Genomics Data Carpentry Workshop

Monday, April 28, 2025 - Tuesday, April 29, 2025

start-time 9:00 am - 4:30 pm
end-time Visitor Center, MBZUAI Campus, Masdar City, Abu Dhabi
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Welcome
Code of Conduct
Surveys
People
Program
Setup
Registration

Welcome to the first Data Carpentry Genomics Workshop at MBZUAI, organized by the Computational Biology and Cancer Regulatory Genomics (CBCRG) Lab, Computational Biology Department at MBZUAI, in collaboration with the Center for Genomics and Systems Biology (CGSB), NYU Abu Dhabi. This interactive hands-on workshop aims to build regional capacity in genomics and computational biology, empowering participants with foundational genomics data science skills and highlighting MBZUAI's commitment to advancing precision medicine and digital public health in the UAE and beyond.

General Information

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.

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 (click here).

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

  • The room is wheelchair / scooter accessible.
  • Accessible restrooms are available.

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.

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Directions

Code of Conduct

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.

Report a Code of Conduct Incident

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Instructors

  • Aziz Khan
    Assistant Professor of Computational Biology, MBZUAI
    Group Leader, Computational Biology & Cancer Regulatory Genomics Lab
    View Profile
  • Nizar Drou
    Core Bioinformatics Lead Developer
    New York University, Abu Dhabi
    View Profile
  • Eduardo Beltrame
    Assistant Professor of Computational Biology, MBZUAI
    View Profile

Helpers

  • Muhammad Arshad
    Bioinformatics Data Analyst
    New York University, Abu Dhabi
  • Nadine Hosny El Said
    Postdoctoral Associate
    New York University, Abu Dhabi
  • Luiz Maniero
    Visiting PhD Candidate
    Computational Biology Department, MBZUAI
  • Jayaram Radhakrishnan
    Bioinformatics Infrastructure Engineer
    New York University, Abu Dhabi
  • Nabil Rahiman
    Research Data Scientist
    New York University, Abu Dhabi
  • Giuseppe-Antonio Saldi
    Data Scientist
    New York University, Abu Dhabi
 

Program on 28 April, 2025

Morning
09:00 AM - 09:30 AM
Welcome and Workshop Introductions
09:30 AM - 10:00 AM
Data Tidiness
10:00 AM - 10:30 AM
Planning for NGS Projects
10:30 AM - 10:45 AM
Examining Data on the NCBI SRA Database
10:45 AM - 11:00 AM
Morning Tea/Coffee Break
Mid Morning
11:00 AM - 11:05 AM
Why of Cloud Computing
11:05 AM - 11:15 AM
Logging onto Cloud
11:15 AM - 12:00 PM
Fine Tuning Your Cloud Setup
12:00 PM - 01:00 PM
Lunch Break
Afternoon
01:00 PM - 01:15 PM
Introducing the Shell
01:15 PM - 01:45 PM
Navigating Files and Directories
01:45 PM - 02:30 PM
Working with Files and Directories
02:30 PM - 02:45 PM
Afternoon Tea/Coffee Break
02:45 PM - 03:30 PM
Redirection
03:30 PM - 04:15 PM
Project Organization
04:15 PM
Wrap-Up
04:30 PM
End of Day 1 Program

Program on 29 April, 2025

Morning
09:00 AM - 10:00 AM
Assessing Read Quality
10:00 AM - 10:45 AM
Trimming and Filtering
10:45 AM - 11:00 AM
Morning Tea/Coffee Break
11:00 AM - 12:00 PM
Variant Calling Workflow
12:00 PM - 01:00 PM
Lunch Break
01:00 PM - 02:30 PM
Automating a Variant Calling Workflow
Afternoon
02:30 PM - 02:45 PM
Afternoon Tea/Coffee Break
02:45 PM - 03:15 PM
Data Roundtripping
03:15 PM - 04:15 PM
Which Cloud for My Data?
04:15 PM
Wrap-Up
04:30 PM
End of Day 2 Program and Event

Setup

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.



Venue

Visitor Center, MBZUAI Campus, Masdar City

Abu Dhabi, United Arab Emirates

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