Genomics on The Carpentries

DC Genomics Workshop, UC Davis, January 2018

Wed, 28 Mar 2018 00:00:00 +0000

This post originally appeared on the Data Carpentry website

From January 24-25 (Thursday and Friday) we held a Data Carpentry Genomics workshop at UC Davis, led by Sue McClatchy. This was a “sold out” workshop, which filled up about a day after the registration went live. This indicates to us that we should host it again!

Overall, it was a great workshop. The learning workflow included:

Data organization and management -> Introduction to the shell -> Downloading sequencing data files -> QC (fastqc and trimming) -> Assembly -> Variant calling

Genomics Bug BBQ

Mon, 18 Sep 2017 00:00:00 +0000

This post originally appeared on the Data Carpentry website

Bug BBQ starting today, Monday, September 18th!

Be a part of the Genomics Data Carpentry lesson release! We held an Issue Bonanza last month to identify everything from typos to updates in code blocks and had some discussions on broader re-organization. Our next step is to go through and resolve those issues and determine ordering of the lessons.

To help us get over the finish line we’re having a Bug BBQ September 18th - 19th (whatever this is in your time zone!) to squash as many of these bugs as we can, and continue discussions. The Bug BBQ is also an opportunity for you to engage with our world-wide community. For more info about the event, read-on and visit our Bug BBQ Etherpad.

Upcoming Publication of Genomics Materials

Thu, 17 Aug 2017 00:00:00 +0000

This post originally appeared on the Data Carpentry website

There’s been a lot of exciting work on the Genomics workshop materials over the past several months. A massive reorganization of the materials is underway, splitting the workshop into two separate tracks - one including R and the other including a variant-calling workflow. A host of folks have volunteered to serve as Maintainers for the revamped lessons, and others have joined a Curriculum Advisory Committee to provide high-level guidance on the workshop as a whole.

Genomics Interest

Wed, 14 Jun 2017 00:00:00 +0000

This post originally appeared on the Data Carpentry website

Last month, we announced an upcoming revamp for the Data Carpentry Genomics lessons and asked you to let us know how you would like to be involved. We’ve had a tremendous amount of interest from the community, with 78 people indicating their enthusiasm for being a part of this effort.

Twenty-nine people volunteered to serve as Maintainers for the Genomics lessons. You will all be receiving an email shortly with more information about this role. Welcome to the Maintainer team!

Call for Contributions: Moving Ahead with Genomics Data Carpentry

Wed, 03 May 2017 00:00:00 +0000

This post originally appeared on the Data Carpentry website

Way back in March of 2015, a group of 27 Carpentry community members gathered at Cold Spring Harbor for the first Data Carpentry Hackathon on a set of lessons and assessments for Genomics Data Carpentry. From the beginning, we wanted these lessons to be driven by, and useful to the large community of biologists who are (or will be) working with large genomics dataset datasets; perhaps as many as 90% of biologists.