Apr 28-29, 2025
9:00 am - 4:30 pm
Instructors: Aziz Khan, TBD
Helpers: TBD
The Carpentries project comprises the Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach foundational computational and data science skills to researchers.
Want to learn more and stay engaged with The Carpentries? Carpentries Clippings is The Carpentries' biweekly newsletter, where we share community news, community job postings, and more. Sign up to receive future editions and read our full archive: https://carpentries.org/newsletter/
Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. 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 "Good Enough 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: Visitor Center, MBZUAI, Masdar City, Abu Dhabi. Get directions with OpenStreetMap or Google Maps.
When: Apr 28-29, 2025; 9:00 am - 4:30 pm 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. The workshop organizers have checked that:
We are dedicated to providing a positive and accessible learning environment for all. We do not require participants to provide documentation of disabilities or disclose any unnecessary personal information. However, we do want to help create an inclusive, accessible experience for all participants. We encourage you to reach out to workshop organizers and share any information that would be helpful to make your Carpentries experience accessible.
Glosario is a multilingual glossary for computing and data science terms. The glossary helps learners attend workshops and use our lessons to make sense of computational and programming jargon written in English by offering it in their native language. Translating data science terms also provides a teaching tool for Carpentries Instructors to reduce barriers for their learners.
Contact: Please email aziz.khan@mbzuai.ac.ae 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.
| Morning | Project organization and management |
| 09:00 | Welcome and workshop introductions |
| 09:30 | Data Tidiness |
| 10:00 | Planning for NGS Projects |
| 10:30 | Examining Data on the NCBI SRA Database |
| 10:45 | Coffee |
| Mid-Morning | Introduction to cloud computing for genomics: Part I |
| 11:00 | Why of cloud computing |
| 11:05 | Logging onto Cloud |
| 11:15 | Fine tuning your Cloud Setup |
| 12:00 | Lunch break |
| Afternoon | Introduction to the command line for genomics |
| 1:00 | Introducing the Shell |
| 1:15 | Navigating Files and Directories |
| 13:45 | Working with Files and Directories |
| 14:30 | Coffee |
| 14:45 | Redirection |
| 15:30 | Project Organization |
| 16:15 | Wrap-up |
| 16:30 | END |
| Morning | Genomic data wrangling and processing |
| 09:00 | Assessing Read Quality |
| 10:00 | Trimming and Filtering |
| 10:45 | Coffee |
| 11:00 | Variant Calling Workflow |
| 12:00 | Lunch break |
| 13:00 | Automating a Variant Calling Workflow |
| Afternoon | Introduction to cloud computing for genomics: Part II |
| 14:30 | Coffee |
| 14:45 | Data roundtripping |
| 15:15 | Which Cloud for my data? |
| 16:15 | Wrap-up |
| 16:30 | END |
To participate in a Data Carpentry workshop, you will need access to software 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 Data Carpentry Genomics workshops can be found at the workshop overview site
.