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 |