January - December 2022

Where: online
Registration: here
Paymenthere
email: Jeannette Martins This email address is being protected from spambots. You need JavaScript enabled to view it.
phone: +1-530-754-5357

 

 

UC Davis offers 1-week and 2-week intensive courses in Metabolomics, but many researchers cannot contribute so much time! Therefore, we are offering 'Bits and Bites' of some of the most popular parts of our intensive courses plus newly added short courses, see below. We hope to see you there! 

This 10-part short course series will feature in-depth topics in untargeted metabolomics such as Bayesian statistics, a deeper look into MS-DIAL, fundamental courses in mass spectrometry, lipidomics, and so many others. Each short course can be taken individually or you can select multiple Bites. Participants will gain a deeper insight into current software, methods, and pitfalls. Each session starts promptly at 9 a.m. (Pacific Time) and will take approx. 4 hours. The courses will be conducted in a highly interactive manner, with the use of freely available software and databases.  The tuition is $150 per Bite.

Bits & Bites # 01:
Fundamentals of Mass Spectrometry
Date: January 13, 2022
Instructor: Dr. Uri Keshet, UC Davis
Required software: None 
Participant prerequisites: None
Short description of the course: In this short course, we will cover a wide range of topics related to mass spectrometry practices and answer some frequently asked questions about the use and capabilities of such instruments. We'll go over a brief history of mass spectrometry and highlight some technological advances in mass spectrometry.  More importantly, we will cover how a mass spectrometer works from ionization to different mass analyzer types. Lastly, we will also focus on the fundamentals of metabolomics-based mass spectrometry and key ideas to think about when planning your mass spectrometry experiments for untargeted metabolomics.
 
Bits & Bites # 02:
Fundamentals of Lipidomics
Date: February 3, 2022
Instructor: Dr. Tong Shen, UC Davis
Required software: None 
Participant prerequisites: None 
Short description of the course: In this short course, we will cover topics related to lipids and systems-level scale analysis of lipids (lipidomics):
  • Introduction to lipids, classification, and functions
  • Mass spectrometry-based lipidomics, separation techniques, and perspectives on other novel technologies Case studies of lipidomics applications Entire experimental pipeline— design, sample
  • extraction, analysis, data processing, identification, statistical methods, and visualization/interpretation resources
  • Quality control and standardization Participants will gain a high-level overview of lipidomics in order to determine suitable strategies for their own research.

 Students and scientists will gain a high-level overview of lipidomics in order to determine suitable strategies for their own research.

Bits & Bites # 03:
Using MSDIAL to generate accurate comprehensive LC-MS/MS metabolomics datasets
Date: March 3, 2022 
Instructor: Dr. Jacob Folz, UC Davis
Required software: MS-DIAL Version of the tool to be used will be announced closer to the course date. 
Participant prerequisites: Basic understanding of LC-MS and understanding of how MS/MS spectra are used in metabolite identification. 
Short description of the course: Back by popular demand, this short course will focus on how to perform fine-tuned curation of processed LC-MS/MS data generated through MS-DIAL including compound identification, data quality analysis, and unknown feature reduction. Data from rat blood plasma analyzed using LC-MS/MS with MS/MS data collected in a data-dependent manner will be used to generate an example dataset, but the methods and techniques are applicable to many different sample types.
 
Bits & Bites # 04:
Introduction to the GNPS Ecosystem - Tools, Visualizations, and Data
Date: March 31, 2022

Instructor: Dr. Mingxun Wang, UC San Diego & Ometa Labs
Required software: None 
Participant prerequisites: GNPS Account, no programming experience necessary.
Short description of the course: We want to familiarize the entire community on how to look at their data using classical molecular networking on GNPS by reanalyzing public MassIVE data with classical molecular networking, visualizing raw mass spec data with GNPS Dashboard, and searching/contextualizing MS/MS data with MASST. The goals of the short course are to: 
  • Select spectrum files and metadata from MassIVE public dataset
  • Run classical molecular network workflow
  • Qualitatively compare between cohorts with molecular networks
  • Visualize LC/MS Data Interactively - GNPS Dashboard
  • Search Public Data with MASSTIdentify putative compounds
  • Visualize your molecular families
 
Bits & Bites #05:
Fundamentals of Metabolism
Date: April 7, 2022
Instructor: Dr. Oliver Fiehn, UC Davis
Required software: None 
Participant prerequisites: None
Short description of the course: Metabolism defines life. Metabolism generates energy for the cell, but it also makes building blocks for proteins and DNA. Importantly, metabolism also produces signaling molecules that regulate physiology across organs in addition to cellular mechanisms. What are the blind spots of metabolomics data today? How can we use metabolomics data to understand metabolic networks in cells, organs, and body fluids? How much can biochemical pathways be trusted in guiding our understanding, and how much do we need to extend our scope of metabolism to integrate transporters, feedback regulation, and novel epimetabolites? In this short course, we will review major concepts in metabolism and regulation of enzymes, give practical examples of how to carefully interpret metabolomic results, and set a foundation of chemical reactions that govern metabolism in the cell.
 
