General Information

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.

We will cover Welcome and overview of genomic data, Introduction to command line, Command line continued and Variant Calling and Workflow Automation. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.

Who: The course is aimed at graduate students and other researchers.

Where: Lawrence Berkeley National Laboratory, Building 59, Room 3101. 1 Cyclotron Rd, Berkeley, CA. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail Erin Scharfstein at ecscharfstein@lbl.gov for more information.

Preliminary Schedule

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Etherpad: http://pad.software-carpentry.org/2017-08-07-LBNL.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Setup

To participate in a Data Carpentry workshop, you will need working copies of the software named below. Please make sure to install everything before the start of your workshop. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Mac users

1. Java
2. Filezilla
3. Integrative Genomics Viewer (IGV) (You will need to enter your email address; don't worry, they don't send spam.)

Windows users

1. Putty (Download putty.exe)
2. Java
3. Filezilla
4. Integrative Genomics Viewer (IGV) (You will need to enter your email address; don't worry, they don't send spam.)

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.