Special Announcements

Schedule

Sunday, October 15
7:00-8:00 Meet & Greet in the bar

Everyone
 
Monday, October 16
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
7:00-9:30 Review Session: program structure

TAs
 
Tuesday, October 17
9:00-10:30 Python I: python1 overview, running python, PyCharm, syntax, data types and variables

Simon
10:30-12:00 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
dinner
7:00-9:30 Review Session:

TAs
 
Wednesday, October 18
9:00-10:30 Python III: sequences, strings, lists, tuples

Simon
10:30-12:00 Python III Problem set

TAs
lunch
2:00-3:30 Python IV: loops, dictionaries, sets

Sofia
3:30-5:00 Python IV Problem set

TAs
5:00-6:00 Wine and Cheese on Hershey upstairs veranda

Everyone
dinner
7:00-9:30 Review Session

TAs
 
Thursday, October 19
9:00-10:30 Python V: iterables, I/O and files

Simon
10:30-12:00 Python V problem set

TAs
lunch
2:00-3:30 Python VI: regular expressions

Sofia
3:30-5:00 Python VI problem set

TAs
dinner
7:00-9:30 Review Session

TAs
 
Friday, October 20
9:00-10:30 Python VII: Functions, scope, modules

Simon
10:30-12:00 Python VII problem set

TAs
lunch
2:00-3:30 Python VIII: exceptions, data structures

Simon
3:30-5:00 Python VIII problem set

TAs
dinner
7:00-9:30 Review Session

TAs
 
Saturday, October 21
All day Free Time
Relax, have some fun!!

Everyone
 
Sunday, October 22
9:00-10:30 Bioinf tools overview I: what's coming; define bioinf concepts: gene prediction, alignment, searching, assembly

Simon
10:30-12:00 Catch up on problem sets

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

Mike
3:30-5:00 NGS problem set

TAs
dinner
7:00-9:30 Review Session

TAs
Monday, October 23
9:00-10:30 Python IX: Biopython

Simon
10:30-12:00 Biopython problem set

TAs
lunch
2:00-3:30 bioinf tools overview II: GMOD and JBrowse

Scott Cain, Ontario Institute for Cancer Research
3:30-5:00 Managing Genomic Data
Sample Tripal install (GDR--Apple, strawberry, etc)
Sample JBrowse install (WormBase dev site)
Demo Apollo site (user:demo@demo.com, password demo)
Sample InterMine site (FlyMine)

Scott Cain, Ontario Institute for Cancer Research
7:00-7:45 Cocktails at the bar (associated with the splicing meeting)

7:45-9:00 banquet (No normal 5:30 - 7:30 dinner)

9:00-11:00? Field trip: Carrington's Genomics Research Station, Huntington

Everyone
 
Tuesday, October 24
9:00-10:30 Sequence Similarity Search I: Sequence similarity search I

Bill Pearson
10:30-12:00 Sequence Similarity Search workshop I
FASTA search web service
Most partial domains in proteins are alignment and annotation artifacts

Bill Pearson
lunch
2:00-3:30 Sequence Similarity Search II: Sequence similarity search I
alignment data
problems

Bill Pearson
5:30-5:45 Projects overview

dinner
7:00-9:30 Review Session Open questions

TAs
 
Wednesday, October 25
9:00-10:30 Ontologies: Controlled vocabulary
GO:Dowwnload annotations page
GO:Understanding the columns
GO:Gene Ontology Wiki
GO: LAGO - GO term finder
GO: DAVID - Over representation tool
GO: Making high level GO summaries
GO: Use and misuse of the gene ontology annotations S Rhee et al.
GO: Ten Quick Tips for Using the Gene Ontology
SO: Sequence Ontology
HPO: Human Phenotype Ontology
HPO: Browser
HPO: Phenomizer
OBO: Places to find biomedical ontologies
NCBO: Places to find biomedical ontologies

Karen Eilbeck, Univeristy of Utah
10:30-12:00 Ontology workshop
go file

Karen Eilbeck, Univeristy of Utah
lunch
2:00-3:30 Guest Lecture V: Ethics and Reproducibility in research

Jan Witkowski, Executive Director Banbury Centre, Cold Spring Harbor Laboratory
3:30-5:30 Genome Assembly: Genome Assembly

Deb
dinner
7:00 Project proposals due
7:00-9:00 Genome Assembly workshop

Deb
Thursday, October 26
All day Free Time
Relax, have some fun!!

Everyone
 
Friday, October 27
9:00-10:30 RNAseq: RNAseq

Brian Haas, The Broad Institute
10:30-12:00 RNAseq workshop I
Exercise 1: Counting kmers
Exercise 2: Estimating gene expression levels
Exercise 3: Filtering DE results

Brian Haas, The Broad Institute
lunch
2:00-4:00 RNAseq workshop II

Brian Haas, The Broad Institute
4:00-5:00 Guest Lecture: Structural Variation

Lukas Kuderna, Universitat Pompeu Fabra
5:5:30 Pizza dinner at Hershey (little vincents?)
5:30-6:00 project prep: Jupyter Notebooks

Simon
6:00-9:00 Student informal project discussion and costume prep

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

Everyone
 
Saturday, October 28
9:00-9:30 Signup for Final Project groups

Everyone
All day Group Projects

Everyone
2:00 Group Photo (meet at the back door of Hershey)

Everyone
All day Group Projects

Everyone
 
Sunday, October 29
All day Group Projects

Everyone
 
Monday, October 30
9:00-12:00 Group Projects

Everyone
lunch
2:00-4:00 Final Project wrap up

Everyone
4:00-6:00 Final Project Presentations - Hershey West

Everyone
6:00-6:45Open bar - Blackford Bar
6:45-10:00 Course banquet
 
Tuesday, October 31
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


Participants

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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
Michael Campbell Cold Spring Harbor Laboratory, Cold Spring Harbor, NY mcampbel -- at -- cshl.edu
Xengie Doan Stowers Institute for Medical Research, Kansas City, MO Xdo-- at -- stowers.org
Lukas Kuderna Universitat Pompeu Fabra, Bracelona, SPAIN lukas.kuderna -- at -- upf.edu>--
Demitri Muna Cold Spring Harbor Laboratory, Cold Spring Harbor, NY muna -- at -- cshl.edu
Deborah Triant University of Florida dtriant -- at -- virginia.edu
 
 
Guest Lecturers
Scott Cain Ontario Institute for Cancer Research, Medina, OH scott -- at -- scottcain.net
Karen Eilbeck University of Utah, Sale Lake City, UT keilbeck --at -- genetics.utah.edu
Brian Haas Broad Institute, Cambridge, MA bhaas -- at -- broadinstitute.org
WilliamPearson University of California, Davis, CA wrp --at-- virginia.edu
Tomas Marques-Bonet Universitat Pompeu Fabra, Barcelona, Spain tomas.marques -- at -- upf.edu