Programming for Biology 2025
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Jessen Bredeson
Eric Ross
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Jessen Bredeson
Eric Ross
| Sunday, October 12 | |
|---|---|
| 7:00-8:00 | Meet & Greet in the bar 🎉
Everyone |
| Monday, October 13 | |
| 9:00 | Welcome & Orientation Security & Safety Briefing 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 Simon & Sofia |
| 3:30 - 5:00 |
Unix II problem set TAs |
| 5:30 - 7:00 | Dinner |
| 7:00 - 8:00 | Github & VSCode
TAs |
| 8:00 - 10:00 | Problem Sets: Continue Unix TAs |
| Tuesday, October 14 | |
| 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 15 | |
| 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 - 7:00 | Dinner |
| 7:00 - 8:00 | Review Session TAs |
| 8:00 - 10:00 | Problem Sets TAs |
| Thursday, October 16 | |
| 9:00 - 10:00 | Python VI: I/O and files Simon |
| 10:00 - 12:30 | Python VI problem set TAs |
| 12:30 - 2:00 | Lunch |
| 2:00 - 3:30 | Python V: Dictionaries, sets Sofia |
| 3:30 - 5:30 | Python V problem set TAs |
| 5:30 - 7:00 | Dinner |
| 7:00 - 8:00 | Review session TAs |
| 8:00 - 9:00 | Problem sets TAs |
| Friday, October 17 | |
| 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 - 5:30 | Python VIII Problem set Python IX Problem set TAs |
| 6:00-8:00 | 🍕CSHL Pizza Party🍕 Everyone |
| 🕉 💃 KAROKE DANCE PARTY 🕺 🕉 TAs |
|
| Saturday, October 18 | |
| Free day | Relax, have some fun!! Everyone |
| Sunday, 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 |
| 6:00 - 7:00 | Dinner |
| 7:00 - 8:00 | Ethics and reproducibility Simon |
| 8:00 - | Review Session TAs |
| Monday, 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 | 🐍 Mamba package manager 🐍 Jessen |
| 3:00 - 5:00 | Problem Sets TAs |
| 5:00 - 7:00 | Dinner |
| 7:00 - 8:00 | HPC Workflows with Python, Unix and Mamba TBD |
| 8:00 - 10:00 | Problem sets TAs |
| Tuesday, October 21 | |
| 9:00 - 12:30 | Introduction to coding with AI and debugging Simon |
| 12:30 - 2:00 | Lunch |
| 2:00 - 5:30 | Live Coding with AI and debugging Simon |
| 5:30 - 7:00 | Dinner |
| 7:00 - 8:00 | Live AI Coding Demo Colin |
| Wednesday, 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 | Student Collaboration Night- learn by teaching! Problem Sets TA night off |
| Thursday, October 23 | |
| 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 - 2:00 | Class Picture Meet outside of Hershey! |
| 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 | Project Proposals Due
email to smr -at- stowers.org and prochnik -at- gmail.com |
| 7:00 - 8:00 | Coding with AI and Debugging Simon |
| Friday, October 24 | |
| 9:00 - 12:30 | Organize Rooms get Project Teams Together
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 |
| Saturday, October 25 | |
| 9:00 - 12:30 | Group Projects Everyone |
| 12:30 - 2:00 | Lunch |
| 2:00 - 5:00 |
Group Projects Everyone |
| 5:00 - 7:00 | Dinner |
| 7:00 - 10:00 |
Group Projects Everyone |
| Sunday, October 26 | |
| 9:00-12:30 | Group Projects Everyone |
| 12:30-2:00 | Lunch |
| 2:00-5:00 |
Group Projects Everyone |
| Monday, October 27 | |
| 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 TBD 🕺 |
| Tuesday, October 28 | |
| 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 |
| Co-Instructor | Jessen Bredeson | DOE Joint Genome Institute | jessenbredeson - at - gmail.com |
| Co-Instructor | Eric Ross | Stowers Institute for Medical Research | ejr - at - stowers.org |
| Teaching Assistant | Riley Kellermeyer | University of Minnesota | kell3262 - at - umn.edu |
| Teaching Assistant | Joshua Lynch | joshua.kevin.lynch - at - gmail.com | |
| Teaching Assistant | Ken Youens-Clark | University of Arizona | kyclark - at - arizona.edu |
| Teaching Assistant | Taylor Pio | Emory University | taylor.pio - at - emory.edu |
| Teaching Assistant | Rebekah (Bekah) Kim | Harvard University | rebekahkim - at - fas.harvard.edu |
| Teaching Assistant | Colin Diesh | University of California, Berkeley | colindiesh - at - gmail.com |
| Lecturer | Brian Haas | Broad Institute | bhaas - at - broadinstitute.org |
| Lecturer | Bill Pearson | University of Virginia | wrp - at - virginia.edu |
| Participant | Pauline DiGianivittorio | Children's Hospital of Philadelphia | digianivip - at - chop.edu |
| Participant | Giancarlo Gonzalez | University of Puerto Rico | giancarlogonzalezfeliu - at - gmail.com |
| Participant | Huishi Toh | Meharry Medical College | huishi.toh - at - mmc.edu |
| Participant | Esraa Gabal | Purdue University | egabal - at - purdue.edu |
| Participant | Sara Pini | University of Modena and Reggio Emilia | sara.pini - at - unimore.it |
| Participant | Theresa (Tess) Kelly | Oregon Health and Science University | kellythe - at - oshu.edu |
| Participant | Emma Saart | Feinstein Institute for Medical Research | esaart - at - northwell.edu |
| Participant | Anastasia Rusnak | Binghamton University | arusnak1 - at - binghamton.edu |
| Participant | Jane Liu | Pomona College | jane.liu - at - pomona.edu |
| Participant | Pia-Yael Hartig | Institute of Molecular Biology | p.hartig - at - imb-mainz.de |
| Participant | Zilin Xianyu | Mayo Clinic | Xianyu.Zilin - at - mayo.edu |
| Participant | Caroline Harrer | The Rockefeller University | charrer - at - rockefeller.edu |
| Participant | Grace Beggs | Princeton University | gb1683 - at - princeton.edu |
| Participant | Ananya Nidamangala Srinivasa | University of Massachusetts Amherst | anidamangala - at - umass.edu |
| Participant | Hea Jin Hong | Yale University | heajin.hong - at - yale.edu |
| Participant | Walter Orellana | University of Utah | walter.orellana - at - hci.utah.edu |
| Participant | Julianne Fazekas | Baylor University | julianne_fazekas1 - at - baylor.edu |
| Participant | Vivian Li | The Rockefeller University | yli03 - at - rockefeller.edu |
| Participant | Josiah Murray | Medical College of Wisconsin | jmurray - at - mcw.edu |
| Participant | Calvin Herman | The Rockefeller University | cherman - at - rockefeller.edu |