Programming for Biology 2023
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
| 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 |
