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DTSTART;TZID=Asia/Dubai:20250428T090000
DTEND;TZID=Asia/Dubai:20250429T163000
DTSTAMP:20260513T140344
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SUMMARY:Genomics Data Carpentry Workshop
DESCRIPTION:Welcome\nCode of Conduct\nSurveys\nPeople\nProgram\nSetup\nRegistration\n \n \n\n\nWelcome 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. \nGeneral Information\nThe 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. \nData 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. \nFor more information on what we teach and why\, please see our paper “Good Enough Practices for Scientific Computing“. \nWho: 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. \nWhere: Visitor Center\, MBZUAI\, Masdar City\, Abu Dhabi. Get directions with OpenStreetMap or Google Maps. \nWhen: Apr 28-29\, 2025; 9:00 am – 4:30 pm Add to your Google Calendar. \nRequirements: 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). \nAccessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that: \n\nThe room is wheelchair / scooter accessible.\nAccessible restrooms are available.\n\nWe 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. \nGlosario 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. \nContact: Please email aziz.khan@mbzuai.ac.ae for more information. \nRoles: To learn more about the roles at the workshop (who will be doing what)\, refer to our Workshop FAQ. \n\n   Register Now\n \n \n\n Directions \n\n    \n    \n\n\n\nCode of Conduct\nEveryone 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. \n\n   Report a Code of Conduct Incident\n\n\n\nSurveys\nPlease be sure to complete these surveys before and after the workshop. \n• Pre-workshop Survey \n• Post-workshop Survey \n\n\nInstructors\n\n\n    \n    \n      Aziz Khan\n      Assistant Professor of Computational Biology\, MBZUAI\n      Group Leader\, Computational Biology & Cancer Regulatory Genomics Lab\n      View Profile\n  \n\n    \n    \n      Nizar Drou\n      Core Bioinformatics Lead Developer\n      New York University\, Abu Dhabi\n      View Profile\n    \n  \n\n    \n    \n      Eduardo Beltrame\n      Assistant Professor of Computational Biology\, MBZUAI\n      View Profile\n    \n  \n\nHelpers\n\n\n    \n    \n      Muhammad Arshad\n      Bioinformatics Data Analyst\n      New York University\, Abu Dhabi\n    \n  \n\n    \n    \n      Nadine Hosny El Said\n      Postdoctoral Associate\n      New York University\, Abu Dhabi\n    \n  \n\n   \n    \n      Luiz Maniero\n      Visiting PhD Candidate\n      Computational Biology Department\, MBZUAI\n    \n  \n\n\n\n    \n    \n      Jayaram Radhakrishnan\n      Bioinformatics Infrastructure Engineer\n      New York University\, Abu Dhabi\n    \n  \n\n    \n    \n      Nabil Rahiman\n      Research Data Scientist\n      New York University\, Abu Dhabi\n    \n  \n\n    \n    \n      Giuseppe-Antonio Saldi\n      Data Scientist\n      New York University\, Abu Dhabi\n    \n  \n\n \n\n\nProgram on 28 April\, 2025\n\n\nMorning\nProject Organization and Management\n09:00 AM – 09:30 AM\nWelcome and Workshop Introductions\n09:30 AM – 10:00 AM\nData Tidiness\n10:00 AM – 10:30 AM\nPlanning for NGS Projects\n10:30 AM – 10:45 AM\nExamining Data on the NCBI SRA Database\n10:45 AM – 11:00 AM\nMorning Tea/Coffee Break\nMid Morning\nIntroduction to Cloud Computing for Genomics: Part I\n11:00 AM – 11:05 AM\nWhy of Cloud Computing\n11:05 AM – 11:15 AM\nLogging onto Cloud\n11:15 AM – 12:00 PM\nFine Tuning Your Cloud Setup\n12:00 PM – 01:00 PM\nLunch Break\nAfternoon\nIntroduction to the Command Line for Genomics\n01:00 PM – 01:15 PM\nIntroducing the Shell\n01:15 PM – 01:45 PM\nNavigating Files and Directories\n01:45 PM – 02:30 PM\nWorking with Files and Directories\n02:30 PM – 02:45 PM\nAfternoon Tea/Coffee Break\n02:45 PM – 03:30 PM\nRedirection\n03:30 PM – 04:15 PM\nProject Organization\n04:15 PM\nWrap-Up\n04:30 PM\nEnd of Day 1 Program\n\n\nProgram on 29 April\, 2025\n\n\nMorning\nGenomic Data Wrangling and Processing\n09:00 AM – 10:00 AM\nAssessing Read Quality\n10:00 AM – 10:45 AM\nTrimming and Filtering\n10:45 AM – 11:00 AM\nMorning Tea/Coffee Break\n11:00 AM – 12:00 PM\nVariant Calling Workflow\n12:00 PM – 01:00 PM\nLunch Break\n01:00 PM – 02:30 PM\nAutomating a Variant Calling Workflow\nAfternoon\nIntroduction to Cloud Computing for Genomics: Part II\n02:30 PM – 02:45 PM\nAfternoon Tea/Coffee Break\n02:45 PM – 03:15 PM\nData Roundtripping\n03:15 PM – 04:15 PM\nWhich Cloud for My Data?\n04:15 PM\nWrap-Up\n04:30 PM\nEnd of Day 2 Program and Event\n \n \n\n\nSetup\nTo 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. \nWe 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. \nThe setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site.
URL:https://mbzuai.ac.ae/event/genomics-data-carpentry-workshop/
LOCATION:Visitor Center\, MBZUAI Campus\, Masdar City\, Abu Dhabi\, United Arab Emirates
ATTACH;FMTTYPE=image/jpeg:https://sambzuaiwpprd01.blob.core.windows.net/mbzuaiwpprd01/2025/04/Genomics-Data-Carpentry.jpg
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