Programming for Biology 2024
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
| 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 | VS Code Riley |
| 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 | Miniconda package manager Jessen |
| 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 |
| 6:00-8:00 | 🍕CSHL Pizza Party🍕 Everyone |
| 7:00-8:00 | Pandas Riley |
| 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 | Unit Testing
Ken |
| 8:00- | Evening off - see you at the bar? Everyone |
| Sunday, October 20 | |
| 9:00-10:30 | Bioinformatics 1, Python Pipelines 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 Part 2 Brian Haas |
| 3:30-5:00 | Workshop TAs |
| 5:00-7:00 | Dinner |
| 7:00 - 8:00 | Ethics and reproducibility Simon |
| Wednesday, October 23 | |
| 9:00-11:00 | Next Gen Sequencing technologies Anoja Perera |
| 11:00-12:30 | Next Gen Sequencing Workshop: File Types and Analysis Jessen Bredeson |
| 12:30-2:00 | Lunch |
| 2:00-3:30 | Genome Assembly lecture Deb Triant |
| 3:30-5:00 | Genome Assembly workshop TAs |
| 5:00-6:00 | 🏃 Run, Walk, Jog, Get Vitamin D and fresh air! 🏃
TAs |
| 6:00-7:00 | Dinner |
| 7:00 | Project Proposal Overview |
| 7:00-8:00 | Genome assembly programming exercises Deb |
| 8:00-10:00 | Problem sets TAs |
| Thursday, October 24 | |
| 9:00-11:00 | Sequence Similarity Part 1 Bill Pearson |
| 11:00-12:30 | Gene homology workshop TAs |
| 12:30-2:00 | Lunch |
| 2:00-3:30 | Sequence Similarity Part2 Bill Pearson |
| 3:30-5:00 | Gene homology Workshop Pt 2 TAs |
| 5:00-7:00 | Dinner |
| 7:00-8:30 | Open Source Software for Data Sharing Scott Cain |
| 10:00 | Project Proposals Due
email to smr -at- stowers.org and prochnik -at- gmail.com |
| Friday, October 25 | |
| 9:00-12:30 | Start here for install Image Processing Workshop Jay Unruh |
| 12:30-2:00 | Lunch |
| 2:00-2:30 | 📷 Course Photo: Meet at Hershey, downstairs, south door (backside)
Everyone |
| 2:30-4:00 | Python debugging and awk Simon |
| 4:00-6:00 | Problem sets TAs |
| 6:00-8:00 | 🍕 Pizza Party🍕 Everyone |
| 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. |
| 10:00 - | 🪩 🕺 Post-conference disco! 🕺 🪩 (Biondi? Bush? Follow the music...) |
| Saturday, October 26 | |
| 8:30-9:00 | Project sign ups |
| 9:00-9:30 | Room Rerrangement TAs |
| 9:30-10:00 | 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 |
| 9:00 - 😴 |
🎃 Halloween Party 👻 (Bush) |
| 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 |
| 3:00-5:00 | 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-????? | 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 CientÃficas 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 |