CFDE Metabolomics Workbench Virtual Summer Workshop 2024

UCSD Metabolomics Workbench (MW, https://www.metabolomicsworkbench.org/), as part of the NIH Common Fund Data Ecosystem (CFDE, https://commonfund.nih.gov/dataecosystem) is pleased to announce a 4-day virtual Summer Workshop on July 22-25, 2024 for researchers, students, educators and to anyone who is interested in learning about metabolomics and their integration with other omics data towards a better understanding of their role in health and disease. Registration is free but required.

Targeted audience: while open to all, these groups may find it most useful.

1. Biomedical researchers, clinicians and undergraduate/graduate students working in metabolomics or integrative multi-omics.

2. Educators and undergraduate/graduate and high-school students attending courses in Biochemistry and Biology.

Registration:

Please register here. Please contact mmaurya@ucsd.edu for any issues with registration. If prompted to SIGN-IN into Google account, logout from all Google accounts in the browser, reopen the browser and login into one Google account.

Registration deadline extended: July 19, 2024

If you have registered but have not received the Zoom webinar information, please contact mmaurya@ucsd.edu or shankar-admin@ucsd.edu.

Mode of delivery:

When: July 22-25, 2024, lectures/presentations by the teams during 8-11 AM PST (Los Angeles time).

Online via Zoom: Zoom link will be provided in July for all registered participants.

Suggested prerequisites:

1. Some background in metabolomics and its role in health and disease.

2. If the user is interested in incorporating metabolomics data and related tools in their research, then programming experience in R and Python, and knowledge of Jupyter notebooks will be useful.

3. Some experience in using GitHub will be beneficial.

Schedule summary:

1. Day 1: Introduction, Overview of the National Metabolomics Data Repository (NMDR) / Metabolomics Workbench (MW), MW tools and features.

2. Day 2: Common Fund Data Ecosystem (CFDE)-related tools developed by MW, Our GitHub repositories and Demonstration of the metadata search at the CFDE Portal.

3. Day 3: MW-knowledge graph and CFDE Playbook Workflow Builder tool.

4. Day 4: Re-demonstration of some of the tools and open for participants sharing their results and experiences, questions, discussion, and feedback.

We look forward to your participation and meeting you online. Click here to provide feedback on the workshop.

Detailed Schedule:

Day	Presenter(s)	Session	Time
Day 1 July 22	Mano Maurya, Eoin Fahy	Overall introduction [Mano Maurya] - Objectives of the workshop; presentations, demo, hands-on exploration; participants encouraged to share the outcome of their explorations on the last day. Introductory Lecture [Eoin Fahy] - The role of metabolites such as lipids (e.g., cholesterol, glycerides), carbohydrates, and small molecules in health and disease.	8:00 - 8:30 AM PST
	Eoin Fahy	Overview of the National Metabolomics Data Repository (NMDR) / Metabolomics Workbench (MW) - Various tutorials related to the MW resources, such as data from metabolomics studies, metabolite naming standards such as RefMet, metabolic pathway databases. Key URLs: https://www.metabolomicsworkbench.org/	8:30-9:15 AM PST
		Break	9:15-9:45 AM PST
	Eoin Fahy	MW Tools and Features - Various tools and APIs available at MW, e.g., statistical analyses and visualizations, structure tools, search, MetStat and REST-based data access. Key URLs: https://www.metabolomicsworkbench.org/data/analyze.php, https://www.metabolomicsworkbench.org/data/metstat_form.php, https://www.metabolomicsworkbench.org/tools/mw_rest.php	9:45-10:30 AM PST
		Hands-on session: Explore/Q/A.	10:30-11 AM PST
Day 2 July 23	Sumana Srinivasan, Mano Maurya	CFDE Biomedical Data Commons Workbench (BDCW) - Various tools and APIs available under CFDE BDCW, e.g., MetGENE, MetENP and MetNet. Key URLs: https://bdcw.org, https://bdcw.org/MetGENE/, https://github.com/metabolomicsworkbench/MetENP, https://github.com/metabolomicsworkbench/MetNet	8:00-8:45 AM PST
		Hands-on session: Explore/Q/A.	8:45-9:30 AM PST
	Mano Maurya	GitHub Repo Walkthrough - A demonstration of our GitHub repository. Online browsing. Key URLs: https://github.com/metabolomicsworkbench	9:30-9:45 AM PST
		Break	9:45-10 AM PST
	Shivaramakrishna Srinivasan, Sumana Srinivasan, Mano Maurya	Demonstration of the CFDE Data Portal - Searching MW metadata at the CFDE information/data portal. Key URLs: https://info.cfde.cloud/, https://data.cfde.cloud/	10-10:30 AM PST
		Hands-on session: Explore/Q/A.	10:30-11 AM PST
Day 3 July 24	Srinivasan Ramachandran, Ethan Sanchez	CFDE - Graph Query Interface - An introduction to graph database and Cypher query. Neo4j-based graph query interface for intuitive and interactive data search/discovery. Key URLs: https://neo4j.com/	8:00-8:45 AM PST
		Hands-on session: Explore/Q/A.	8:45-9:00 AM PST
		Break	9:00-9:15 AM PST
	Mano Maurya, Sumana Srinivasan	CFDE Playbook Workflow Builder (PWB) Tool - Access and use of the CFDE BDCW APIs through the CFDE PWB tool. Key URLs: https://playbook-workflow-builder.cloud, https://github.com/MaayanLab/Playbook-Workflow-Builder/	9:15-9:45 AM PST
		Hands-on session: Explore/Q/A.	9:45-10:15 AM PST
Day 4 July 25	All	Open Session - Re-demonstration of some of the tools, then participants share results and experiences from their explorations. Questions, discussion, and feedback.	8-11 AM PST; including a 15-30-minute break