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
2:00-3:30 Aligners

Alex Dobin
3:30- 5:00 Aligners: STAR

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

TAs
7:00-10:00 Problems sets

TAs
 
Wednesday, October 24
9:00-10:30 RNASeq

Brian Hass
10:30-12:30 RNA-seq problem set

12:30 Lunch
2:00 Group Photo: Meet on lawn behind Blackford
Afternoon Continue Working on RNAseq Workshop followed by Problem sets
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
9:00-11:00 GMOD

Scott Cain
11:00-12:30 GMOD Workshop

TAs
Afternoon and Evening Free Time
Relax, have some fun!!

Everyone
 
Friday, October 26
9:00-11:00 Intro to Ontologies

Nicole Vasilevsky
11:00-12:30 Ontologies Workshop

TAs
Afternoon Protein Function and Annotation

Paul Thomas
5:00-6:00 Wine and Cheese sign up for projects
8:00-8:30 Start Projects: 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
4:00-6:00 Project Presentations

Everyone
6:00-6:45 Cocktails in Blackford Bar
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


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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 joseph.orkin -- at -- ucalgary.ca
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 Campbell10X Genomicskeilbeck --at -- genetics.utah.edu
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
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