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A Data Carpentry Workshop

Langebio, Cinvestav Unidad Irapuato

June 1-2, 2016

9:00 am - 4:30 pm

Instructors: Jason Williams, John Fonner

Helpers: Beto Bermúdez, Rubén Rellán Álvarez, Covando, Selene L. Fernandez-Valverde, Dagoberto Armenta, Jacob Israel

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 Cloud computing and command line for genomics and Data analysis and visualization in R. 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: Libramiento Norte Carretera Leon Km 9.6, 36821 Irapuato, Gto., Mexico. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail for more information. Registration is directly through CyVerse at

Pre-Survey: Please take this pre-survey prior to the workshop.


Day 2: 9AM - 4:30PM

Morning: Using Linux to organize and process Genomics Data
Intro to the Linux Shell - Searching and Metadata Jason
Project Organziation and Documentation John
'For' loops - QC of Sequencing Data Jason
Afternoon: Using Linux to Automate
Automating Analyses - Shell Scripting Selene
Creating Workflows - Varient Calling Workflow Selene
Workshop Conclusion Please take the post-survey

Post Workshop

How to Make This Work on Your Own
Launching Your Own Cloud Instances On Your Own

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


To participate in a Data Carpentry workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) 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.

Please follow these Setup Instructions.

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.