Special Announcements

Schedule

Sunday, October 14
7:00-8:00 Meet & Greet in the bar

Everyone
 
Monday, 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

TAs
8:00-10:00 Problem Sets Unix

TAs
 
Tuesday, 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 Wine and Cheese on Hershey upstairs balcony

Everyone
6:00-7:00 Dinner: Pizza in Hershey
7:00-7:30 Text Editors

TAs
Emacs Presentation, Emacs Reference Card
VI Presentation, VI Commands Cheatsheet, VI Table Cheatsheet
7:30-8:30 Review Session

TAs
8:30-10:00 Problem Sets

TAs
 
Wednesday, 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
Dinner
7:00-8:00 Python V: Dictionaries, sets

Sofia
7:00-8:00 Review Session

TAs
8:00-10:00 Python V Problem set

TAs
 
Thursday, 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
Dinner
7:00-8:00 Review Session

TAs
8:00-10:00 Problem Sets

TAs
 
Friday, October 19
9:00-10:30 Python VIII: Data structures, exceptions

Sofia
10:30-12:30 Python VIII Problem set

TAs
Lunch
2:00-3:30 Python IX: Functions, Scope, Modules

Simon
3:30-5:00 Python IX Problem Set

TAs
Dinner
7:00-8:00 Review Session

TAs
8:00-10:00 Problem Sets

TAs
 
Saturday, October 20
All day Free Time
Relax, have some fun!!

Everyone
 
Sunday, October 21
9:00-10:30 Python X: Classes

BioPython: BioPython

Simon
10:30-12:30 Python X Problem Set
BioPython Problem Set


TAs
Lunch
2:00-3:30 Next Gen Sequencing: File formats: fasta, fastq, bam, vcf

Mike Campbell
3:30-5:30 NGS problem set

NGS workshop walkthrough

TAs
5:30-7:00 Dinner
7:00-9:00 Structural Variation

Tomas Marques
9:00-9:20 Project Overview and Proposal Instructions

Sofia & Simon
9:30 Tour of J.T. Carringtons Genome Resource Center, Huntington

ALL
Monday, October 22
9:00-10:30 Sequence Homology Part 1: Homology and Alignments

Brandi Cantarel
10:30-12:30 Homology and Alignments Workshop

TAs
Lunch
2:00-3:30 Sequence Homology Part 2: Protein Domains and Distant Relatives

Brandi Cantarel
3:30-5:00 Protein Domains and Distant Relatives Workshop

TAs
5:00-5:30 Genome Assembly, start running assembler before dinner

Debra Triant
5:30-7:00 Dinner

7:00-9:00 Genome Assembly

Debra Triant
9:00-10:00 Problem Sets/Finish Genome Assembly Workshop

TAs
 
Tuesday, October 23
9:00-10:30 Bioinformatics and Useful Tools
Simon
10:30-12:30 Work on old problem sets

TAs
Lunch
2:00- 5:00 Aligners

Alex Dobin
7:00-8:00 Review Session (optional - ask students)

TAs
7:00-10:00 Problems sets

TAs
 
Wednesday, October 24
Morning RNASeq

Brian Hass
Lunch
Afternoon Ontology problem set
GO file

Dinner
7:00-8:00 Ethics And Reproducibility in Research

Sofia
Simon
7:00-10:00 Problems sets

TAs
12:00 Turn in Project Proposals by Midnight

Thursday, October 25
Morning Bioinformatic Tools

Scott Cain
Afternoon and Evening Free Time
Relax, have some fun!!

Everyone
 
Friday, October 26
Morning Ontologies

Nicole Vasilevsky
Afternoon Protein Function and Annotation

Paul Thomas
5:00-6:00 Wine and Cheese
7:00-9:00 Start Projects: sign up, first group discussion, move tables

TAs
9:00-?:00 Halloween Party! (Clarkston Dinning room)

Everyone
 
Saturday, October 27
All day Group Projects

Everyone
 
Sunday, October 28
All day Group Projects

Everyone
 
Monday, October 29
9:00-12:00 Group Projects

Everyone
Lunch
9:00-12:00 Project Presentations

Everyone
6:45-10:00 Course banquet
 
Tuesday, 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


Valid XHTML 1.0 Strict

Instructors
Simon Prochnik Itrexon, South Sam Fransisco, 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 josephorkin -- at -- gmail.com
Lukas Kuderna Institue de Biologia Barcelona, Spain lukas.kuderna -- at -- upf.edu
Shasta Webb University of Calgary Calgary, Canada shasta.webb -- at -- ucalgary.ca
 
 
Guest Lecturers
Scott Cain Ontario Institute for Cancer Research, Medina, OH scott -- at -- scottcain.net
Michael Campbell
Brandi Cantarel UTSW Medical Center, Dallas TX
Alexander Dobin Cold Spring Harbor Laboratory, Cold Spring Harbor NY
Brian Haas Broad Institute, Cambridge, MA bhaas -- at -- broadinstitute.org
Tomas Marques-Bonet Universitat Pompeu Fabra Barcelona, Spain
Paul Thomas University of Southern California, Los Angeles CA
Deborah Triant University of Virgina, Chorlottesville, VA
Nicole Vasilevsky Oregon Health & Science University, Portland, OR
WilliamPearson University of California, Davis, CA wrp --at-- virginia.edu
Tomas Marques-Bonet Universitat Pompeu Fabra, Barcelona, Spain tomas.marques -- at -- upf.edu