GlyGen & CFDE Biocuration2024 Workshop
Title: GlyGen and Common Fund Data Ecosystem (CFDE) Bioinformatics Workshop
When: 10 AM - 1 PM, March 5th, 2024
Attendees are kindly asked to ensure their devices are fully charged prior to the workshop, as accommodating simultaneous charging for all devices may prove challenging.
Register here (free registration): REGISTRATION IS CLOSED. If you are interested in a two hour virtual workshop on May 1st, 2024 (11 AM US Eastern Time) please register HERE.
Please register to get workshop-related material and also transportation details from the Indian Biological Data Centre (IBDC) (the main conference venue) to Univ. of Delhi South Campus (UDSC) (workshop venue: Biotech Auditorium, USDC). Due to traffic conditions, it might be a one-hour taxi ride.
Note: We have filled all available spots for this workshop. New registrants will be placed on a waiting list. Main conference participants will receive priority. Everyone who is waitlisted will have a chance to join an upcoming online workshop. We'll keep you informed.
Venue: Biotech Auditorium, Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India.
Organizing Committee: Raja Mazumder (GlyGen, CFDE), Jeet Vora (GlyGen, CFDE), Suvarna Nadendla (CFDE), Saurabh Raghuvanshi (Univ. of Delhi), Sonia Balyan (IBDC), Utkarsh Raghuvanshi (UDSC), Mike Tiemeyer (GlyGen, CFDE, remote), Rene Ranzinger (GlyGen, CFDE, remote)
Abstract
An interactive 3-hour in-person bioinformatics workshop is scheduled for March 5th, 2024, from 10 AM to 1 PM. Blending training sessions with hands-on activities the workshop is designed for students, post-docs, and early investigators interested in bioinformatics analysis and knowledgebase development. Attendees will be able to participate using their cell phones, mobile devices, or laptops. This workshop marks a continuation of the Glycan Function Workshop series initiated last year during Biocuration 2023 in Padua, Italy. The focus of the workshop will be on bioinformatics analysis use cases that span exploration of glycan and protein function, gene mutations, gene expression, and how biocuration along with large-scale analysis, querying, and filtering of data can reveal insights into biomolecule function. NIH's Common Fund Data Ecosystem will also be presented.
This workshop aims to provide attendees with practical skills in bioinformatics analysis. Best practices in knowledgebase development and biocuration will also be discussed, fostering seamless integration into existing resources worldwide and making data findable, accessible, interoperable, and reusable. There will also be a feedback session to identify gaps in current resources.
Schedule
| Time | Duration | Topic | Presenter(s) |
|---|---|---|---|
| 10 - 11:00 am | 60 min | Welcome and introduction. An overview of GlyGen and the NIH-funded Common Fund Data Ecosystem (CFDE) will be presented to provide attendees with the scope of scientific questions these resources can answer. Other key resources such as UniProtKB, NCBI, and EBI will be introduced to showcase how certain use cases and scientific questions require cross-resource queries.
Glycobiology, GlyGen and other resources (20 mins)
Other resources needed for the example use case
Common bioinformatics searches (BLAST, ID mapping, Site Search, Supersearch, Filtering) (20 mins) CFDE (20 mins)
|
Raja, Jeet, Suvarna |
| 11:00 - 11:30 am | 30 min | Scientific Question Co-Development. A collaborative session with the audience will be held to formulate scientific questions addressable through the introduced resources.
Example format - As a (user profile) (e.g. As a Microbiologist, Glycobiologist) - I want (requirement) (e.g. I want a list of human glycosyltransferases) - So that (benefit) (e.g. so that I can evaluate their expression in cancer) Field of Study: (e.g. glycobiology, rare disease) Name: Jeet Vora Email: jeetvora@gwu.edu |
Raja, Jeet Suvarna |
| 11:30 - 12:00 pm | 30 min | Refreshment Break. | - |
| 12:00 - 1:00 pm | 60 min | Hands-On Session and Q&A. Participants, alongside presenters, will use their laptops or mobile devices to answer the formulated scientific questions. Discussion on opportunities and challenges presented by these bioinformatics resources. | All |
Presentation/Discussion Sessions
Each presentation/discussion session will demonstrate the use and practice of GlyGen and CFDE portals and tools. Participants are allowed to ask questions during each session. All the unanswered questions will be addressed by the presenters during the Q&A session at the end of the workshop.
Presenters & Local Organizing Committee Members
Raja Mazumder (George Washington University) (ORCID: 0000-0001-8823-9945)
Jeet Vora (George Washington University) (ORCID: 0000-0002-5317-1458)
Suvarna Nadendla (University of Maryland, Baltimore)
Sonia Balyan (Indian Biological Data Centre)
Utkarsh Raghuvanshi (University of Delhi, South Campus)
Workshop Logistics
Participants need to bring their laptops and/or smartphones to the workshop. This workshop is being held in conjunction with the 17th Annual International Biocuration Conference (https://ibdc.rcb.res.in/biocuration2024/)
Transportation - Bus departures from two different pickup points have been arranged on the morning of March 5, 2024.
Bus Departure Timings:
- RCB, Faridabad: 8:00 A.M (For other participants)
- Vivanta Surajkund: 8:30 A.M (For participants staying at Vivanta Surajkund)
Acknowledgment
NIH funds 1R24GM146616-01 and 1OT2OD032092
Contact
For questions about registration or general inquiries, please contact:
Raja Mazumder: mazumder@gwu.edu
Jeet Vora: jeetvora@gwu.edu