22 - 23 Oct 2025
9:00am - 5.00pm MYT
Instructors: Bryan Wee
Helpers: Timothy Jinam, Chai Li Chin, Wong Hong Kin, Shirley Tan
This workshop is open to postgraduate students (Master’s or PhD level) and researchers who are planning to generate and/or analyse genome sequence data using open-source command-line tools.
To help us understand how the workshop fits with your work, we’ll ask you to complete a short questionnaire about how genomics is relevant to your research or professional role. If you’re interested in joining, please fill out the registration form below. As places are limited, participants will be selected based on how relevant the workshop is to their current or upcoming work.
A recommendation from a scientific or clinical sponsor such as your supervisor, line manager, or head of department, is also required to support your application.
Registration Fees*:
*Registration includes morning tea, lunch and afternoon tea.
**Full-time or part-time enrolled Master’s or PhD students
Registration will close on Monday, 29th September 2025 or when all places have been filled.
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.
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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: 172, Rock Road, 93200, Kuching, Sarawak. Get directions with OpenStreetMap or Google Maps.
When: 22 - 23 Oct 2025; 9:00am - 5.00pm MYT 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 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 unimas-datacarpentry-genomics-2025@sidc.org.my 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.
Please be sure to complete these surveys before and after the workshop.
| Before starting | Pre-workshop survey |
| Morning | Project Organization and Management |
| 09:00 | Welcome and workshop introductions |
| 09:30 | Good data organisation |
| 10:00 | Planning for genomics projects |
| 10:30 | Accessing publicly available genomic data |
| 10:45 | Tea Break |
| Mid-Morning | Intro to Cloud for Genomics: Part I |
| 11:00 | Why cloud computing |
| 11:15 | Logging into the cloud |
| 11:45 | Customising your cloud setup |
| 12:15 | Lunch |
| Afternoon | Introduction to the Command Line |
| 13:00 | Shell basics |
| 13:30 | File and directory navigation |
| 14:45 | File management |
| 15:25 | Tea Break |
| 15:45 | Redirection of output |
| 16:30 | Automation |
| 16:45 | Organising project files (if time permits) |
| Morning | Genomic Data Processing using Command Line Tools |
| 09:00 | Introduction to the genomic data |
| 09:15 | Assessing read quality |
| 10:30 | Tea break |
| 11:00 | Trimming and filtering |
| 12:00 | Lunch |
| 13:00 | Variant calling workflow |
| 14:00 | Automating a variant calling workflow (if time permits) |
| Afternoon | Intro to Cloud for Genomics: Part II |
| 15:00 | Tea break |
| 15:15 | Working with the cloud |
| 15:30 | Transferring data in the cloud |
| 16:15 | Wrap-up and discussion |
| 16:45 | Post-workshop survey |
To participate in a Data Carpentry workshop, you will need access a working spreadsheet program (e.g. Microsoft Excel). If you don’t have a spreadsheet program already, you can use LibreOffice. It’s a free, open source spreadsheet program. Directions to install are included for each Windows, Mac OS X, and Linux systems. For Windows, you will also need to install either Git Bash, PuTTY, or the Ubuntu Subsystem. 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.
During the workshop we will be using Amazon Web Services (AWS) instances (cloud-based virtual machines) that will be set up for you. Depending on your operating system, there may be some additional software required. Please refer to the instructions found at the workshop overview site. We will be using the "Required additional software + Option A" option, so you only need to install the "Required additional software". If you would like install the tools on your own computer after the workshop, please refer to the "Option B: Using the lessons on your local machine"
.