Programming for Biology 2022
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
| Sunday, October 9 | |
|---|---|
| 7:00-8:00 | Meet & Greet in the bar
Everyone |
| Monday, October 10 | |
| 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 |
| 11:30-2:00 | 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 | Review Session: Unix tips and tricks
Coding best practices TAs |
| 8:00-10:00 | Problem Sets Unix TAs |
| Tuesday, October 11 | |
| 9:00-10:30 | Python I: Overview, running python, syntax, data types and variables Simon |
| 10:30-12:30 | Python I problem set TAs |
| 11:30-2:00 | 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 | 🏃 Run, Walk, Jog, Get Vitamin D and fresh air! 🏃
TAs |
| 6:00-7:00 | Dinner 🐟 🐟 🐟 🐟 🧅 |
| 7:00-8:00 | Review Session TAs TAs |
| 8:00-10:00 | Problem Sets TAs |
| Wednesday, October 12 | |
| 9:00-10:30 | Python III: Sequences, strings Simon |
| 10:30-12:30 | Python III Problem set TAs |
| 11:30-2:00 | Lunch |
| 2:00-3:30 | Python IV: Lists, tuples, loops Sofia |
| 3:30-5:00 | Python IV Problem set TAs |
| 5:00-6:00 | Wine and Cheese 🍷 🧀 |
| 6:00-7:00 | Dinner |
| 7:00-10:00 | Problem Sets TAs |
| Thursday, October 13 | |
| 9:00-10:30 | Python V: Dictionaries, sets Sofia |
| 10:30-11:30 | Python V problem set TAs |
| 11:30-12:00 | Python VI: I/O and files Simon |
| 12:00-12:30 | Python VI problem set TAs |
| 12:30-2:00 | 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 14 | |
| 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 |
| 11:30-1:30 | Lunch |
| 1:30-3:00 | 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 | Review Session TAs |
| 8:00-10:00 | Problem Sets TAs |
| Saturday, October 15 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Sunday, October 16 | |
| 9:00-10:30 | Python XI: Python XI BioPython: BioPython Sofia |
| 10:30-12:30 |
Python XI Problem Set
BioPython Problem Set TAs |
| 11:30-2:00 | Lunch |
| 2:00-3:00 | Next Gen Sequencing: Technologies Molly Zeller |
| 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 Simon |
| 8:00-9:00 | Any Problem Sets TAs |
| Monday, October 17 | |
| 9:00-10:30 | Python Pipelines: Simon |
| 10:30-12:30 | Workshop TAs |
| 11:30-2:00 | Lunch |
| 2:00-3:30 | Genome Assembly: Part 1 Canu Assembler Deb Triant |
| 3:30-5:00 | Genome Assembly Workshop TAs |
| 5:30-7:00 | Dinner |
| 7:00-7:45 | Ethics And Reproducibility in Research Simon |
| 7:45-9:00 | Any Problem Sets TAs |
| Tuesday, October 18 | |
| 9:00-10:30 | 🐛 Transcriptomes and RNAseq Part 1: Brian Haas |
| 10:30-12:30 | Workshop TAs |
| 11:30-2:00 | Lunch |
| 2:00-3:30 | 🦋 Transcriptomes and RNAseq Part2: Brian Haas |
| 3:30-5:00 | Workshop TAs |
| 5:30-7:00 | Dinner |
| 7:00-8:00 | Problem Sets TAs |
| Wednesday, October 19 | |
| 9:30-10:00 | Final Project Overview (In Hershey) Simon and Sofia |
| 11:00-11:30 | Introduction to Jupyter Notebooks (In Hershey) Cynthia |
| 9:30-11:30 | Work on Project Proposals/Problem Sets TAs |
| 11:30-2:00 | Lunch |
| 2:00-3:30 | Image Processing (In Hershey) Jay Unruh |
| 3:30-5:30 | Image Processing Workshop |
| 5:30-7:00 | Dinner |
| By 7:00pm | Submit project proposal via email to Simon and Sofia |
| 7:00-8:00 | Open Source Software for Data Sharing (In Bush) Scott Cain |
| 8:30 | Patio Party at Biondi Everyone |
| Thursday, October 20 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Friday, October 21 | |
| 9:00-11:00 | Sequence Similarity Part1 Bill Pearson |
| 11:00-12:30 | Workshop TAs |
| 1:30-3:30 | Sequence Similarity Part2 Bill Pearson |
| 3:30-5:00 | Workshop TAs |
| 5:30-7:00 | Dinner |
| 7:00-8:00 | Project Signup and Room Rerrangement TA |
| 8:00-9:00 | First Project Group Meeting TAs |
| Saturday, October 22 | |
| 9:00-11:30 | Group Projects Everyone |
| 11:30-2:00 | Lunch |
| Group Projects Everyone |
|
| 5:30-7:00 | Dinner |
| Group Projects Everyone |
|
| Sunday, October 23 | |
| 9:00-11:30 | Group Projects Everyone |
