| Home | C. elegans | AcePerl | Gramene | Reactome | GMOD | Course | DAS | WWW |
Suzanna Lewis, PhD
Lincoln Stein, MD,PhD
James Tisdall, PhD
Simon Prochnik, PhD
October 20-November 2, 2004
Lectures meet in the Bush fireplace room.
Workshops are held in the Bush auditorium.
| WEDNESDAY OCTOBER 20 | |
|---|---|
| 9:00 | Welcome & Orientation Lincoln Stein |
| 9:30-11:00 | Using the UNIX Operating System 1 Files, directories, commands, text editors Lincoln Stein |
| 11:00-12:30 | Workshop: Getting to know UNIX Lincoln Stein, Tutors |
| 2:00-3:30 | Perl Scripting 1 Expressions, operators, basic I/O Simon Prochnik |
| 3:30-5:30 | Workshop: Perl basics Simon Prochnik, Tutors |
| 7:00-8:00 | Review Session Jan Aerts |
| 8:00-11:00 | Workshop: Perl/independent projects Tutors |
| THURSDAY OCTOBER 21 | |
| 9:00-10:00 | Using the UNIX Operating System 2 Input/Output Redirection, Command Pipes, Job and Process Control Simon Prochnik |
| 10:00-12:30 | Workshop: UNIX 2 Simon Prochnik, Tutors |
| 2:00-3:00 | Perl Scripting 2 Control structures: what is Truth? Jim Tisdall |
| 3:00-5:00 | Workshop: Perl Jim Tisdall |
| 7:00-8:00 | Review Session Mike Dybbs |
| 8:00-11:00 | Workshop: Perl/independent projects |
| FRIDAY OCTOBER 22 | |
| 9:00-10:00 | Perl Scripting 3 Arrays and Hashes Suzi Lewis |
| 10:00-12:30 | Workshop: Perl Suzi Lewis |
| 2:00-4:30 | Lecture: Sequence Similarity Analysis William Pearson |
| 4:30-6:00 | Wine & Cheese Reception Racker Room Blackford Hall |
| 7:00-8:00 | Perl Debugging Steven Lembark |
| 8:00-11:00 | Workshop: Perl/independent projects Tutors |
| SATURDAY OCTOBER 23 | |
| 9:00-10:00 | Lecture: The BLAST Algorithm Mark Yandell |
| 10:30-11:30 | Lecture: Interpreting BLAST Statistics Mark Yandell |
| 2:00-3:00 | Workshop: Sequence Similarity Analysis Jim Tisdall |
| 4:00-5:00 | Perl Scripting 4 Loops and Filehandles Jim Tisdall |
| 7:00-8:00 | Review Session Joshua Stein |
| SUNDAY OCTOBER 24 | |
| 9:00-2:00 | Free Time to Relax! |
| 2:00-3:00 | Perl Scripting 5 Regular Expressions Simon Prochnik |
| 3:00-4:00 | Brainstorming for final projects Lincoln Stein, Simon Prochnik |
| 7:00-8:00 | Perl Scripting 6 Subroutines Mike Dybbs |
| 8:00-11:00 | Workshop: Perl/Independent Projects Tutors |
| MONDAY OCTOBER 25 | |
| 9:00-11:00 | Final Project assignment Simon Prochnik, Lincoln Stein |
| 11:00-12:00 | Guest Lecture: The Tsao of Perl George Hartzell |
| 2:00-3:00 | Perl Scripting 7 Using Perl Modules Lincoln Stein |
| 3:00-5:30 | Workshop: Perl/independent projects Tutors |
| 7:00-8:00 | Publishing Biological Data on the Web 1: Writing in HTML George Hartzell |
| 8:00-11:00 | Workshop: Perl/independent projects Tutors |
| TUESDAY OCTOBER 26 | |
| 9:00-10:00 | Relational Databases 1: Introduction to Databases and SQL Suzi Lewis |
| 10:00-12:00 | Workshop: Databases and SQL Suzi Lewis |
| 2:00-3:00 | Lecture: Modeling Biological Data in Relational Databases Rob Peitzsch |
| 3:00-5:30 | Workshop: Relational databases Tutors |
| 7:00-8:00 | Relational Databases 2: Calling Relational Databases from Perl Jim Tisdall |
| 8:00-11:00 | Workshop: Perl/independent projects Tutors |
| WEDNESDAY OCTOBER 27 | |
| 9:00-10:00 | Guest Lecture: Biological Ontologies Michael Ashburner |
| 11:00-12:00 | The Tsao of Perl Simon Prochnik |
