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: 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.