SODA Meetups And Workshops
SODA Meetups And Workshops
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SODAMeets is a platform where data generators and computational scientists can share their use of software/data. For each meeting, we will have two speakers present on software or data they would like to share with the community, emphasizing how these software/data are used. Click Here to add to our SODA Meetups to your google calendar. Please check your email for the Zoom link and password, sent out the day before the meetup.
SODA Meetup August 2025
Dr. Shipei Xing
UCSD
Structural annotation of full-scan MS data: A unified solution for LC-MS and imaging MS analyses
SODA Meetup April 2025
Dr. Huaxu Yu
UC Davis
MassCube: a Python framework for end-to-end metabolomics data processing from raw files to phenotype classifiers
Dr. Yasin El Abeied
UCSD
The remaining size of the dark metabolome
SODA Meetup February 2025
Dr. Mihir Mongia
Meta
Processing Gargantuan Amounts of Tandem Mass Spectrometry Data Lightning Fast
Dr. Mingxun Wang
Assistant Prof., UC Riverside
MassQL - An new language to unify query data in metabolomics based mass spectrometry
SODA Meetup December 2024
Dr. Gabi Kastenmüller
Computational Health Center, Helmholtz Munich
The HuMet Repository: An interactive resource of time-resolved metabolite profiles for exploring human metabolism under challenges
Dr. Courtney Jean Smith
MD/PhD Student, Department of Genetics, Stanford University School of Medicine
microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data
SODA Meetup August 2024
Dr. Nick Rigel, Ohio State University
ORISE Postdoctoral Fellow at EPA Office of Research and Development (ORD)
metLinkR: an R package for automated linking of metabolite identifiers to common names
Andrew Patt, Bioinformatics Scientist
National Center for Advancing Translational Sciences
metLinkR: an R package for automated linking of metabolite identifiers to common names
SODA Workshop May 2024
GNPS
Drs. Ipsita Mohanty and Simone Zuffa
Drs. Ipsita Mohanty and Simone Zuffa and will provide hands-on training for the GNPS Dashboard and microbeMASST.
Publication: https://www.nature.com/articles/s41564-023-01575-9
SODA Meetup April 2024
Dr. Troy Ferland
ORISE Postdoctoral Fellow at EPA Office of Research and Development (ORD)
EPA’s NTA WebApp Replication Experiment: A cost-benefit analysis of NTA study design
Simone Zuffa, PhD
UC San Diego
microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data
SODA Workshop March 2024
Asari - Dr. Joshua Mitchell and Dr. Shuzhao Li
In this one-hour workshop, Presenters Dr. Joshua Mitchell and Dr. Shuzhao Li will demonstrate Asari, a Python program for high-resolution LC-MS metabolomics data preprocessing, geared for reproducibility and performance (GitHub, Publication). The demo will also include a web version and a fully featured pipeline, pcpfm, to automate all steps in data processing, including QC, annotation and data wrangling.
Links:
Publication - https://www.nature.com/articles/s41467-023-39889-1
pcpfm - https://www.biorxiv.org/content/10.1101/2024.02.13.580048v1
Google Colab Notebooks: https://github.com/shuzhao-li-lab/asari_pcpfm_tutorials
SODA Meetup February 2024
Dr. Hani Habra
NIST NRC Postdoctoral Fellow
Inter-Laboratory Alignment and Analysis of LC-MS Metabolomics and Lipidomics Data
Dr. Eoin Fahy
Metabolomics Workbench Bioinformatics Project Manager, University of California San Diego
RefMet: a reference nomenclature for metabolomics
SODA Meetup December 2023
Dr. Hunter Mosely
Professor, Department of Molecular and Cellular Biochemistry, University of Kentucky
A Cautionary Tale About Properly Vetting Datasets for Supervised Machine Learning Predicting Metabolic Pathway Involvement
Fleming Kretschmer
PhD-Student, Chair for Bioinformatics, Friedrich Schiller University Jena
RepoRT: A comprehensive repository for small molecule retention times
SODA Meetup October 2023
Dr. Tao Huan
Assistant Professor, Department of Chemistry, University of British Columbia
Preparing High-Quality Tandem Mass Spectra for Metabolite Annotation and Unknown Discovery
Dr. Yuanyue Li
Assistant Project Scientist, Fiehn Lab, West Coast Metabolomics Center, UC Davis
Flash entropy search to query all mass spectral libraries in real time
SODA Meetup Feburary 2023
Dr. Jeremy Koelmel
Krystal Pollitt Lab, Yale University
Interactive Visualizations for Lipid and Homologous Series Discovery
Dr. Matthias S. Klein
Assistant Professor, The Ohio State University
Untargeted NMR metabolomics using the mrbin package
Previous Speakers
Previous Speakers
Name
Name
Shuzhao Li & Joshua Mitchell
Michael Judge
Rui Pinto
Xiaotao Shen
Xinsong Du
Patrik Bjärterot,
Matthias Klein
Jeremy Koelmel
Yue Wu
Alex Smirnov
Sean Colby
Daniel Hitchcock
Andy Patt
Yuri Corilo
Sadjad Fakouri-Baygi
Olatomiwa Bifarin
Yuanyue Li
Hunter Moseley
Joel Lapin
Christopher Jurich
Tom Metz
Oliver Fiehn
Mark Styczinski
Date
Date
8/8/2023
8/8/2023
6/13/2023
6/13/2023
4/11/2023
4/11/2023
2/14/2023
2/14/2023
12/13/2022
12/13/2022
10/11/2022
08/09/2022
08/09/2022
04/12/2022
04/12/2022
02/08/2022
02/08/2022
12/14/2021
12/14/2021
10/19/2021
10/19/2021
10/12/2021
10/12/2021
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Favorite Carbonated Beverage
Ginger Beer and Thumbs Up
Cheerwine and Blenheim
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Sanpellegrino
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Homemade 35PSI CW
Ginger Beer
Coke Zero
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Cherry Coke Zero
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Ginger Ale
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