Jan 26-27, 2017
9:00 am - 4:30 pm
Instructors: Sue McClatchy, Dan Gatti, Eric Ma, Bob Freeman, Brian Teague, Asli Uyar
Helpers: David LaPointe, Albert Tai, Norbert Kremer
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 Introduction to the Shell and Cloud Computing, The Shell and Project Setup, Know Your Data 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 workshop is sponsored by the graduate Immunology Program and is open primarily to graduate students, faculty and postdoctoral fellows in immunology.
Where: 145 Harrison Avenue, Boston, Massachusetts. 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 diana.pierce@tufts.edu for more information.
Morning | Introduction to the Shell and Cloud Computing |
Afternoon | The Shell and Project Setup |
Morning | Know Your Data |
Afternoon | Variant Calling and Workflow Automation |
Etherpad: http://pad.software-carpentry.org/2017-01-26-tufts.
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.
Morning | Introduction to the Shell and Cloud Computing |
09:00 | Workshop overview |
09:30 | Using cloud computing for genomics |
10:00 | Introduction to Unix: navigating, paths, shortcuts |
10:45 | Coffee/tea break |
11:00 | Introduction to Unix: examining files, modifying, writing |
12:00 | Lunch on your own |
Afternoon | The Shell and Project Setup |
13:00 | Introduction to Unix: searching and redirection |
13:45 | Shell scripts |
14:30 | Coffee/tea break |
14:45 | Shell scripts (cont) |
15:45 | Genomics planning |
16:45 | Wrap-up |
Morning | Know Your Data |
09:00 | Introduction to the workshop dataset |
09:15 | Examining data on the NCBI SRA database |
09:45 | QC of NGS data |
10:45 | Coffee/tea break |
11:00 | QC of NGS data (cont) |
12:00 | Lunch on your own |
Afternoon | Variant Calling and Workflow Automation |
13:00 | Variant calling workflow (QC, alignment, variant calling) |
14:00 | Automating the workflow |
14:30 | Coffee/tea break |
14:45 | Automating the workflow (cont) |
16:45 | Wrap-up |
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.
Mac users
Windows users
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.