GlyGen CFDE Biocuration2024 Workshop: Difference between revisions

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{{DISPLAYTITLE:GlyGen & CFDE Biocuration2024 Workshop}}
{{DISPLAYTITLE:GlyGen & CFDE Biocuration2024 Workshop}}


'''This workshop provides an opportunity to learn about glycobiology and introduce bioinformatics resources to answer a biological questions.'''
Title: GlyGen and Common Fund Data Ecosystem (CFDE) Bioinformatics Workshop
 
When: March 8th, 2024, from 9 AM to 1 PM
 
Organizing Committee: Raja Mazumder (GlyGen, CFDE), Jeet Vora (GlyGen, CFDE), Suvarna Nadendla (CFDE), Mike Tiemeyer? (GlyGen, CFDE, remote), Rene Ranzinger? (GlyGen, CFDE, remote)
 
Venue: 17th Annual International Biocuration Conference, India (https://ibdc.rcb.res.in/biocuration2024/)
 
'''This workshop provides an opportunity to learn about glycobiology and introduce bioinformatics resources to answer biological questions.'''


'''2-hour GlyGen & NIH Common Fund Data Ecosystem (CFDE) workshop'''
'''2-hour GlyGen & NIH Common Fund Data Ecosystem (CFDE) workshop'''
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== Abstract ==
== Abstract ==


Glycobiology is the study of the structure, production, biology, and evolution of sugars and glycans, which are found in all cells in nature. Glycans are enzymatically attached to other macromolecules, primarily proteins, and lipids, in a process known as glycosylation. This post-translational modification plays an important role in protein folding, function, and cellular interactions. It is essential to study the dynamic changes in glycosylation and biosynthetic pathways, as glycans modulate normal biological functions and are involved in most major human diseases. The National Institutes of Health (NIH) and the National Institute of General Medical Sciences (NIGMS) have provided funding for the worldwide research project GlyGen, which aims to advance glycoscience studies by integrating various multi-omics and glycobiology knowledge. GlyGen exists as an online portal that allows users to browse various glycan and protein data via a wide range of unique yet complementary resources. Users can utilize the portal's features to investigate  questions related to biology and glycobiology  and examine detailed glycan and protein data.
An interactive 4-hour in-person bioinformatics workshop is scheduled for March 5th, 2024, from 9 AM to 1 PM. Blending training sessions with hands-on activities the workshop is It will be 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 (<nowiki>https://wiki.glygen.org/Glycan_Function_Workshop_2023</nowiki>) 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 more and how biocuration along with large-scale analysis, querying, and filtering of data can reveal insights into biomolecule function.


In addition, Common Fund Data Ecosystem (CFDE) is an NIH funded project that pools all of common fund recipients into one association which compiles resources and databases to enable users to explore and connect bioinformatics knowledge networks. By launching a series of cooperative projects that bring together eight Common Fund Data Coordinating Centers (DCCs), the CFDE took a significant step toward developing this resource. These projects will help create this functional ecosystem for addressing important biological questions, such as locating novel molecular pathways and shedding light on disease mechanisms. A crosscut metadata model (C2M2) is implemented in CFDE to properly integrate all of the input, as well as assist in the standardization of other data from the DCCs.
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.
 
The purpose of this workshop is to bring together high school students who are interested in developing early-on research knowledge and skills in biochemistry, glycobiology, computer science, and bioinformatics. Each presenter will demonstrate glycan and protein analysis using GlyGen and CFDE tools described above, followed by a Q&A session at the end of the workshop. The attendees will gain basic knowledge on how to efficiently use bioinformatics resources to answer biological questions and provide valuable feedback on the user experience perspective which aids in the continuous development of GlyGen.


