Data Carpentry: BEACON @ MSU

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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 Intro to genomics files, Working in the Shell, and . 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 upper level undergraduate students, early graduate students, and others with no computational genomics experiance.

Where: Biomedical and Physical Sciences Building, 567 Wilson Road, Room 1441. 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 lsmead@msu.edu for more information.

Schedule

Monday

	09:00	Data organization and management
		Break 10:30 - 10:45
	10:45	Working with genomics file types
	12:00	Lunch Noon - 1
	01:00	Introduction to command line
		Break 3:00 - 3:15
	3:15	Wrangling and processing genomic data-Shell scripting

Etherpad: https://etherpad.wikimedia.org/p/MSU_DataCarpentry_Jan2016 (insert the URL for your Etherpad if you're using one).
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 described software.

Windows users: Install Gitbash before arriving at the workshop. (or at least download the installers) before the start of your workshop.

Mac and Linux users: No additional software is required

Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Download the Git for Windows installer.
Run the installer and follow the steps bellow:
1. Click on "Next".
2. Click on "Next".
3. Click on "Next".
4. Click on "Next".
5. Click on "Next".
6. Select "Use Git from the Windows Command Prompt" and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
8. Select "Use Windows' default console window" and click on "Next".
9. Click on "Next".
10. Click on "Finish".

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

The default shell in all versions of Mac OS X is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

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.

A Data Carpentry Workshop

BEACON @ MSU