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)

Important links:

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) Glycobiology Introduction GlyGen introduction Concept of entry pages in knowledgebases Starting use-case in GlyGen Other resources needed for the example use case UniProtKB NCBI (RefSeq, PubChem) EBI (ChEBI) Common bioinformatics searches (BLAST, ID mapping, Site Search, Supersearch, Filtering) (20 mins) CFDE (20 mins) CFDE introduction Ontologies and controlled vocabularies Data model Findability of data and Cross Data Coordination Center (DCC) searches Cloud-based analysis on CAVATICA	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. Participants will write out their questions/usecases during this session and finalize them during the break. The usecases can be added here 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:

1. RCB, Faridabad: 8:00 A.M (For other participants)
2. 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