Data Carpentry Genomics Workshop
University of Amsterdam
13 - 14 December 2017
9:00 - 16.30
Instructors:
Dennis Schmitz, Sam Nooij, Marc Galland, Anita Schürch
Helpers:
Zsofia Koma, Like Fokkens
13 - 14 December 2017
9:00 - 16.30
Instructors: Dennis Schmitz, Sam Nooij, Marc Galland, Anita Schürch
Helpers: Zsofia Koma, Like Fokkens
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 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.
Where:
Roeterseilandcampus, Amsterdam, room E0.15.
Get directions with
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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 a.c.schurch@umcutrecht.nl for more information.
Preliminary Schedule
Surveys
Please be sure to complete these surveys before and after the workshop.
13 December
| 09:00 | Introduction to Data Carpentry | AS |
| 09:30 | Introduction to the Data Set | AS |
| 09:45 | Data management | AS |
| 10:00 | Coffee break | |
| 10:15 | Data management continued | AS |
| 11:00 | Introducting the shell | SN |
| 11:45 | Navigating Files and Directories | SN |
| 12:30 | Lunch break | |
| 13:00 | Working with Files and Directories | SN |
| 13:45 | Redirection | SN |
| 15:00 | Coffee break | |
| 15:15 | Writing scripts | SN |
| 15:45 | Project Organization | SN |
| 16:30 | Wrap up day 1 | AS |
14 December
| 09:00 | Data Wrangling and Processing - Assessing Read Quality | MG |
| 10:00 | Coffee break | |
| 10:15 | Data Wrangling and Processing - Trimming and Filtering | DS |
| 11:00 | Data Wrangling and Processing - Variant calling workflow | DS |
| 12:30 | Lunch break | |
| 13:00 | Data Wrangling and Processing - Automating | DS |
| 14:30 | Coffee break | |
| 14:45 | Intro to cloud computing | AS |
| 16:30 | Wrap up | AS |
Etherpad: http://pad.software-carpentry.org/2017-12-13-amsterdam.
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. 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.