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
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
1:30-2:00 Class photo: meet at back door of Hershey (South side)
We'll have our photo taken on the lawn between Hershey and the main road
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 GMOD and JBrowse workshop

Scott Cain, Ontario Institute for Cancer Research
dinner
7:00-7:15 Project overview

7:00-9:30 Review Session

TAs
 
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

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

Bill Pearson
10:30-12:00 Sequence Similarity Search workshop II

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

TAs
10:30ish? Submit project proposals
email to Simon and Sofia before midnight

Simon, Sofia
 
Wednesday, October 25
9:00-10:30 Ontologies: Controlled vocabulary

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

Karen Eilbeck, Univeristy of Utah
lunch
2:00-3:30 Genome Assembly: Genome Assembly

Deb
3:30-5:00 Genome Assembly workshop

Deb
dinner
7:00-8:00 Guest Lecture V: Ethics and Reproducibility in research

Jan Witkowski, Executive Director Banbury Centre, Cold Spring Harbor Laboratory
8:00-10:00 Problem sets
Review Session

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

Brian Haas, The Broad Institute
lunch
2:00-3:30 Variant calling Variant calling
3:30-5:00 Programming task
dinner
7:00-9:30 Guest Lecture I: Structural Variation

Tomas Marques, Universitat Pompeu Fabra
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
 
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 - Hotchkiss Dining room, upstairs Blackford
 
Tuesday, October 31
after breakfast Depart

Everyone

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