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 |