What is ASU Genomics?
ASU Genomics is a group of students, faculty, and staff interested in learning, teaching and doing genomics and bioinformatics research.
For announcements about upcoming genomics workshops at Arizona State University, please join our google group: https://groups.google.com/forum/#!forum/asu_genomics.
Workshops are organized and managed by Melissa Wilson Sayres. To volunteer to run a session (1hr, 2hr, half-day or whole-day), please email: melissa.wilsonsayres at asu dot edu.
For people interested in getting started with bioinformatics, here's what we recommend: https://github.com/WilsonSayresLab/BioinformaticsIntroduction
Computing for Research. BIO 498 and BIO/EVO 598 (syllabus)
Shawn Rupp, Ph.D. Biology, Bioinformatics concentration: Comparative Genomics and Novel Bioinformatics Methodology Applied to the Green anole Reveal Unique Sex Chromosome Evolution
Past workshops and notes:
Nov 2016: Protein analysis (Daren Thifualt - Slides and Paper; 11 participants)
Nov 2016: Design and Analysis of Amplicon Sequencing for Targeted Multiplexed Genotyping (Shanshan Yang - WebCast; 12 participants)
Nov 2016: Reference-based genome assembly (Tim Webster - GitHub; 8 participants)
Nov 2016: An introduction to using R (Rick Simpson - Zip File of Notes; 13 participants)
Oct 2016: Uncertainty & Sensitivity Analysis (Anuj Mubayi, Dheeraj Lokam - Slides, GitHub; 9 participants)
Sep 2016: Simple Shell Scripting (Jeremy Mills and Melissa Wilson Sayres - Slides, Example Scripts, and Command Cheat Sheet; 23 participants)
Sep 2016: Interacting with the cluster: SSH/SFTP, SLURM batch scripts (Darren Thifault - Slides and Commands; 23 participants)
Aug 2016: R for Reproducible Molecular Evolution (David Winter - Notes; 20 particpants)
May 2016: De Novo Genome Assembly Using Next Generation Sequence Data (Marc Tollis - Slides; 45 participants)
May 2016: CoGe workshop (Eric Lyons and Blake Joyce - Slides and Notes; 35 participants)
March 2016: Awk tutorial (Maria Nieves Colon - GitHub; 34 participants)
February 2016: Introduction to Command Line (Melissa Wilson Sayres - Codecademy; 15 participants)
January 2016: The Galaxy Project - usegalaxy.org (Anton Nekrutenko - Agenda; 48 participants)
January 2016: Python bootcamp (Wilson Sayres lab; 15 participants)
BIO 598: Computing for Research (1 credit option to participate in all, or register individually).
This is a series of two-hour hands-on workshops:
August 29 - Introduction to Supercomputing at ASU, Melissa Wilson Sayres
September 12 - Interacting with the cluster: SSH/SFTP, SLURM batch scripts, Darren Thifault
September 26 - Useful Shell Scripting, Jeremy Mills & Melissa Wilson Sayres
October 24 - Uncertainty quantification and sensitivity analysis, Anuj Mubayi
November 7 - Designing and implementing a pipeline for reference-based genome assembly, Tim Webster
November 21 - Protein analysis, Daren Thifualt
December 5 - Stochastic modeling and simulations, Lokam Dheeraj
BIO 591: Research Computing Brown Bag (1 credit option to participate in all, or register individually)
This is a series of one hour discussion-based seminars over lunch on different research computing topics.
September 9 – Welcome to Research Computing, Host: Melissa Wilson Sayres
September 16 – Shell scripting, Host: Jeremy Mills
September 23 – Accessing the cluster, Host: Darren Thifault
September 30 – User Feedback: Training needs, Outreach, Communications Host: Marisa Brazil
October 7 – Decision Theatre Network, Host: Jon Miller
October 14 – What does Research Computing offer? Host: Brandon Mikkelsen
October 21 – Types of protein analysis, Host: Darren Thifault
October 28 – Finance and HPC, Host: Geoff Smith
November 4 – Genomics and HPC, Host: Tim Webster
November 11 – Veteran’s Day – No Brown bag
November 18 – Research Computing across ASU, Host: Brandon Mikkelsen
November 25 – Thanksgiving Break – No brown bag
December 2 – Informatics funding, Host: OKED representative
References I found useful at some point
- Current Topics in Genomics 2014 lectures from the NIH
- Statistics visualizations by Emil Kirkegaard
- Plotting in R: by Claus Wilke and Hadley Wickham
- R Reference Card by Tom Short
- R for beginners by Emmanuel Paradis
- Statistics for Biologists collection at Nature
- Homebrew - For downloading/installing on Mac. Original code by Max Howell, Website by Remi Prevost.
- Perl 5 By Example - Intro to programming in perl. By David Medinets.
- vi cheat sheet by Lagmonster.
Parsing and Analysis
- Bedtools: Dealing with Bed files, by Aaron Quinlan
- PGDSpider: Conversion tool for population genomics data types.
- Galaxy: Open source, web-based platform for data intensive biological research.
- DAVID: Database for Annotation, Visualization and Integrated Discovery
- GORILLA: Gene Ontology enRIchment anaLysis and visuaLizAtion tool
- Databases for teaching: Ernest, Morgan; Brown, James; Valone, Thomas; White, Ethan P. (2015): Portal Project Teaching Database
Viewing phylogenetic trees
- FigTree by Andrew Rambaut (cite website).
- ITOL: Interactive Tree of Life by Letunic and Bork (2007).
- Dendroscopeby Daniel H. Hudson (paper here).
For browsing: more comprehensive collections of bioinformatics resources
- ExPASy Bioinformatics Resource Portal
- Bioinformatics Resources collected by Anil Jegga
- Online Bioinformatics Resources Collection (OBRC) by the Health Sciences Library System at the University of Pittsburgh
Writing and Publishing