May 03-04, 2018
9:00am - 4:00pm
Instructors: Nima Hejazi, Adam Orr
Helpers: Nurgul Kaplan, Shi Wang
Data Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: 1 Cyclotron Road, Berkeley, CA 94720, Building 54, Room 130. Get directions with OpenStreetMap or Google Maps.
When: May 03-04, 2018. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (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.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email ecscharfstein@lbl.gov , ajorr1@asu.edu or nhejazi@berkeley.edu for more information.
Please be sure to complete these surveys before and after the workshop.
| Early Morning | Project organization and management |
| Coffee Break | |
| Late Morning | Introduction to the command line |
| Lunch Break | |
| Afternoon | Command line continued |
| Coffee Break | |
| Evening | Command line continued |
| Early Morning | Data wrangling and processing |
| Coffee Break | |
| Late Morning | Data wrangling continued |
| Lunch Break | |
| Afternoon | Data wrangling continued |
| Coffee Break | |
| Evening | Introduction to cloud computing for genomics |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
This workshop is designed to be run on pre-imaged Amazon Web Services (AWS) instances. All the software and data used in the workshop are hosted on an Amazon Machine Image (AMI). For information about how to use the workshop materials, see the setup instructions on the main workshop page.
Windows users should download and install PuTTY.
The project organization lesson requires a working spreadsheet program. If you don’t have a spreadsheet program already, you can use LibreOffice. It’s a free, open source spreadsheet program.