== Schedule ==
== Schedule ==
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|-
|-
|-
|-
|1 - 1:15 pm
|9 - 9:45 am
|10 min
|45 min
|Welcome and introduction (to presenters and HIVE Lab)
|Welcome and introduction. An overview of GlyGen (www.glygen.org) and the NIH-funded Common Fund Data Ecosystem (<nowiki>https://app.nih-cfde.org/</nowiki>) will be presented to provide attendees with the scope of scientific questions these resources can answer. Other key resources such as UniProtKB, CFDE, NCBI, and EBI will be introduced to showcase how certain use cases and scientific questions require cross-resource queries.
|All
|Raja, Jeet
|-
|-
|1:15 - 1:35 pm
|9:45 - 10:30 am
|20 min
|45 min
|Basics of glycobiology
|Scientific Question Co-Development. A collaborative session with the audience will be held to formulate scientific questions addressable through the introduced resources.
|All
|Raja, Jeet Suvarna
|-
|-
|1:35 - 1:55 pm
|10:30 - 10:50 am
|20 min
|20 min
|GlyGen Introduction and GlyGen BLAST
|Refreshment Break.
|Naina Bethi
| -
|-
|-
|1:55 - 2:15 pm
|10:50 - 12:30 pm
|20 min
|100 min
|GlyGen Mapper and Structure Browser
|Hands-On Session. Participants, alongside presenters, will use their laptops or mobile devices to answer the formulated scientific questions.
|All
|All
|-
|-
|2:15 - 2:20 pm
|12:30 - 1:00 pm
|5 min
|30 min
|Break
|Round Table Discussion. The final half-hour will be dedicated to a round table discussion on opportunities and challenges presented by these bioinformatics resources.
|Raja, Jeet, Suvarna
|-
|
|
|
|
|
|-
|-
|2:20 - 2:40 pm
|
|20 min
|
|CFDE home page and main portal (chart and data filler demonstration)
|
|Sanvi Desai
|
|-
|-
|2:40 - 3:00 pm
|
|20 min
|
|CFDE data portals and tools (Gene and Drug Landing Page Aggregator; EGFR demonstration)
|
|Nikhil Vattathara
|
|-
|3:00 - 3:10 pm
|10 min
|Q&A
|All
 
 
|}
|}


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== Presentation/Discussion Sessions ==
== Presentation/Discussion Sessions ==
Each presentation/discussion session will demonstrate the use and practice of corresponding GlyGen and CFDE portal and tools. Audience are allowed to ask questions during each session by raising hands or posting the questions in the chat. All the unanswered questions will be addressed by the presenters during the Q&A session at the end of the workshop.
Each presentation/discussion session will demonstrate the use and practice of corresponding GlyGen and CFDE portal and tools. Audience 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.
 
== Organization Committee ==
 
Naina Bethi (ORCID ID: [https://orcid.org/0009-0005-9409-2739 0009-0005-9409-2739])
 
Sanvi Desai (ORCID ID: [https://orcid.org/0009-0009-3376-5708 0009-0009-3376-5708])
 
Nikhil Vattathara (ORCID ID: [https://orcid.org/0009-0000-4747-1473 0009-0000-4747-1473])
 
This workshop is organized by high-school students as part of their eight week internship.
 
== Workshop Testimonials ==


"Running the workshop was a lot of exposure and experience that I did not think i would get to experience as a high schooler. It taught me a different form of collaboration and team work which was very interesting and fun. I am grateful for the experience, and proud of the work that was put in and the final product." - Summer 2023 intern workshop organizer from Freedom High School
== In-person Organization Committee ==


"I am proud of the workshop my team and I were able to able to put together and host. Preparing and conducting this workshop was a learning experience for me as I was never previously given this sort of opportunity. It was fun and interesting to collaborate with the other interns on this, and learn about the topics we discussed as well. I'm very grateful for the experience and the chance to create this workshop." - Summer 2023 intern workshop organizer from Freedom High School
Raja Mazumder


"Conducting this workshop was an amazing and very new experience that taught me so much and gave me so much hands-on experience. It taught me how to effectively communicate and collaborate with a group of peers to produce an amazing end result. The field specifically, glycobiology is very interesting and the tools that we learned about will be very helpful for future research. I am very thankful for the opportunity to learn and conduct a workshop." - Summer 2023 intern workshop organizer from Thomas Jefferson High School for Science and Technology
Jeet Vora


"I loved the workshop and thought it was very informative and interactive. Everything was very thoroughly explained and I loved how we were able to explore the website ourselves, as well. I would definitely recommend this to others who want to explore this field, as well as people who know anything about this field yet, because I learned a lot of new information." - Student A from Freedom High School
Suvarna Nadendla


"I really enjoyed the workshop! I thought it was a great opportunity to get a solid overview about glycobiology. Before this workshop I had no idea about this branch of science. It was super interesting to see the tools and history of glycobiology. I also liked how it was run by interns. I would recommend other to explore this field." - Student B from St. Paul VI Catholic High School
== Workshop Logistics ==


"This workshop provided me with a unique opportunity to learn about the field of bioinformatics, and the role it plays in conducting biomedical research. I liked how everyone explained  the topic very thoroughly, and in a very organized manner. I would definitely recommend others to explore this field." - Student C from Freedom High School
Participants need to bring their laptops and/or smartphones to the workshop.


