Programming for Biology 2018
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
Simon Prochnik, Ph.D.
Sofia Robb, Ph.D.
| Sunday, October 14 | |
|---|---|
| 7:00-8:00 | Meet & Greet in the bar
Everyone |
| Monday, October 15 | |
| 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 |
| Lunch | |
| 2:00-3:30 | Unix 2: Text Editors,Git for Beginners Sofia |
| 3:30-5:00 |
Unix II problem set TAs |
| Dinner | |
| 7:00-8:00 | Review Session: Unix TAs |
| 8:00-10:00 | Problem Sets Unix TAs |
| Tuesday, October 16 | |
| 9:00-10:30 | Python I: Overview, running python, syntax, data types and variables Simon |
| 10:30-12:30 | Python I problem set TAs |
| 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 on Hershey upstairs balcony Everyone |
| 6:00-7:00 | Dinner: Pizza in Hershey |
| 7:00-7:30 | Text Editors TAs Emacs Presentation, Emacs Reference Card VI Presentation, VI Commands Cheatsheet, VI Table Cheatsheet |
| 7:30-8:30 | Review Session TAs |
| 8:30-10:00 | Problem Sets TAs |
| Wednesday, October 17 | |
| 9:00-10:30 | Python III: Sequences, strings Simon |
| 10:30-12:30 | Python III Problem set TAs |
| Lunch | |
| 2:00-3:30 | Python IV: Lists, tuples, loops Sofia |
| 3:30-5:00 | Python IV Problem set TAs |
| Dinner | |
| 7:00-8:00 | Python V: Dictionaries, sets Sofia |
| 7:00-8:00 | Review Session TAs |
| 8:00-10:00 | Python V Problem set TAs |
| Thursday, October 18 | |
| 9:00-10:30 | Python VI: I/O and files Simon |
| 10:30-12:30 | Python VI problem set TAs |
| Lunch | |
| 2:00-3:30 | Python VII: regular expressions Sofia |
| 3:30-5:00 | Python VII problem set TAs |
| Dinner | |
| 7:00-8:00 | Review Session TAs |
| 8:00-10:00 | Problem Sets TAs |
| Friday, October 19 | |
| 9:00-10:30 | Python VIII: Data structures, exceptions Sofia |
| 10:30-12:30 | Python VIII Problem set TAs |
| Lunch | |
| 2:00-3:30 | Python IX: Functions, Scope, Modules Simon |
| 3:30-5:00 | Python IX Problem Set TAs |
| Dinner | |
| 7:00-8:00 | Review Session TAs |
| 8:00-10:00 | Problem Sets TAs |
| Saturday, October 20 | |
| All day | Free Time Relax, have some fun!! Everyone |
| Sunday, October 21 | |
| 9:00-10:30 | Python X: Classes BioPython: BioPython Simon |
| 10:30-12:30 |
Python X Problem Set
BioPython Problem Set TAs |
| Lunch | |
| 2:00-3:30 | Next Gen Sequencing: File formats: fasta, fastq, bam, vcf Mike Campbell |
| 3:30-5:30 | NGS problem set NGS workshop walkthrough TAs |
| 5:30-7:00 | Dinner |
| 7:00-9:00 | Structural Variation Tomas Marques |
| 9:00-9:20 | Project Overview and Proposal Instructions Sofia & Simon |
| 9:30 | Tour of J.T. Carringtons Genome Resource Center, Huntington ALL |
| Monday, October 22 | |
| 9:00-10:30 | Sequence Homology Part 1: Homology and Alignments Brandi Cantarel |
| 10:30-12:30 | Homology and Alignments Workshop TAs |
| Lunch | |
| 2:00-3:30 | Sequence Homology Part 2: Protein Domains and Distant Relatives Brandi Cantarel |
| 3:30-5:00 | Protein Domains and Distant Relatives Workshop TAs |
| 5:00-5:30 | Genome Assembly, start running assembler before dinner Debra Triant |
| 5:30-7:00 | Dinner |
| 7:00-9:00 | Genome Assembly Debra Triant |
| 9:00-10:00 | Problem Sets/Finish Genome Assembly Workshop TAs |
