Does[0]compute? - Computational Biology Discussion Group

Does[0]compute? (pronounced “Does naught compute?”), is intended to foster a discussion about best practices in computational biology.

The next meeting will be in 213 Borlaug Hall on 10 June 2016, 2:00-3:00 pm. Please bring a computer to use during the discussion.

For more information, sign up for the Google group, “Biocomputing Discussion Group”.

Subscribe to a
calendar of Does[0]compute? meetings.

Upcoming Meetings

06/10/2016
Smith KW (2015) Cython: A Guide for Python Programmers
Chapter 3: Python in Depth
Discussion Leaders: Paul Hoffman

06/24/2016
Grus H (2015) Data Science from Scratch: First Principles with Python
Chapter 9: Getting Data
Discussion Leaders:

06/10/2016
Goodlife P (2014) Becoming a Better Programmer: A Handbook for People Who Care About Code
Chapter 3: Write Less Code!
Discussion Leaders:


Past Meetings

05/20/2016
Jones MO (2014) Advanced Python for Biologists
Chapter 8: Module and testing
Discussion Leaders:
Skylar Wyant & Colin Pierce

05/06/2016
Jones MO (2014) Advanced Python for Biologists
Chapter 7: Exception handling
Discussion Leaders:
Li Lei & Peter Morrell

04/22/2016
Jones MO (2014) Advanced Python for Biologists
Chapter 6: Iterators, comprehensions & generators
Discussion Leaders:
Thomas Kono & Kevin Silverstein

04/15/2016
Jones MO (2014) Advanced Python for Biologists
Chapter 5: Functional Python
Discussion Leaders:
Paul Hoffman & Chaochih Liu

03/25/2016
Jones MO (2014) Advanced Python for Biologists
Chapter 4: Object Oriented Python
Discussion Leaders:
Felipe Reyes & Skylar Wyant

03/11/2016
Jones MO (2014) Advanced Python for Biologists
Chapter 3: Complex Data Structures
Discussion Leaders: Jeff Neyhart &
Li Lei

02/26/2016
Jones MO (2014) Advanced Python for Biologists
Chapters 1: Introduction
Chapter 2: Recursion and Trees
Discussion Leaders: Thomas Kono & Chaochih Liu

02/12/2016
Model ML (2009) Bioinformatics Programming Using Python: Practical Programming for Biological Data. O’Reilly Media, Inc. 528 p.
Chapter 1. Primitives
Chapter 2. Names, Functions, and Modules

Discussion Leaders: Shawn Goggins & Paul Hoffman

01/29/2016
Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M et al. (2014) Best practices for scientific computing. PLoS Biol 12: e1001745.
Discussion Leaders:
Shawn Goggins & Jeff Neyhart

12/10/2015 - Note Special Date
Compeau P, Pevzner P (2015) Bioinformatics algorithms: an active learning approach. 2nd Edition, Volume 1. Active Learning Publishers LLC. 384 p.
Chapter 6: Are there fragile regions in the human genome?: Combinatorial algorithms
Discussion Leaders: Allison Haaning &
Li Lei

11/12/2015
Compeau P, Pevzner P (2015) Bioinformatics algorithms: an active learning approach. 2nd Edition, Volume 1. Active Learning Publishers LLC. 384 p.
Chapter 5: How do we compare DNA sequences?: Dynamic programming
Discussion Leaders:
Chaochih Liu & Joseph Guhlin

10/29/2015
Compeau P, Pevzner P (2015) Bioinformatics algorithms: an active learning approach. 2nd Edition, Volume 1. Active Learning Publishers LLC. 384 p.
Chapter 4: How do we sequence antibiotics?: Brute force algorithms
Discussion Leaders:
Diana Trujillo & Paul Hoffman

10/15/2015
Compeau P, Pevzner P (2015) Bioinformatics algorithms: an active learning approach. 2nd Edition, Volume 1. Active Learning Publishers LLC. 384 p.
Chapter 3: How do we assemble genomes?: Graph algorithms
Discussion Leaders:
Kevin Silverstein & Shawn Goggins

10/08/2015 - 2:30 pm - Note Special Date & Time
Compeau P, Pevzner P (2015) Bioinformatics algorithms: an active learning approach. 2nd Edition, Volume 1. Active Learning Publishers LLC. 384 p.
Chapter 2: Which DNA patterns play the role of molecular clocks?: Randomized algorithms
Discussion Leader: Trina Kuriger-Laber


09/24/2015
Compeau P, Pevzner P (2015) Bioinformatics algorithms: an active learning approach. 2nd Edition, Volume 1. Active Learning Publishers LLC. 384 p.
Chapter 1: Where in the genome does DNA replication begin?: Algorithm warmup
Discussion Leader:
Jean-Michel Michno

08/07/2015 - Note Date
Handling Sequence Data: Variant detection - use of sets of known variants, de-duplication, realignment, etc.
Be sure to have read Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools; Chapter 10: Working with Sequence Data
Discussion Leaders:
Getiria Onsongo & Paul Hoffman

06/26/2015
Handling Sequence Data: Reference based read mapping and de novo assembly
Be sure to have read Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools; Chapter 10: Working with Sequence Data
Discussion Leaders:
Kevin Dorn & Chaochih Liu

05/29/2015
Handling Sequence Data: Read quality and FASTQ files
Be sure to have read Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools; Chapter 10: Working with Sequence Data
Discussion Leaders:
John Garbe & Diana Trujillo

04/17/2015
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 13: Databases and Other Out-of-Memory Solutions
Discussion Leaders:
Getiria Onsongo & Rob Schaefer

04/03/2015
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 12: Bioinformatics Shell Scripting, Writing Pipelines, and Parallelizing Tasks
Discussion Leaders:
Joseph Guhlin & Jean-Michel Michno

03/06/2015
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 11: Working with Alignment Data
Discussion Leaders:
Tom Kono & Ying Zhang

02/20/2015
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 10: Working with Sequence Data
Discussion Leaders: Fengli Fu &
Lauren Mills

02/06/2015
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 9: Working with Range Data
Discussion Leaders:
Christy Henzler & Justin Anderson

01/23/2015
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 8: A Rapid Introduction to the R Language
Discussion Leaders: Derek Nedvek &
Micah Gerhart

12/12/2014
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 7: Unix Data Tools

Discussion Leaders: Joshua Baller & Lauren Mills

11/14/2014
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 6: Bioinformatics Data

Discussion Leaders: Peter Morrell & John Garbe

10/31/2014
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 5: Git for Scientists

Discussion Leaders: Derek Nedvek & Yancy Ribbens

10/17/2014
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 1: How to Learn Bioinformatics
Chapter 2: Setting Up and Managing a Bioinformatics Project

Discussion Leaders: Chaochih Liu & Derek Nedvek

10/03/2014
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 4: Working with Remote Machines
Discussion Leaders:
Ana Gonzales & Justin Anderson

09/19/2014
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Revisiting Chapter 3: Remedial UNIX Shell
Discussion Leaders:
Tom Kono & Kevin Silverstein

09/12/2014
Buffalo V (2014) Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Sebastopol, CA: O’Reilly Media. 300 p.
Chapter 3: Remedial UNIX Shell
Discussion Leaders: Tom Kono & Kevin Silverstein

Page Updated: 05 June 2016