Jason Williams on The Carpentries

Genomics Workshop Pilot and BugBBQ at University of Arizona

Wed, 15 May 2019 00:00:00 +0000

This post originally appeared on the Data Carpentry website

This February, a small group of committed community members, led by Taylor Reiter at the University of California, Davis, completed a major update to the Data Carpentry Genomics curriculum. A huge thank you to everyone who contributed! This update included significant changes to both the data set and the software used for the lessons, modernizing the workshop and keeping it relevant to researchers working in the genomics field. The new version of this curriculum is already live and will be officially published in the upcoming lesson release in June.

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.

Building Genomics Data Analysis Capacity at NWU

Wed, 07 Dec 2016 00:00:00 +0000

This post originally appeared on the Data Carpentry website

The North-West University in South Africa boasts two next generation sequencing (NGS) platforms and additionally receive terabytes of NGS data annually from local and international service providers. Research projects with NGS components exist in the areas of Microbiology, Zoology, Botany, Nutrition, Agriculture, and more.

The three biggest challenges experienced by researchers and postgraduate students in terms of data analysis are as follow:

many of the students entering NGS projects have limited prior exposure to molecular techniques such as Sanger sequencing and PCR, and genetics concepts;
there is limited access to bioinformatics support and training (although there is lots of access to short interventions like 1- or 2-day workshops with no sustained follow-up);
and they are not aware of the range of research compute infrastructures which are available to them.

In September 2016, the NWU eResearch Initiative helped to establish a Genomics Hacky Hour (GHH) Study Group to support postgraduate students and researchers using NGS technologies. The original intention of the GHH was to bring researchers together to work on their current projects. However, limited shared NGS vocabulary hampered constructive communication amongst researchers and it was decided that specific topics would be discussed during the first few sessions, lead by a study group leader.

2016 Election: Jason Williams

Thu, 14 Jan 2016 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

#2016 Election: Jason Williams

With benthic sensuous pleasure I offer up myself as candidate for the 2016 Steering Committee.

There are those (mom, the U.S. Department of Justice) who have labeled my apoplectic fits a sign of ‘weakness’, but I have found them to be a source of extraordinary strength. With this strength I pledge to bring Software Carpentry to places no one imagined it could (or should) go. As other candidates hail HYDRA, I’m proud to be the first and only candidate to come out in favor of all the things you believe in, and strongly (though perhaps not uncategorically) opposed to the things that displease you.

Assessment Update - 2015

Tue, 22 Dec 2015 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

About a year ago, I hoped to help answer the question, "Is our students learning?" We are now a bit closer to an answer, and I wanted to update the community about what we have accomplished this year. First, I want to thank and acknowledge the assessment subcommittee and Blake Joyce, who helped to define tasks, possibilities, and provided significant feedback. Especially here I wanted to thank Daniel Chen, Jeramia Ory, and Rayna Harris who put in a lot of hours moving things along.

2015 Election: Jason Williams

Wed, 14 Jan 2015 00:00:00 +0000

This post originally appeared on the Software Carpentry website.

"You can trust in Jason, he's your friend!" — Decent People

I can't recall ever running in an election - rule by fiat is what "just feels right" to me. I have on occasion thought about running for office but I usually lack ambition (although I'm attracted to power). The fantasy of being the candidate people vote for even though he is clearly against their interest just makes my pedipalps tingle. So, when I learned about the Software Carpentry Foundation election, I thought, "let's try that!"