March 22, 2023
9:00 am - 12:30 pm EDT
Instructors: John Bradley (Duke), Matthew Thompson (OSU)
Helpers: Elizabeth Campolongo (OSU), Steve Chang (OSU), Jim Balhoff (RENCI), Hilmar Lapp (Duke)
This workshop is inspired by the format of The Carpentries-type workshops. It combines lessons from the Carpentries Incubator. (Lessons in the incubator are in early development and thus much less mature than lessons in the core curriculum.) In contrast to "regular" Carpentries workshops, the total length of instruction for this workshop is only a half day. However, as for regular Carpentries workshops, this course will be highly interactive and hands-on. Participants will use their own laptops throughout the course, and are encouraged to help one another.
The Carpentries develops and teaches workshops on the foundational coding and data skills needed to conduct research. Its target audience is researchers worldwide, including those who have little to no prior computational experience.
For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".
This is a pilot workshop, meaning the lessons being taught are under active development. We would appreciate any feedback you can give about the content of the lessons, and suggestions for how they could be further improved.
Who: This workshop is aimed at NextGens and other researchers across the Imageomics Institute. The lessons assume you have some basic knowledge of Python and some previous exposure to the Bash command line shell. The workshop is held as part of the Imageomics All-Hands meeting, and unless notified otherwise is currently not open to others for registration.
Where: 175 Pomerene Hall, 1760 Neil Ave., Columbus, Ohio 43210. Get directions with OpenStreetMap or Google Maps.
When: March 22, 2023. 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).
Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, 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 hilmar.lapp@duke.edu , john.bradley@duke.edu or thompson.4509@osu.edu for more information.
Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.
Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Please be sure to complete these surveys before and after the workshop.
This workshop is teaching lessons from The Carpentries Incubator.
| Before starting | Pre-workshop survey |
| 9-10am | Reproducible Computational Environments Using Containers: Introduction to Docker |
| Break |
| 10.30am-12.30pm | Workflow Automation using Snakemake |
| During lunch | Post-workshop survey |
| END |
The lesson taught in this workshop is being piloted and a precise schedule is yet to be established. The workshop will include one break of about 15 minutes.
To participate in a Imageomics workshop, you will need access to software and other resources as described below. 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.
The setup instructions for the Imageomics workshop lessons are the following:
.