== Acknowledgement ==
== Acknowledgement ==


Raja Mazumder (ORCID: [https://orcid.org/0000-0001-8823-9945 0000-0001-8823-9945]) – Principal Investigator at GW
Raja Mazumder (ORCID: [https://orcid.org/0000-0001-8823-9945 0000-0001-8823-9945])  
 
Jingyue Wu (ORCID: [https://orcid.org/0000-0001-8523-2676 0000-0001-8523-2676]) – Supervisor


Jeet Vora (ORCID: [https://orcid.org/0000-0002-5317-1458 0000-0002-5317-1458]) – Co-supervisor
Jeet Vora (ORCID: [https://orcid.org/0000-0002-5317-1458 0000-0002-5317-1458])  


Supported by the GlyGen team at The George Washington University
Supported by funds from NIH to the GlyGen-CFDE team at The George Washington University


== Contact ==
== Contact ==
'''For questions about registration or general inquiries, please contact:'''  
'''For questions about registration or general inquiries, please contact:'''  


Jingyue Wu: jingyue.wu@email.gwu.edu
Raja Mazumder: mazumder@gwu.edu


Jeet Vora: jeetvora@gwu.edu
Jeet Vora: jeetvora@gwu.edu

Revision as of 16:57, 29 December 2023


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

When: March 8th, 2024, from 9 AM to 1 PM

Organizing Committee: Raja Mazumder (GlyGen, CFDE), Jeet Vora (GlyGen, CFDE), Suvarna Nadendla (CFDE), Mike Tiemeyer? (GlyGen, CFDE, remote), Rene Ranzinger? (GlyGen, CFDE, remote)

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

This workshop provides an opportunity to learn about glycobiology and introduce bioinformatics resources to answer biological questions.

2-hour GlyGen & NIH Common Fund Data Ecosystem (CFDE) workshop

Date & Time: Monday August 7th, 2023, 1 - 3 pm Eastern Time

Photo & Video Recording Release Form: https://communications.gwu.edu/photo-video-release

Abstract

An interactive 4-hour in-person bioinformatics workshop is scheduled for March 5th, 2024, from 9 AM to 1 PM. Blending training sessions with hands-on activities the workshop is It will be 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 (https://wiki.glygen.org/Glycan_Function_Workshop_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 more and how biocuration along with large-scale analysis, querying, and filtering of data can reveal insights into biomolecule function.

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)
9 - 9:45 am 45 min Welcome and introduction. An overview of GlyGen (www.glygen.org) and the NIH-funded Common Fund Data Ecosystem (https://app.nih-cfde.org/) will be presented to provide attendees with the scope of scientific questions these resources can answer. Other key resources such as UniProtKB, CFDE, NCBI, and EBI will be introduced to showcase how certain use cases and scientific questions require cross-resource queries. Raja, Jeet
9:45 - 10:30 am 45 min Scientific Question Co-Development. A collaborative session with the audience will be held to formulate scientific questions addressable through the introduced resources. Raja, Jeet Suvarna
10:30 - 10:50 am 20 min Refreshment Break. -
10:50 - 12:30 pm 100 min Hands-On Session. Participants, alongside presenters, will use their laptops or mobile devices to answer the formulated scientific questions. All
12:30 - 1:00 pm 30 min Round Table Discussion. The final half-hour will be dedicated to a round table discussion on opportunities and challenges presented by these bioinformatics resources. Raja, Jeet, Suvarna


Presentation/Discussion Sessions

Each presentation/discussion session will demonstrate the use and practice of corresponding GlyGen and CFDE portal and tools. Audience 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.

In-person Organization Committee

Raja Mazumder

Jeet Vora

Suvarna Nadendla

Workshop Logistics

Participants need to bring their laptops and/or smartphones to the workshop.

Acknowledgement

Raja Mazumder (ORCID: 0000-0001-8823-9945)

Jeet Vora (ORCID: 0000-0002-5317-1458)

Supported by funds from NIH to the GlyGen-CFDE team at The George Washington University

Contact

For questions about registration or general inquiries, please contact:

Raja Mazumder: mazumder@gwu.edu

Jeet Vora: jeetvora@gwu.edu

Retrieved from "https://wiki.glygen.org/index.php?title=GlyGen_CFDE_Biocuration2024_Workshop&oldid=2769"