00 | Gbrowse: the generic genome browser Scott Cain, Ontario Inst. for Cancer Research |
| lunch | |
| 3:00 SHARP | Class Picture on the back patio |
| 2:00-4:00 | Next Gen Sequencing II Jeremy |
| 4:30-5:00 | Final Project Discussion Everyone |
| dinner | |
| 7:00-8:30 | Gene expression, transcript reconstruction, and analysis Win Hide, Harvard and SANBI |
| Wednesday, October 20 | |
| 9:00-12:00 | Sequence Similarity William Pearson, Univ of Virginia |
| lunch | |
| 2:00-3:30 | Sequence Similarity workshop William Pearson, Univ of Virginia |
| 4:30-5:30 | Final Project Presentations Everyone |
| dinner | |
| 7:05-8:30 | De Novo Short Read Assembly Jeremy |
| 8:45-9:00 | Final Project Assignment Announcement Instructors |
| 9:00-10:00 | Review Session (optional) - Problem set #7 source code |
| Thursday, October 21 | |
| 9:00-10:30 | Molecular Evolution I Emina Begovic |
| 10:30-12:00 | Problem Sets TAs |
| lunch | |
| 2:00-3:30 | Molecular Evolution II Emina Begovic |
| 3:30-5:00 | Problem Sets TAs |
| dinner | |
| 7:00-10:00 | Projects TAs |
| Friday, October 22 | |
| 9:00-10:30 | Genetic variation and deep sequencing Richard McCombie |
| 10:30-12:00 | Problem Sets TAs |
| lunch | |
| 2:00-3:30 | Introduction to R Jeremy |
| 3:30-5:00 | Projects TAs |
| dinner | |
| 8:00-?:00 | Halloween Party! TAs |
| Saturday, October 23 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Sunday, October 24 | |
| 9:00-12:00 | Projects TAs |
| lunch | |
| 2:00-3:30 | Ontologies Suzi |
| 2:00-5:00 | Projects TAs |
| dinner | |
| 7:00-8:30 | Protein Function, Panther Paul Thomas, SRI |
| Monday, October 25 | |
| 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 |
| All day | Projects TAs |
| Tuesday, October 26 | |
| 9:00-12:00 | Final Project Presentation Everyone |
| Instructors | ||
|---|---|---|
| Suzanna Lewis | University of California, Berkeley | suzi -- at -- berkeleybop.org |
| Simon Prochnik | University of California, Berkeley | prochnik -- at -- gmail.com |
| Jim Tisdall | DuPont Experimental Station | tisdall -- at -- tisdall.net |
| Tutors | ||
| Jer-Ming Chia | Cold Spring Harbor Laboratory | chia -- at -- cshl.edu |
| Ken Youens-Clark | Cold Spring Harbor Laboratory | kyclark.cshl -- at -- gmail.com |
| Ed Lee | University of California, Berkeley | elee -- at -- berkeleybop.org |
| Jeremy Leipzig | DuPont Crop Genetics/CHOP | leipzig -- at -- gmail.com |
| Dave Messina | Stockholm University | David.Messina -- at -- sbc.su.se |
| Sofia Robb | University of Utah | sofia -- at -- neuro.utah.edu |
| Jim Thomason | Cold Spring Harbor Laboratory | thomason -- at -- cshl.edu |
| Guest Lecturers | ||
| Emina Begovic | University of California, Berkeley | emina -- at -- socrates.berkeley.edu |
| Scott Cain | Ontario Institute for Cancer Research | scott -- at -- scottcain.net |
| Stephane Deschamps | DuPont Corporation | stephane.deschamps -- at -- cgr.dupont.com |
| Winston Hide | Harvard University, South African National Bioinformatics Institute | whide -- at -- hsph.harvard.edu |
| Sheldon McKay | University of Arizona | smckay -- at -- email.arizona.edu |
| Richard McCombie | Cold Spring Harbor Laboratory | mccombie -- at -- cshl.edu |
| William Pearson | University of Virginia | wrp -- at -- virginia.edu |
| Paul Thomas | SRI International | paul.thomas -- at -- sri.com |
| Students | ||
| Galeb Abu-Ali | US Food and Drug Administration | galeb.abu-ali -- at -- fda.hhs.gov |
| Batool Akhtar-Zaidi | Case Western Reserve University (CWRU) | bxa21 -- at -- case.edu |
| Stefan Ameres | University of Massachusetts Medical School | stefan.ameres -- at -- umassmed.edu |
| Marco Cristancho | National Center for Coffee Research - CENICAFÃ | marco.cristancho -- at -- cafedecolombia.com |
| Della David | University of California San Francisco | della.david -- at -- ucsf.edu |
| Angelica Maria Delgado Vega | Uppsala University | angelica.delgado -- at -- genpat.uu.se |
| Margaret Frank | Cornell University | mhf47 -- at -- cornell.edu |
| Zhanna Hakhverdyan | Rockefeller University | zhakhverdy -- at -- mail.rockefeller.edu |
| Anthony Hall | University of Liverpool | anthony.hall -- at -- liv.ac.uk |
| Anna Lopatina | Russian Academy of Sciences | night_sun -- at -- mail.ru |
| Iago Lowe | University of California Davis | izlowe -- at -- ucdavis.edu |
| David Lowry | University of Texas at Austin | davidbryantlowry -- at -- gmail.com |
| Zhuoyu Ni | Cornell University | zn12 -- at -- cornell.edu |
| Anne O'Donnell | Columbia University | aeo2102 -- at -- columbia.edu |
| Megumi Onishi-Seebacher | European Molecular Biology Laboratory | megumi.onishi.seebacher -- at -- embl.de |
| Magdalini Polymenidou | University of California in San Diego | mpolymen -- at -- ucsd.edu |
| Laura Robertson | U.S. Geological Survey (USGS) | lrobertson -- at -- usgs.gov |
| Nadin Rohland | Harvard Medical School | nrohland -- at -- genetics.med.harvard.edu |
| Shawn Rynearson | Eccles Institute of Human Genetics | shawn.rynearson -- at -- gmail.com |
| Julia Sandberg | Royal Institute of Technology, SciLife Lab | julia.sandberg -- at -- scilifelab.se |
| Andrea Schorn | Cold Spring Harbor Laboratory | aschorn -- at -- cshl.edu |
| Grace Teng | Yale University | grace.teng -- at -- yale.edu |