13 - 14 December 2017
9:00 - 16.30
Instructors: Dennis Schmitz, Sam Nooij, Marc Galland, Anita Schürch
Helpers: Zsofia Koma, Like Fokkens
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 is on working with genomics data and data management and analysis for genomics research.
We will cover project organization and management, introduction to the command line, data wrangling and processing and introduction to cloud computing for genomics. 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.
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 firstname.lastname@example.org for more information.
Please be sure to complete these surveys before and after the workshop.
|09:00||Introduction to Data Carpentry||AS|
|09:30||Introduction to the Data Set||AS|
|10:15||Data management continued||AS|
|11:00||Introducting the shell||SN|
|11:45||Navigating Files and Directories||SN|
|13:00||Working with Files and Directories||SN|
|16:30||Wrap up day 1||AS|
|09:00||Data Wrangling and Processing - Assessing Read Quality||MG|
|10:15||Data Wrangling and Processing - Trimming and Filtering||DS|
|11:00||Data Wrangling and Processing - Variant calling workflow||DS|
|13:00||Data Wrangling and Processing - Automating||DS|
|14:45||Intro to cloud computing||AS|
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.