!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> Programming for Biology 2024

Special Announcements

Schedule



Sunday, October 13
7:00-8:00 Meet & Greet in the bar 🎉

Everyone
 
Monday, October 14
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 15
9:00-10:30 Python I: Overview, running python, syntax, data types and variables

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

TAs
12:30-2:00 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 Wine and Cheese 🍷 🧀
6:00-7:00 Dinner
7:00-8:00 Review Session

TAs
8:00-10:00 Problem Sets

TAs
 
Wednesday, October 16
9:00-10:30 Python III: Sequences, strings

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

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

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

TAs
5:00-6:00 ☀ Go outside! Rest your eyeballs 👁👁, Run, Walk, Jog
6:00-7:00 Dinner
7:00-8:00 Review Session

TAs
8:00-10:00 Problem Sets

TAs
 
Thursday, October 17
9:00-10:30 Python V: Dictionaries, sets

Sofia
10:30-12:30 Python V problem set

TAs
 
12:30-2:00 Lunch
2:00-3:30 Python VI: I/O and files

Simon
3:30-5:00 Python VI 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 18
9:00-10:30 Python VII: Regular expressions

Sofia
10:30-12:30 Python VII problem set

TAs
12:30-2:00 Lunch
2:00-3:00 Python VIII: Data structures

Python IX: Exceptions

Sofia
3:00-5:00 Python VIII Problem set

Python IX 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
8:00-10:00 Problem sets

TAs
 
Saturday, October 19
9:00-10:30 Python X: Functions, Scope, and Modules

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

TAs
12:30-2:00 Lunch
2:00-3:00 Python XI: Python XI, classes

BioPython: BioPython

Sofia
3:00-5:00 Python XI Problem Set
BioPython 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

TBD
8:00-10:00 Problem sets

TAs
 
Sunday, October 20
9:00-10:30 Bioinformatics 1, Python Pipelines:Bioinformatics tools

Simon
10:30-12:30 Problem Sets

TAs
12:30-2:00 Lunch
2:00-3:00 Coding with AI

Simon
3:00-5:00 Problem Sets

TAs
5:00-7:00 Dinner

7:00-8:00 Review

TBD
8:00-10:00 Problem sets

TAs
 
Monday, October 21
Free day Relax, have some fun!!

Everyone
 
Tuesday, October 22
9:00-10:30 🐛 Transcriptomes and RNAseq Part 1:

Brian Haas
10:30-12:30 Workshop

TAs
12:30-2:00 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
Simon
 
Wednesday, October 23
9:00-11:00 Next Gen Sequencing technologies

Anoja Perera
11:00-12:30 Next Gen Sequencing: File Types and Analysis

Jessen Bredeson
12:30-1:45 Lunch
1:00-3:30 Genome Assembly lecture

Deb Triant
3:30-5:00 Genome Assembly workshop

TAs
5:00-7:00 Dinner
1:00-3:30 Genome Assembly lecture

Deb Triant
3:30-5:00 Genome Assembly workshop

TAs
 
Thursday, October 24
9:00-11:00 Sequence Similarity Part 1

Bill Pearson
11:00-12:30 Gene homology workshop

TAs
12:30-1:30 Lunch
1:30-3:30 Sequence Similarity Part2

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

TAs
1:30-5:00 Sequence Similarity Part 2

Bill Pearson
5:00-7:00 Dinner
7:00-8:30 Open Source Software for Data Sharing

Scott Cain
8:30-10:00 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.
 
Friday, October 25
9:00-11:00 Image Processing

Jay Unruh
11:00-12:30 Image Processing Workshop

TAs
12:30-1:30 Lunch
1:30-5:00 GO Terms and Phylogeny

Paul Thomas
5:00-7:00 Dinner
7:00 Project Proposals

email to smr -at- stowers.org and prochnik -at- gmail.com
 
Saturday, October 26
8:30-9:00 Project sign ups
9:00 Room Rerrangement

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

TAs
10:00-12:30 Group Projects

Everyone
12:30-2:00 Lunch
2:00-5:00
Group Projects

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

Everyone
 
Sunday, October 27
9:00-12:30 Group Projects

Everyone
12:30-2:00 Lunch
2:00-5:00
Group Projects

Everyone
 
Monday, October 28
9:00-12:30 Group Projects

Everyone
12:30-2:00 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 39
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 Ken Youens-Clark University of Arizona kyclark - at - arizona.edu
Teaching Assistant Eric Ross Stowers Institute for Medical Research ejr - at - stowers.org
Teaching Assistant Riley Kellermeyer San Antonio Zoo rileykellermeyer - at - gmail.com
Teaching Assistant Robert Dalipovic Binghamton University rdalipo1 - at - binghamton.edu
Teaching Assistant Maria (Majo) Blanco Salazar Stowers Institute for Medical Research MBlancoSalazar - at - stowers.org
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 Ankit Sharma Brandeis University ankitsharma - at - brandeis.edu
Participant Lola Takhirov University of Southern California, Los Angeles takhirov - at - usc.edu
Participant Harshad Ingle Washington University in St. Louis hingle - at - wustl.edu
Participant Chan Young Park Chonnam National University Medical school mose6606 - at - gmail.com
Participant Caitlin Millett The Feinstein Institutes for Medical Research cmillett - at - northwell.edu
Participant Henry Arnold University of Utah henry.arnold - at - hci.utah.edu
Participant Taylor Pio Emory University taylor.pio - at - emory.edu
Participant Rebekah Kim Harvard University rebekahkim - at - fas.harvard.edu
Participant Isobel Fetter University of California, Santa Cruz ifetter - at - ucsc.edu
Participant Rada Malko Indiana University rmalko - at - iu.edu
Participant Konstantin Queitsch Oregon Health & Science queitsch - at - ohsu.edu
Participant Timothy Schwanitz Princeton University ts5103 - at - princeton.edu
Participant Jorge Antonio Tzec Interian Centro de Investigación Científicas de Yucatan jorgetzec - at - gmail.com
Participant Upendra Chalise University of Minnesota uchalise - at - umn.edu
Participant Johanna Seitz-Holland Brigham and Women's Hospital jseitz - at - bwh.harvard.edu
Participant Nathan Harper The Rockefeller University nharper - at - rockefeller.edu
Participant Rajendra Pangeni Nova Southeastern University rpangeni - at - nova.edu

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