A Data Carpentry Workshop
The Donald Danforth Plant Science Center
June 17, 2017
9:00 am - 5:00 pm
Instructors:
Bo Ji, Catalina Anghel
Helpers:
Alex Harkess, Patricia Baldrich
June 17, 2017
9:00 am - 5:00 pm
Instructors: Bo Ji, Catalina Anghel
Helpers: Alex Harkess, Patricia Baldrich
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.
The focus of this workshop will be on working with genomics data and data management and analysis for genomics research. We will cover data organization, connecting to and using cloud computing, the command line for sequence quality control and bioinformatics workflows. We will not be teaching any particular bioinformatics tools, but the foundational skills that will allow you to conduct any analysis and analyze the output of a genomics pipeline.
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: Mary and Oliver Langenberg Theater, 975 North Warson Road, St. Louis, MO. 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 catalina.v.anghel@gmail.com for more information.
Etherpad
Link: http://pad.software-carpentry.org/2017-06-17-stlouis.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Surveys
Please be sure to complete these surveys before and after the workshop.
Schedule
Morning: 9:00AM - 12:00PM
| Module 1: Data and project organization | |
| Intro to Data Carpentry | Bo |
| Intro to Data and Genomics Data Tidiness (brief overview) | Bo |
| Module 2: Using cloud computing for genomics | |
|
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| Connecting to the Cloud in 5 Minutes or Less | Bo |
| Module 3: Introduction to the command line | |
| Using the Command Line (Shell) | Bo (a short introduction by Catalina) |
Afternoon: 1PM - 5:00PM
| Module 3, continued (if needed): Command line | |
| Using the Command Line (Shell) | Catalina |
| Module 4: Running bioinformatics programs and creating workflows | |
|
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| QC of Sequence Data | Catalina |
| Automating Workflows (up until the shell script) | Catalina |
Post Workshop
| Alignment and Variant Calling | Automating Workflows | On Your Own |
| Variant Calling | On Your Own |
| How To Make This Work Your Own | Launching Your Own Cloud Instances | On Your Own |
Setup
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.