Special Announcements

Schedule



Everyone

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

Everyone
 
Monday, October 16
9:00 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
12:30-2:00 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 Meet the instructors, Review Session: Unix tips and tricks, Coding best practices

TAs
8:00-10:00 Problem Sets: Continue Unix

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

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

TAs
12:00-2:00 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 Wine and Cheese 🍷 🧀
6:00-7:00 Dinner
7:00-8:00 Review Session

TAs
8:00-10:00 Problem Sets

TAs
 
Wednesday, October 18
9:00-10:30 Python III: Sequences, strings

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

TAs
12:00-2:00 Lunch
2:00-3:30 Python IV: Lists, tuples, loops

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

TAs
5:00-6:00 ☀ Go outside! Rest your eyeballs 👁👁, Run, Walk, Jog
6:00-7:00 Dinner
7:00-8:30 Python V: Dictionaries, sets

Sofia
8:30-10:00 Python V problem set

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

Simon?
10:30-12:00 Python VI problem set

TAs
12:00-2:00 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 20
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
12:30-2:00 Lunch
2:00-3:00 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 Miniconda package manager

Jessen
8:00-9:00 Problem sets

TAs
9:00-10:00 Party! 💃🕺🪩

Everybody
 
Saturday, October 21
Free day Relax, have some fun!!

Everyone
 
Sunday, October 22
9:00-10:30 Python XI: Python XI, classes

BioPython: BioPython

Sofia
10:30-12:00 Python XI Problem Set
BioPython Problem Set

TAs
12:00-2:00 Lunch
2:00-3:00 Next Gen Sequencing: Technologies

Anoja Perera
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

8:00-9:00 Problem Sets

TAs
 
Monday, October 23
9:00-10:30 Bioinformatics 1, Python Pipelines:Bioinformatics tools

Simon
10:30-12:00 Problem Sets

TAs
12:00-2:00 Lunch
2:00-3:30 Genome Assembly: Part 1 Canu Assembler

Deb Triant
3:30-5:00 Genome Assembly Workshop: Workshop link

TAs
5:00-7:00 Dinner

7:00-8:30 Genome Assembly: Part 2 Canu Assembler

Deb Triant
7:00-10:00 Problem Sets
TAs
Tuesday, October 24
9:00-10:30 🐛 Transcriptomes and RNAseq Part 1:

Brian Haas
10:30-12:00 Workshop

TAs
12:00-2:00 Lunch
2:00-3:30 🦋 Transcriptomes and RNAseq Part2:

Brian Haas
3:30-5:00 Workshop

TAs
5:00-7:00 Dinner

7:00 - 10:00 Problem Sets
Student Collaboration night (TA night off): It is an excellent learning experience to help others find and fix bugs. Try explaining a concept.
 
Wednesday, October 25
9:00-10:30 GO Terms and Phylogeny

Paul Thomas
10:30-12:00 Functional annotation workshop

TAs
12:00-1:45 Lunch
1:45-2:00 📷Course Photo: Meet at Hershey, downstairs, north door

Everyone
2:00-3:30 Open Source Software for Data Sharing

Scott Cain
3:30-5:00 Continuation of protein functional annotation workshop

TAs
5:00-7:00 Dinner
7:00-8:30 Analysis of non-coding RNA and repetitive sequences in the genome

Andrea Schorn
8:30 - 10:00 Problem Sets

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

Everyone
 
Friday, October 27
9:00-11:00 Sequence Similarity Part1

Bill Pearson
11:00-12:00 Gene homology workshop

TAs
12:00-1:30 Lunch
1:30 Project Proposals Due

email to smr -at- stowers.org and prochnik -at- gmail.com
1:30-3:30 Sequence Similarity Part2

Bill Pearson
3:30-5:00 Gene homology Workshop Pt 2

TAs
5:00-7:00 Dinner
7:00-9:00 Image Processing

Jay Unruh

Image Processing Workshop

🎃Halloween Party👻 (Bush)
 
