Special Announcements

Schedule

Sunday, October 9
7:00-8:00 Meet & Greet in the bar

Everyone
 
Monday, October 10
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
11:30-2:00 Lunch
2:00-3:30 Unix 2: Text Editors,Git for Beginners
Sofia
3:30-5:00 Unix II problem set

TAs
5:30-7:00 Dinner
7:00-8:00 Review Session: Unix tips and tricks Coding best practices

TAs
8:00-10:00 Problem Sets Unix

TAs
 
Tuesday, October 11
9:00-10:30 Python I: Overview, running python, syntax, data types and variables

Simon
10:30-12:30 Python I problem set

TAs
11:30-2:00 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 🏃 Run, Walk, Jog, Get Vitamin D and fresh air! 🏃
TAs
6:00-7:00 Dinner 🐟 🐟 🐟 🐟 🧅
7:00-8:00 Review Session

TAs
TAs
8:00-10:00 Problem Sets

TAs
 
Wednesday, October 12
9:00-10:30 Python III: Sequences, strings

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

TAs
11:30-2:00 Lunch
2:00-3:30 Python IV: Lists, tuples, loops

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

TAs
5:00-6:00 Wine and Cheese 🍷 🧀
6:00-7:00 Dinner
7:00-10:00 Problem Sets

TAs
 
Thursday, October 13
9:00-10:30 Python V: Dictionaries, sets

Sofia
10:30-11:30 Python V problem set

TAs
11:30-12:00 Python VI: I/O and files

Simon
12:00-12:30 Python VI problem set

TAs
12:30-2:00 Lunch
2:00-3:30 Python VII: regular expressions

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

TAs
5:00-6:00 Run, Walk, Jog, Get Vitamin D and fresh air:
TAs
6:00-7:00 Dinner
7:00-8:00 Review Session

TAs
8:00-10:00 Problem Sets

TAs
 
Friday, October 14
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
11:30-1:30 Lunch
1:30-3:00 Python X: Functions, Scope, and Modules

Simon
3:00-5:00 Python X Problem set
TAs
5:00-6:00 🏃 Run, Walk, Jog, Get Vitamin D and fresh air! 🏃
TAs
6:00-7:00 Dinner
7:00-8:00 Review Session

TAs
8:00-10:00 Problem Sets

TAs
 
Saturday, October 15
All day Free Time
Relax, have some fun!!

Everyone
 
Sunday, October 16
9:00-10:30 Python XI: Python XI

BioPython: BioPython

Sofia
10:30-12:30 Python XI Problem Set
BioPython Problem Set


TAs
11:30-2:00 Lunch
2:00-3:00 Next Gen Sequencing: Technologies

Molly Zeller
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


Simon
8:00-9:00 Any Problem Sets


TAs
 
Monday, October 17
9:00-10:30 Python Pipelines:

Simon
10:30-12:30 Workshop

TAs
11:30-2:00 Lunch
2:00-3:30 Genome Assembly: Part 1 Canu Assembler

Deb Triant
3:30-5:00
Genome Assembly Workshop
TAs
5:30-7:00 Dinner

7:00-7:45 Ethics And Reproducibility in Research

Simon
7:45-9:00
Any Problem Sets
TAs
Tuesday, October 18
9:00-10:30 🐛 Transcriptomes and RNAseq Part 1:

Brian Haas
10:30-12:30 Workshop

TAs
11:30-2:00 Lunch
2:00-3:30 🦋 Transcriptomes and RNAseq Part2:

Brian Haas
3:30-5:00 Workshop

TAs
5:30-7:00 Dinner

7:00-8:00 Problem Sets


TAs
 
Wednesday, October 19
9:30-10:00 Final Project Overview (In Hershey)

Simon and Sofia
11:00-11:30 Introduction to Jupyter Notebooks (In Hershey)

Cynthia
9:30-11:30 Work on Project Proposals/Problem Sets

TAs
11:30-2:00 Lunch
2:00-3:30 Image Processing (In Hershey)

Jay Unruh
3:30-5:30 Image Processing Workshop
5:30-7:00 Dinner
By 7:00pm Submit project proposal via email to Simon and Sofia

7:00-8:00 Open Source Software for Data Sharing (In Bush)

Scott Cain
8:30 Patio Party at Biondi

Everyone
 
Thursday, October 20
All day Free Time
Relax, have some fun!!

