GlyGen & CFDE Biocuration2024 Workshop

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Title: GlyGen and Common Fund Data Ecosystem (CFDE) Bioinformatics Workshop

When: 10 AM - 1 PM, March 5th, 2024

Register here (free registration): WORKSHOP REGISTRATION

Please register to get workshop-related details and also transportation details from the Indian Biological Data Centre (IBDC) (the main conference venue) to Univ. of Delhi South Campus (UDSC) (the workshop venue).

Venue: Univ. of Delhi South Campus. 17th Annual International Biocuration Conference, India (https://ibdc.rcb.res.in/biocuration2024/)

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.

GlyGen and other resources (20 mins)

  • GlyGen introduction
  • Common bioinformatics searches (BLAST, ID mapping, text search, supersearch, filtering)
  • 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)

CFDE (40 mins)

  • CFDE introduction
  • Ontologies and controlled vocabularies
  • Data model & data portal
  • 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.
  • Example questions (3-5 questions)
  • Participants will write out their questions/usecases during this session and finalize them during the break
 Raja, Jeet Suvarna
11:30 - 12:00 pm 30 min Refreshment Break.
  • Deposit questions in post-it notes on a board
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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.

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

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