Upcoming Training: High-throughput Sequencing Data at UC Davis

We’re excited to announce our 10th consecutive workshop on analyzing sequencing data, ANGUS 2019!

Please see http://ivory.idyll.org/dibsi/ANGUS.html, or below, for all the details.

July 1 – July 12, 2019
University of California, Davis


This workshop is organized and hosted by Dr. C. Titus Brown and
Dr. Karen Word. Please contact us at dibsi.training@gmail.com.

This intensive two-week summer course introduces attendees with a strong biology background to the practice of analyzing big shotgun sequencing data sets (Illumina, PacBio, and Nanopore). We introduce students to computational thinking and large-scale data analysis on UNIX platforms, and cover genome and transcriptome analysis. We also cover computational topics including R scripting, software installation with bioconda, cloud computing, and building efficient and automated workflows. We use hands-on tutorials, live coding, group notes, and in-class exercises to support an effective learning experience.

Lead instructors for 2019:

Mike Lee
Sateesh Peri
Taylor Reiter
Marian Schmidt

Confirmed lecturers for 2019:

Meg Staton
Erich Schwarz
Phillip Brooks


Registration is now open until June 1!

Please also see the Frequently Asked Questions for 2019.

No prior programming experience is required, although bravery in the face of the unknown is necessary!  A year or more of graduate school in biological sciences is strongly suggested. Faculty, postdocs, and research staff are more than welcome, as are researchers from industry.

The 2019 schedule is up!

We plan to run multiple independent classrooms of 20 – 30 participants each. Each classroom will have two lead instructors and four to five TAs and helpers. In 2019, we will provide both introductory and intermediate tracks to accommodate all levels of learners.

We strive to provide a welcoming and inclusive environment and work hard to accommodate learner needs. This course supports and encourages diversity by creating an environment in which people can communicate effectively and share their unique talents. This diversity of talents enriches the course by fueling creativity, innovation, and success!


What will I learn if I attend?


Our goal for these two weeks is to get students to the point where they are ready to begin analyzing their own data on a computer cluster and are more comfortable with help forums and other online resources to be able to continue advancing their own skills.

Students will gain practical experience in:

– bash shell and R scripting
– Cloud computing/Jetstream
– Installing and running many bioinformatics tools (e.g., BLAST, bwa, samtools)
– Querying mappings and evaluating assemblies
– Running workflows in the cloud and evaluating their results
– Estimating computational resources

Materials from previous courses are available at this link under a Creative Commons/full use+reuse license.

You can read a blog post about the 2015 course at this link.

The course fee will be $950 for this workshop. On-campus housing for
the two weeks of the ANGUS course is $1,005; housing includes breakfast and dinner, but not lunch.

What do people say about this workshop?


Quotes from previous attendees:

“I would climb a mountain and share this awesome program with the rest of the world.”

“We had great teachers and helpers. They made me feel comfortable in making mistakes and learn from them.”

“You don’t have to be a programmer to use or do computational science, and that is awesome!”

“I definitely broke through the difficult “starting” barrier, which was what I hoped to do. Now the techniques don’t seem so opaque and intimidating that I can’t work through them on my own.”

“My entire outlook on computational biology changed. I am much more enthusiastic about continuing to learn and apply computational analyses to my research.”

Computer requirements

You will need to bring a computer that can connect to Wi-Fi, and you should have a modern browser (Google Chrome, Safari, or Firefox) installed. No specific operating system is required.

We will use XSEDE Jetstream academic cloud computing to execute data analysis for the workshop; all analysis will be done remotely.

History

This workshop was run at Michigan State University’s Kellogg Biological Station from 2010 to 2016, with support from the USDA and NIH. Dr. Brown is the founding course director and ran the workshop from 2010 – 2015; Dr. Staton (UTK) and Dr. MacManes (UNH) were the 2016 course directors. In 2017, the course moved to UC Davis with Dr. Brown’s lab, and we were able to expand to serve over 70 learners.

There are now over 350 alumni of the first 9 years!

Register now!

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