Everyone
 
Friday, October 21
9:00-11:00 Sequence Similarity Part1

Bill Pearson
11:00-12:30 Workshop

TAs
1:30-3:30 Sequence Similarity Part2

Bill Pearson
3:30-5:00 Workshop

TAs
5:30-7:00 Dinner
7:00-8:00 Project Signup and Room Rerrangement

TA
8:00-9:00 First Project Group Meeting

TAs
 
Saturday, October 22
9:00-11:30 Group Projects

Everyone
11:30-2:00 Lunch

Group Projects

Everyone
5:30-7:00 Dinner

Group Projects

Everyone
 
Sunday, October 23
9:00-11:30 Group Projects

Everyone
11:30-2:00 Lunch

Group Projects

Everyone
5:30-7:00 Dinner

Group Projects

Everyone
 
Monday, October 24
9:00-12:00 Group Projects

Everyone
11:30-2:00 Lunch
4:00-6:00 Project Presentations

Everyone
6:00-6:45 Cocktails in Blackford Bar
6:45-10:00 Course banquet
 
10:00-?  BIONDI DANCE PARTY PART DEUX 
 
Tuesday, October 25
after breakfast Depart

Everyone

Participants
Instructor Simon Prochnik Triplebar Biotechnology Inc. prochnik - at - gmail.com
Instructor Sofia Robb Stowers Institute for Medical Research smr - at - stowers.org
Teaching Assistant Jessen Bredeson jessenbredeson - at - gmail.com
Teaching Assistant Cynthia Cardinault Centro de Investigación Científica de Yucatán cyntsc10 - at - gmail.com
Teaching Assistant Zachary Konkel The Ohio State University konkel.8 - at - buckeyemail.osu.edu
Teaching Assistant Eric Ross HHMI ejr - at - stowers.org
Teaching Assistant Shasta Webb University of Notre Dame webbshasta - at - gmail.com
Lecturer Brian Haas Broad Institute bhaas - at - broadinstitute.org
Lecturer William Pearson University of Virginia wrp - at - virginia.edu
Lecturer Deborah Triant University of Missouri datriant - at - hotmail.com
Lecturer Jay Unruh Stowers Institute for Medical Research jru - at - stowers.org
Lecturer Molly Zeller University of Wisconsin-Madison zeller2 - at - wisc.edu
Student Bana Abolibdeh Michigan State University libdehba - at - msu.edu
Student Reed Alexander Middle Tennessee State University nra2q - at - mtmail.mtsu.edu
Student Elaine Aquino University of Nevada, Las Vegas aquine1 - at - unlv.nevada.edu
Student Christian Baca The Rockefeller University cbaca - at - rockefeller.edu
Student Melissa Bentley-Ford Atlant VA Healthcare System mrbentl - at - emory.edu
Student Irene Duba Rockefeller University iduba - at - mail.rockefeller.edu
Student Marleny Garcia Lozano Max Planck Institute for Biology marleny.garcia-lozano - at - tuebingen.mpg.de
Student Omar Gutierrez Ruiz Mayo Clinic Graduate School of Biomedical Sciences gutierrezruiz.omar - at - mayo.edu
Student Christina Heil University of Rochester Medical Center christina_heil - at - urmc.rochester.edu
Student Cassandra Herbert University of Cincinnati herbercr - at - mail.uc.edu
Student Nicholas Hilton University of California, Davis nhilton - at - ucdavis.edu
Student Jonathan Jacobs The Ohio State University jacobs.1080 - at - osu.edu
Student Jennifer Jahncke Oregon Health & Science University jahncke - at - ohsu.edu
Student Riley Kellermeyer Stowers Institute for Medical Research rkellermeyer - at - stowers.org
Student Dmitry Kretov Boston University School of Medicine dkretov - at - bu.edu
Student Kyle Leistikow Marquette University kyle.leistikow - at - marquette.edu
Student Meike Lobb-Rabe University of Chicago lobbrabe - at - uchicago.edu
Student Brianda Lopez Aviña University of Kentucky brianda.lavina - at - uky.edu
Student Aparna Mariyam Thomas University of Calgary aparna.mariyamthomas - at - ucalgary.ca
Student Daniel Murphy Washington University School of Medicine DMURPHY26 - at - wustl.edu
Student Mina Peyton University of Minnesota mina.peyton - at - gmail.com
Student Sarah Prostak University of Massachusetts Amherst sprostak - at - umass.edu
Student Carin Ragland Stanford University cragland - at - stanford.edu
Student Esra Sengul University of Oxford esra.sengul - at - dpag.ox.ac.uk
Student Alex Von Schulze The Stowers Institute for Medical Research avonschulze - at - stowers.org

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