CFDE Metabolomics Workbench Virtual Summer Workshop 2024


UCSD Metabolomics Workbench (MW,, as part of the NIH Common Fund Data Ecosystem (CFDE, 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.



Please register here. Please contact 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 or


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: Open for participants sharing their results and experiences, questions, discussion, and feedback.


We look forward to your participation and meeting you online.


Detailed Schedule:





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:

8:30-9:15 AM PST



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:,,

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:,,,

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:

9:30-9:45 AM PST



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:,

10-10:30 AM PST


Hands-on session: Explore/Q/A.

10:30-11 AM PST

Day 3

July 24

Srinivasan Ramachandran, Ethan Sanchez

MW-Knowledge graph - An introduction to knowledge graphs, Neo4j database and Cypher query. Neo4j-based data model and data search/discovery tool.

Key URLs:

8:00-8:45 AM PST

Hands-on session: Explore/Q/A.

8:45-9:30 AM PST



9:30-9:45 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:,

9:45-10:15 AM PST

Hands-on session: Explore/Q/A.

10:15-11:00 AM PST

Day 4 July 25


Open Session - Participants share results and experiences from their explorations. Questions, discussion, and feedback.

8-11 AM PST; including a 15-30-minute break