Programming for Biology 2019
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
| Monday, October 14 | |
|---|---|
| 7:00-8:00 | Meet & Greet in the bar
Everyone |
| Tuesday, October 15 | |
| Welcome & Orientation Simon Prochnik, Sofia Robb, and TAs |
|
| 9:00-10:30 | Unix 1: Unix Overview, The Basics, Advanced Unix Unix cheet sheet Simon |
| 10:30-12:30 | Unix I problem set sequences.nt.fa file for Unix I, problem 6 cuffdiff.txt file for Unix I, problem 10 TAs |
| Lunch | |
| 2:00-3:30 | Unix 2: Text Editors,Git for Beginners Sofia |
| 3:30-5:00 |
Unix II problem set TAs |
| Dinner | |
| 7:00-8:00 | Review Session: Unix tips and tricks
Coding best practices TAs |
| 8:00-10:00 | Problem Sets Unix TAs |
| Wednesday, October 16 | |
| 9:00-10:30 | Python I: Overview, running python, syntax, data types and variables Simon |
| 10:30-12:30 | Python I problem set TAs |
| Lunch | |
| 2:00-3:30 | Python II: Operators, truth, logic, numbers Sofia |
| 3:30-5:00 | Python II problem set TAs |
| 5:00-6:00 | No screen time social on Hershey upstairs balcony Everyone |
| 7:00-8:00 | Review Session TAs TAs |
| 8:00-10:00 | Problem Sets TAs |
| Thursday, October 17 | |
| 9:00-10:30 | Python III: Sequences, strings Simon |
| 10:30-12:30 | Python III Problem set TAs |
| Lunch | |
| 2:00-3:30 | Python IV: Lists, tuples, loops Sofia |
| 3:30-5:00 | Python IV Problem set TAs |
| 7:00-8:00 | Python V: Dictionaries, sets Sofia |
| 8:00-10:00 | Python V Problem set TAs |
| Friday, October 18 | |
| 9:00-10:30 | Python VI: I/O and files Simon |
| 10:30-12:30 | Python VI problem set TAs |
| Lunch | |
| 2:00-3:30 | Python VII: regular expressions Sofia |
| 3:30-5:00 | Python VII problem set TAs |
| 6:00-7:00 | Dinner: Pizza in Hershey |
| 7:00-8:00 | Review Session TAs |
| 8:00-10:00 | Problem Sets TAs |
| Saturday, October 19 | |
| 9:00-10:30 | Python VIII: Data structures Python IX: Exceptions Sofia |
| 10:30-12:30 | Python VIII Problem set Python IX Problem set TAs |
| Lunch | |
| 2:00-3:30 | Python X: Functions, Scope, and Modules Simon |
| 3:30-5:00 | Python X Problem set TAs |
| Dinner | |
| 7:00-8:00 | Review Session TAs |
| 8:00-10:00 | Problem Sets TAs |
| Sunday, October 20 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Monday, October 21 | |
| 9:00-10:30 | Python XI: Python XI BioPython: BioPython Sofia |
| 10:30-12:30 |
Python XI Problem Set
BioPython Problem Set TAs |
| Lunch | |
| 2:00-3:00 | Next Gen Sequencing: Technologies Anoja Perera |
| 3:00-4:00 | Next Gen Sequencing: File Types and Analysis Jessen Bredeson |
| 4:00-5:30 | NGS problem set TAs |
| 5:30-7:00 | Dinner |
| 7:00-8:00 | Introduction to Pandas Daniel |
| 8:00-9:00 | Unfinished Problem Sets TAs |
| 9:00-9:20 | Project Overview and Proposal Instructions Sofia & Simon |
| Tuesday, October 22 | |
| 9:00-10:30 | Sequence Similarity Part 1: Homology and Alignment Bill Pearson |
| 10:30-12:30 | Homology and Alignments Workshop TAs |
| Lunch | |
| 2:00-3:30 | Sequence Similarity Part 2: Protein Domains and Distant Relatives Bill Pearson |
| 3:30-5:00 | Protein Domains and Distant Relatives Workshop TAs |
| 5:30-7:00 | Dinner |
| 7:00-9:00 | Genome Assembly: Part 1 Deborah Triant |
