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: July 15, 2024


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.


Topics covered:

1.     Day 1: Introductory lecture on what are and the role of metabolites such as lipids (e.g., cholesterol, glycerides), carbohydrates, and small molecules in keeping us healthy and in various diseases. About 1 hour lecture.

2.     Day 1: Overview of the National Metabolomics Data Repository (NMDR), served by the Metabolomics Workbench: Various tutorials related to the MW DCC resources, such as data from metabolomics studies, metabolite naming standards and IDs such as RefMet, metabolic pathway databases. About 1 hour lecture and demo.

3.     Day 2: Various tools and APIs available at MW DCC, e.g., statistical analyses and visualizations, structure tools, search, MetStat and REST-based data access. About 1 hour lecture and demo.

4.     Day 2: Searching MW metadata at the CFDE information/data portal. Day 2. About 30 minutes - 1 hour, a brief presentation and online browsing/demo.

5.     Day 2: Various tools and APIs available under CFDE Biomedical Data Commons Workbench (BDCW), e.g., gene ID conversion, MetENP, MetGENE, and MetNet. About 1 hour lecture and demo.

6.     Day 3: How some of the CFDE BDCW tools and APIs can be accessed through the CFDE Workflow Builder tool. About 1 hour lecture and demo.

7.     Day 3: Our GitHub repos. About 30 minutes, a brief presentation and online browsing/demo.

8.     Day 3: MW-Knowledge graph. About 1.5 hours of lecture and demo. An introduction to knowledge graphs, Neo4j database and Cypher query. How a graph data model can be utilized for intuitive and efficient data search/discovery in NMDR.

9.     Day 4: Open for questions, discussion, and feedback.


We look forward to your participation and meeting you online.