| 2:00-3:00 | Perl Scripting 8 References & Objects Brian O'Connor |
| 3:00-5:30 | Workshop: References and Objects Brian O'Connor |
| 7:00-8:00 | Bioperl 1 Aaron Mackey |
| 8:00-11:00 | Workshop: Bioperl 1 Tutors |
| THURSDAY OCTOBER 28 | |
| 9:00-10:00 | Bioperl 2 Aaron Mackey |
| 10:00-12:30 | Workshop: Bioperl 2 Aaron Mackey |
| 2:00-3:00 | Publishing Biological Data on the Web 2 CGI Scripting Lincoln Stein |
| 3:00-5:30 | Workshop: CGI Scripting Tutors |
| 7:00-8:00 | Writing Object-Oriented Modules Brian O'Connor |
| 8:00-11:00 | Workshop: Perl/independent projects Tutors |
| FRIDAY OCTOBER 29 | |
| 9:00-10:00 | Bioinformatics Programming: A Matter of Good Taste George Hartzell |
| 10:00-12:30 | Workshop: Stuff Scott Cain |
| 2:00-3:00 | Lecture: Bio::Graphics Scott Cain |
| 3:00-5:30 | Workshop: Generic Genome Browser Scott Cain |
| 9:00-11:00 | Independent Projects Tutors |
| SATURDAY OCTOBER 30 | |
| 9:00-10:00 | Lecture: Sequence Variation Analysis Gabor Marth |
| 10:00-12:30 | Workshop: Sequence Variation Analysis Gabor Marth |
| 2:00-3:00 | Lecture: Microarray Analysis Olga Troyanskay |
| 4:00-5:00 | Workshop: Microarray Analysis Olga Troyanskay & tutors |
| 7:00-8:00 | Mac OSX Software Installation Workshop Chihiro Yamada |
| 8:00-11:00 | Workshop: Perl/independent projects Tutors |
| SUNDAY OCTOBER 31 | |
| 9:00-12:30 | FREE: Relax! Do your laundry! See NYC! |
| 2:00-5:00 | FREE: Relax! Do your laundry! See NYC! |
| 7:00-8:00 | Answers to PERL Problems Rob Halgren |
| 9:00-11:00 | Independent projects Tutors |
| MONDAY NOVEMBER 1 | |
| 9:00-10:00 | Lecture: Gene Prediction Michael Brent |
| REST OF DAY | Independent projects Tutors |
| 6:00-?? | BANQUET Blackford Hall |
| TUESDAY NOVEMBER 2 | |
| 9:00-12:00 | PRESENT FINAL PROJECTS |
| Graduation Ceremony | |
| Name | Affiliation | Login |
|---|---|---|
| Ivan Acosta | Yale University | iacosta |
| Dimitra Chalkia | Pennsylvania State University | dchalkia |
| Mack Crayton III | UNC Chapel Hill | mcrayton |
| Richard Emes | University College London | remes |
| Marc Gillespie | St. John's University | gillespm |
| Gopal Gopinathrao | Cold Spring Harbor Laboratory | gopinath |
| Derek Goto | Cold Spring Harbor Laboratory | goto |
| William Hsiao | Simon Fraser University | hsiao |
| Belen Hurle | National Human Genome Research Institute | bhurle |
| Joseph Karalius | Seminis Vegetable Seeds | karalius |
| James Kelley | University of Cambridge | jkelley |
| Xialing Liu | The Netherlands Cancer Institute | xliu |
| Marina Mapelli | European Institute of Technology | mapelli |
| Tomas Marques | Universitat Pompeu Fabra | tmarques |
| Cora Mund | DKFZ | cmund |
| Nikolas Nikolaidis | Penn State University | nikolaid |
| Molly Przeworski | Brown University | przewors |
| Andrew Samuelson | Massachusetts General Hospital | samuelso |
| Kairi Tammoja | National Institue for Health Development | ktammoja |
| Soojin Yi | Georgia Institute of Technology | syi |
Funding for this course was provided by NIH grant IT15 HG00048-01. We also wish to thank: Wendy Crowley, Terry Grodzicker, Derek Johnson, Michael Townsend, David Stewart, Peter VanBuren and Andrea Stephenson.
| Home | C. elegans | AcePerl | Gramene | Reactome | GMOD | Course | DAS | WWW |
Lincoln D. Stein, lstein@cshl.edu