Special Announcements

Schedule

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

Books Used in the Course

Learning Python, 5th Edition
Mark Lutz
O'Reilly & Associates

The Linux Command Line
William E. Shotts. Jr.
No Starch Press

Python Cookbook, 3rd Edition
Brian Jones, David Beazley
O'Reilly & Associates


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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