May 10-11, 2018
8:30 am - 5:00 pm
Instructors: Boryana Koseva, Asli Uyar
Helpers: Paola Castro, Olga Botvinnik, Jay Kasberger, Spyros Darmanis, Josh Batson, Angela Oliveira Pisco
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: 499 Illinois St, San Francisco, CA 94158. Get directions with OpenStreetMap or Google Maps.
When: May 10-11, 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 olga.botvinnik@czbiohub.org for more information.
Please be sure to complete these surveys before and after the workshop.
| Morning | Project organization and management |
| Introduction to the command line | |
| Afternoon | Introduction to cloud computing for genomics |
| Data wrangling and processing |
| Morning | Data wrangling and processing (cont'd) |
| Afternoon | Data analysis and visualization in R |
| Evening | Post-workshop survey |
We will use this collaborative document 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.
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.