University of Oslo
Mar 15-16, 2016
9:00 am - 4:30 pm
Instructors: Tracy Teal, Carrie Andrew, Lex Nederbragt
Helpers: Hanna Helgeland, Halfdan Rydbeck, Karin Lagesen, William Brynildsen
General Information
Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain.
The focus of this workshop will be on working with genomics data and data management and analysis for genomics research. We will cover metadata organization in spreadsheets, data organization, connecting to and using cloud computing, the command line for sequence quality control and bioinformatics workflows, and R for data analysis and visualization. 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. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. 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 for any researcher who has data they want to analyze, and no prior computational experience is required.
Where: Niels Henrik Abels hus, Moltke Moes vei 35, Oslo. Get directions with OpenStreetMap or Google Maps.
Requirements: Participants must bring a laptop with a few specific software packages installed (see below). They are also required to abide by Data Carpentry's Code of Conduct.
Contact: Please mail organizers@swcarpentry.uio.no for more information.
Schedule
(NOTE subject to change)Day 1
| 09:00 | Introduction |
| Workshop overview, Introduction to the dataset, Examining data on SRA | |
| 10:30 | Coffee |
| 10:45 | Data organization and tidiness |
| 11:15 | Using cloud computing for genomics |
| 12:00 | Lunch break |
| 13:00 | Introduction to the command line |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
Day 2
| 09:00 | Data wrangling and processing |
| Project setup, Quality control of NGS data, Automating a workflow | |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | R for data analysis and visualization |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
Etherpad: http://pad.software-carpentry.org/2016-03-15-oslo-bio.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Setup
To participate in this Data Carpentry workshop, you will need access to some software. In addition, you will need an up-to-date web browser.
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.