| Tuesday, October 23 | |
| 9:00-10:30 | Bioinformatics and Useful Tools
Simon |
| 10:30-12:30 | Work on old problem sets TAs |
| Lunch | |
| 2:00-3:30 | Aligners Alex Dobin |
| 3:30- 5:00 | Aligners: STAR TAs |
| 7:00-8:00 | Review Session (optional - ask students) TAs |
| 7:00-10:00 | Problems sets TAs |
| Wednesday, October 24 | |
| 9:00-10:30 | RNASeq Brian Hass |
| 10:30-12:30 | RNA-seq problem set |
| 12:30 | Lunch |
| 2:00 | Group Photo: Meet on lawn behind Blackford |
| Afternoon | Continue Working on RNAseq Workshop followed by Problem sets |
| Dinner | |
| 7:00-8:00 | Ethics And Reproducibility in Research Sofia Simon |
| 7:00-10:00 | Problems sets TAs |
| 12:00 | Turn in Project Proposals by Midnight |
| Thursday, October 25 | |
| 9:00-11:00 | GMOD Scott Cain |
| 11:00-12:30 | GMOD Workshop TAs |
| Afternoon and Evening | Free Time Relax, have some fun!! Everyone |
| Friday, October 26 | |
| 9:00-11:00 | Intro to Ontologies Nicole Vasilevsky |
| 11:00-12:30 | Ontologies Workshop TAs |
| Afternoon | Protein Function and Annotation Paul Thomas |
| 5:00-6:00 | Wine and Cheese sign up for projects |
| 8:00-8:30 | Start Projects: move tables TAs |
| 9:00-?:00 | Halloween Party! (Clarkston Dinning room) Everyone |
| Saturday, October 27 | |
| All day | Group Projects Everyone |
| Sunday, October 28 | |
| All day | Group Projects Everyone |
| Monday, October 29 | |
| 9:00-12:00 | Group Projects Everyone |
| Lunch | |
| 4:00-6:00 | Project Presentations Everyone |
| 6:00-6:45 | Cocktails in Blackford Bar |
| 6:45-10:00 | Course banquet |
| Tuesday, October 30 | |
| after breakfast | Depart Everyone |
| Instructors | ||
|---|---|---|
| Simon Prochnik | Itrexon, South Sam Fransisco, CA | prochnik -- at -- gmail.com |
| Sofia Robb | Stowers Institute for Medical Research, Kansas City, MO | sofia2341 -- at -- gmail.com |
| Teaching Assistants | ||
| Jessen Bredeson | University of California, Berkeley, CA | jessenbredeson -- at -- berkeley.edu |
| Kirsten Gotting | University of Wisconsin - Madison, Madison, WI | gotting -- at -- wisc.edu |
| Joseph Orkin | Universitat Pompeu Fabra, Barcelona, Spain | joseph.orkin -- at -- ucalgary.ca |
| Lukas Kuderna | Institue de Biologia Barcelona, Spain | lukas.kuderna -- at -- upf.edu |
| Shasta Webb | University of Calgary, Calgary, Canada | shasta.webb -- at -- ucalgary.ca |
| Guest Lecturers | ||
| Scott Cain | Ontario Institute for Cancer Research, Medina, OH | scott -- at -- scottcain.net |
| Michael Campbell | <--10X Genomics | --> <--keilbeck --at -- genetics.utah.edu | -->
| Brandi Cantarel | UTSW Medical Center, Dallas TX | |
| Alexander Dobin | Cold Spring Harbor Laboratory, Cold Spring Harbor NY | |
| Brian Haas | Broad Institute, Cambridge, MA | bhaas -- at -- broadinstitute.org |
| Paul Thomas | University of Southern California, Los Angeles CA | |
| Deborah Triant | University of Virgina, Chorlottesville, VA | |
| Nicole Vasilevsky | Oregon Health & Science University, Portland, OR | |
| WilliamPearson | University of California, Davis, CA | wrp --at-- virginia.edu |
| Tomas Marques-Bonet | Universitat Pompeu Fabra, Barcelona, Spain | tomas.marques -- at -- upf.edu |