Saturday, October 28
8:30-9:00 Project sign ups
9:00 Room Rerrangement

TA
9:00-10:00 First Project Group Meeting

TAs
10:00-12:00 Group Projects

Everyone
12:00-2:00 Lunch
2:00-5:00
Group Projects

Everyone
5:00-7:00 Dinner
7:00-9:00
Group Projects

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

Everyone
12:00-2:00 Lunch
2:00-5:00
Group Projects

Everyone
6:00-8:00 🍕CSHL Pizza Party🍕
 
Monday, October 30
9:00-12:00 Group Projects

Everyone
12:00-2:00 Lunch
3:30-5:30 Project Presentations
20 min final presentations per group
Everyone
5:30-6:00 Graduation

Everyone
6:00-6:45 Cocktails in Bar
6:45-9:00 Course banquet
9:00-????? DJ and Dancing in Biondi 🕺
 
 
Tuesday, October 31
after breakfast Depart (we love you but go home)

Everyone

Participants
Instructor Simon Prochnik Serenity Comp Bio prochnik - at - gmail.com
Instructor Sofia Robb Stowers Institute for Medical Research smr - at - stowers.org
Teaching Assistant Jessen Bredeson DOE Joint Genome Institute jessenbredeson - at - gmail.com
Teaching Assistant Kirsten Gotting LifeMine gotting - at - wisc.edu
Teaching Assistant Eric Ross Stowers Institute for Medical Research ejr - at - stowers.org
Teaching Assistant Riley Kellermeyer Stowers Institute for Medical Research rileykellermeyer - at - gmail.com
Lecturer Brian Haas Broad Institute bhaas - at - broadinstitute.org
Lecturer Bill Pearson University of Virginia wrp - at - virginia.edu
Lecturer Deb Triant University of Virginia datriant - at - virginia.edu
Lecturer Jay Unruh Stowers Institute for Medical Research jru - at - stowers.org
Lecturer Anoja Pererar Stowers Institute for Medical Research agp - at - stowers.org
Lecturer Andrea Schorn Cold Spring Harbor Laboratory aschorn - at - cshl.edu
Lecturer Paul Thomas University of Southern California pdthomas - at - usc.edu
Participant Melinda Angus-Hill Allen Institute melinda.angushill - at - alleninstitute.org
Participant José Gabriel Barcia Durán NYU Grossman School of Medicine gabriel.barcia - at - nyulangone.org
Participant Maria Blanco Salazar Stowers Institute for Medical Research MBlancoSalazar - at - stowers.org
Participant Clare Cahir The Rockefeller University ccahir - at - rockefeller.edu
Participant Robert Dalipovic Binghamton University rdalipo1 - at - binghamton.edu
Participant Ayushman Dobhal Vaccine Research Center, NIH ayushman.dobhal - at - nih.gov
Participant Gabriela Fort University of Utah gabriela.fort - at - hci.utah.edu
Participant Thompson Gana James Cook University sonyafaf - at - yahoo.com
Participant Minakshi Gandhi Cold Spring Harbor Laboratory mgandhi - at - cshl.edu
Participant Thomas Gebert Baylor College of Medicine gebert - at - bcm.edu
Participant Tiffany Halvorsen Lawrence Livermore National Laboratory halvorsen1 - at - llnl.gov
Participant Danni Jin Yale University danni.jin - at - yale.edu
Participant Ian MacFawn University of Pittsburgh macfawni - at - pitt.edu
Participant Anastasiya Mankouski University of Utah ana.mankouski - at - hsc.utah.edu
Participant Benjamin Muhoya Princeton University bm0211 - at - princeton.edu
Participant Cristina Paraschivescu The Feinstein Institutes for Medical Research cparaschives - at - northwell.edu
Participant David Paulding Cincinnati Children's Hospital Medical Center david.paulding - at - cchmc.org
Participant Riccardo Rossi University of Milan r.rossi44 - at - campus.unimib.it
Participant Shreya Saha University Of Cambridge, UK ss2344 - at - cam.ac.uk
Participant Esra Sengul University of Oxford esra.sengul - at - dpag.ox.ac.uk
Participant Shahar Silverman Yale University shahar.silverman - at - yale.edu
Participant Hannah Toth Ohio State University toth.302 - at - osu.edu
Participant Leah VandenBosch Seattle Childrens Research Institute leah.vandenbosch - at - gmail.com
Participant Camila Vazquez Echegaray Lund University camila.vazquez_echegaray - at - med.lu.se

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