| 9:00-10:00 | Genome Assembly Workshop: Part 1 TAs |
| Wednesday, October 23 | |
| 9:00-10:30 | Genome Assembly: Part 2 Deborah Triant |
| 10:30-12:30 | Genome Assembly Workshop: Part 2 TAs |
| Lunch | |
| 2:00-3:30 | Aligners Alex Dobin |
| 7:00-8:00 | Bioinformatics Useful Tools TAs |
| 8:30 | Tour of J.T. Carrington's Sequencing Centre Everyone |
| Thursday, October 24 | |
| 9:00-10:30 | RNAseq: part 1 Brian Haas |
| 10:30-12:30 | RNAseq Problem Set 1 |
| 11:00-12:00 | Group Photo: Meet on lawn behind Blackford |
| 12:30 | Lunch |
| 2:00-3:30 | RNAseq: Part 2 Brian Haas |
| 3:30-5:30 | RNAseq Problem Set 2 TAs |
| Dinner | |
| 6:45-7:45 | Ethics And Reproducibility in Research Simon |
| 8:00-10:00 | Work on Project Proposals and Problem Sets TAs |
| 12:00 | Turn in Project Proposals by Midnight |
| Friday, October 25 | |
| 9:00-11:00 | GMOD Scott Cain |
| 11:00-12:30 | GMOD Workshop TAs |
| 2:00-3:30 | Gene Function Annotation and Gene Set Analysis Huaiyu Mi |
| 3:30-5:30 | Gene Function Annotation and Gene Set Analysis Workshop TAs |
| 6:00-7:00 | Dinner: Italian Buffet in Hershey |
| 7:00-7:30 | Jupyter Lab Daniel |
| 7:30-8:00 | Project Signup and Room Rearrangement TAs |
| 9:00-Late | Halloween Party! (Clarkston Dinning Room) Everyone |
| Saturday, October 26 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Sunday, October 27 | |
| 9:00-10:00 | Science Lecture Tomas Marques-Bonet |
| Rest of the day | Group Projects Everyone |
| Monday, October 28 | |
| All day | Group Projects Everyone |
| Tuesday, October 29 | |
| 9:00-12:00 | Group Projects Everyone |
| Lunch | |
| 4:00-6:00 | Project Presentations Everyone |
| 6:00-6:45 | Cocktails in Blackford Bar |
| 6:45-10:00 | Course banquet |
| Wednesday, October 30 | |
| after breakfast | Depart Everyone |
| Instructors | ||
|---|---|---|
| Simon Prochnik | Intrexon, South San Francisco, 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, CA | jessenbredeson -- at -- berkeley.edu |
| Kirsten Gotting | University of Wisconsin - Madison, Madison, WI | gotting -- at -- wisc.edu |
| Joseph Orkin | Universitat Pompeu Fabra, Barcelona, Spain | joseph.orkin -- at -- upf.edu |
| Matthew Waas | University of Nebraska Medical Center, Omaha NE | waasmatthew -- at -- gmail.com |
| Shasta Webb | University of Calgary, Calgary, Canada | shasta.webb -- at -- ucalgary.ca |
| Daniel Diaz | Stowers Institute of Medical Research | ddiaz -- at -- stowers.org |
| Guest Lecturers | ||
| Scott Cain | Ontario Institute for Cancer Research, Medina, OH | scott -- at -- scottcain.net |
| Anoja Perera | Stowers Institute for Medical Research, Kansas City, MO | |
| Alexander Dobin | Cold Spring Harbor Laboratory, Cold Spring Harbor NY | |
| Brian Haas | Broad Institute, Cambridge, MA | bhaas -- at -- broadinstitute.org |
| Huaiyu Mi | University of Southern California, Los Angeles CA | huaiyumi --at-- usc.edu |
| Deborah Triant | University of Virgina, Chorlottesville, VA | |
| Bill Pearson | University of California, Davis, CA | wrp --at-- virginia.edu |
| Tomas Marques-Bonet | Universitat Pompeu Fabra, Barcelona, Spain | tomas.marques -- at -- upf.edu |