| 11:30-2:00 | Lunch |
| Group Projects Everyone |
|
| 5:30-7:00 | Dinner |
| Group Projects Everyone |
|
| Monday, October 24 | |
| 9:00-12:00 | Group Projects Everyone |
| 11:30-2:00 | Lunch |
| 4:00-6:00 | Project Presentations Everyone |
| 6:00-6:45 | Cocktails in Blackford Bar |
| 6:45-10:00 | Course banquet |
| 10:00-? | BIONDI DANCE PARTY PART DEUX |
| Tuesday, October 25 | |
| after breakfast | Depart Everyone |
| Participants | |||
|---|---|---|---|
| Instructor | Simon Prochnik | Triplebar Biotechnology Inc. | prochnik - at - gmail.com |
| Instructor | Sofia Robb | Stowers Institute for Medical Research | smr - at - stowers.org |
| Teaching Assistant | Jessen Bredeson | jessenbredeson - at - gmail.com | |
| Teaching Assistant | Cynthia Cardinault | Centro de Investigación Científica de Yucatán | cyntsc10 - at - gmail.com |
| Teaching Assistant | Zachary Konkel | The Ohio State University | konkel.8 - at - buckeyemail.osu.edu |
| Teaching Assistant | Eric Ross | HHMI | ejr - at - stowers.org |
| Teaching Assistant | Shasta Webb | University of Notre Dame | webbshasta - at - gmail.com |
| Lecturer | Brian Haas | Broad Institute | bhaas - at - broadinstitute.org |
| Lecturer | William Pearson | University of Virginia | wrp - at - virginia.edu |
| Lecturer | Deborah Triant | University of Missouri | datriant - at - hotmail.com |
| Lecturer | Jay Unruh | Stowers Institute for Medical Research | jru - at - stowers.org |
| Lecturer | Molly Zeller | University of Wisconsin-Madison | zeller2 - at - wisc.edu |
| Student | Bana Abolibdeh | Michigan State University | libdehba - at - msu.edu |
| Student | Reed Alexander | Middle Tennessee State University | nra2q - at - mtmail.mtsu.edu |
| Student | Elaine Aquino | University of Nevada, Las Vegas | aquine1 - at - unlv.nevada.edu |
| Student | Christian Baca | The Rockefeller University | cbaca - at - rockefeller.edu |
| Student | Melissa Bentley-Ford | Atlant VA Healthcare System | mrbentl - at - emory.edu |
| Student | Irene Duba | Rockefeller University | iduba - at - mail.rockefeller.edu |
| Student | Marleny Garcia Lozano | Max Planck Institute for Biology | marleny.garcia-lozano - at - tuebingen.mpg.de |
| Student | Omar Gutierrez Ruiz | Mayo Clinic Graduate School of Biomedical Sciences | gutierrezruiz.omar - at - mayo.edu |
| Student | Christina Heil | University of Rochester Medical Center | christina_heil - at - urmc.rochester.edu |
| Student | Cassandra Herbert | University of Cincinnati | herbercr - at - mail.uc.edu |
| Student | Nicholas Hilton | University of California, Davis | nhilton - at - ucdavis.edu |
| Student | Jonathan Jacobs | The Ohio State University | jacobs.1080 - at - osu.edu |
| Student | Jennifer Jahncke | Oregon Health & Science University | jahncke - at - ohsu.edu |
| Student | Riley Kellermeyer | Stowers Institute for Medical Research | rkellermeyer - at - stowers.org |
| Student | Dmitry Kretov | Boston University School of Medicine | dkretov - at - bu.edu |
| Student | Kyle Leistikow | Marquette University | kyle.leistikow - at - marquette.edu |
| Student | Meike Lobb-Rabe | University of Chicago | lobbrabe - at - uchicago.edu |
| Student | Brianda Lopez Aviña | University of Kentucky | brianda.lavina - at - uky.edu |
| Student | Aparna Mariyam Thomas | University of Calgary | aparna.mariyamthomas - at - ucalgary.ca |
| Student | Daniel Murphy | Washington University School of Medicine | DMURPHY26 - at - wustl.edu |
| Student | Mina Peyton | University of Minnesota | mina.peyton - at - gmail.com |
| Student | Sarah Prostak | University of Massachusetts Amherst | sprostak - at - umass.edu |
| Student | Carin Ragland | Stanford University | cragland - at - stanford.edu |
| Student | Esra Sengul | University of Oxford | esra.sengul - at - dpag.ox.ac.uk |
| Student | Alex Von Schulze | The Stowers Institute for Medical Research | avonschulze - at - stowers.org |