Bits & Bites # 06: 
Introduction to Bayesian statistics in Metabolomics
Date: May 5, 2022
Instructor: Dr. Christopher Brydges, UC Davis
Required software: JASP (can be downloaded for free from https://jasp-stats.org). Versions of the tool to be used will be announced closer to the course date.
Participant prerequisites: Basic knowledge of statistics (e.g., know what a t-test and a correlation are). No coding experience is needed, and there is no coding taught in this session.
Short description of the course: Bayesian statistics are a useful method for estimating effect sizes and testing the strength of evidence in favor of one hypothesis over another - things that p-values and traditional statistics can't do. However, they are under-utilized in metabolomics research.  This workshop will provide a brief refresher on traditional statistics, teach the basic principles behind Bayesian statistics, learn how to conduct basic Bayesian analyses in JASP (free, open-source software available from https://jasp-stats.org/) and learn how to report the results in the style of a journal article.
 
Bits & Bites # 07: 
Identification of unknown compounds in untargeted metabolomics using freely available software Session 1
Date: September 8, 2022
Instructor: Dr. Arpana Vaniya, UC Davis 
Required software: MS-FINDER for Windows (http://prime.psc.riken.jp/compms/msfinder/main.html) & SIRIUS+CSI:FingerID for Windows (https://bio.informatik.uni-jena.de/software/sirius/). Versions of tools to be used will be announced closer to the course date.
Participant prerequisites: Basic knowledge of computer skills. No coding experience is needed. 
Short description of the course: Compound identification is known as the bottleneck in metabolomics. However, there are many approaches one may consider while tackling this challenge (i.e. mass spectral library search, in silico fragmentation tools, or database searching). This short course will provide an overview of the current status of compound ID in metabolomics, participants will learn how to use freely available in silico fragmentation tool MS-FINDER and SIRIUS+CSI:FingerID, and apply those skills to some unknown challenges.
 
Identification of unknown compounds in untargeted metabolomics using freely available software Session 2
Date: September 9, 2022
Instructor: Dr. Arpana Vaniya, UC Davis 
Required software: CFM-ID 4.0 (http://cfmid4.wishartlab.com/) & MetFrag (https://msbi.ipb-halle.de/MetFrag/). Both CFM-ID and MetFrag are web-based tools, no downloads are required. NIST MS Search 2.3  & Lib2NIST, both tools will be shared closer to the course date.
Participant prerequisites: Basic knowledge of computer skills. No coding experience is needed. 
Short description of the course: In session 2, participants will continue learning additional tools and compound identification approaches. In this short course, participants will learn how to use web-based tools such as MetFrag and CFM-ID and learn how to use MassBank of North America in NIST MS Search. Participants will get a chance to practice on unknown challenges.

Bits & Bites # 08: 
Introduction to Metaboanalyst
Date: October 6, 2022
Instructor: Dr. Jeff Xia, McGill University
Required software: None 
Participant prerequisites: Basic knowledge of computer skills. No coding experience is needed. 
Short description of the course: In this short course, we will cover how to use MetaboAnalyst 5.0, a comprehensive platform dedicated to metabolomics data analysis. There will be a brief overview of data input, processing, and general workflow to perform PCA/PLS-DA/OPLS-DA analysis in MetaboAnalyst 5.0. More importantly, this course will cover how to use different functional analysis methods such as Enrichment Analysis, Pathway Analysis, Joint Pathway Analysis, and Network Analysis. Lastly, participants will also learn how to perform biomarker analysis and statistical analysis with complex metadata.
 
Bits & Bites # 09: 
Fundamentals of Gas Chromatography-MS in Metabolomics
Date: November 3, 2022
Instructor: Dr. Oliver Fiehn, UC Davis and Dr. Uri Keshet, UC Davis
Required software: MS-DIAL for Windows and BinVestigate. Versions of the tool to be used will be announced closer to the course date.
Participant prerequisites: Basic knowledge of computer skills. No coding experience is needed. 
Short description of the course: While LC-MS is all the hype in today's portfolio of metabolomics assays, ranges of small molecules are difficult to impossible to screen in this manner. Volatile compounds in breath, urine, or plant analyses can best be analyzed by GC-MS. Additionally, swaths of primary metabolic intermediates ranging from glycolysis and pentose phosphates to TCA compounds, sugars, and small microbial metabolites are readily and cost-efficiently analyzed by GC-MS. In this short course, we discuss fundamentals of GC-MS, tips for best practice, aspects of instructs of instrumentation, and demonstrate data processing and use of databases. Participants will also learn the current challenges, trends, and developments of GC-MS-based metabolomics.
 
Bits & Bites # 10: 
How to navigate demands in Metabolomics core services
Date: December 1, 2022
Instructor: Dr. Oliver Fiehn, UC Davis
Required software: None 
Participant prerequisites: None
Short description of the course: Biologists and biomedical investigators need metabolomic data but must rely on the services from metabolomic service providers in Universities or private companies. Interests in metabolomics services are very diverse, ranging from PK/PD to untargeted metabolomics, and from flux analysis to absolute quantifications of pathway intermediates. How can metabolomic service cores manage such demands and expectations with limited resources? At UC Davis, we have run metabolomics services for the past 16 years.  In this short course, we will provide a strategic overview on how to deploy tools, spot and fill bottlenecks, assess your core's capacity, scale up from small studies to 1000s of samples and provide high-throughput / high-quality services in a time and cost-efficient manner. We discuss how to consult with clients, how to provide educational resources, and how to manage staff and budgets. Recognizing that there is no one-size-fits-all strategy, we will survey measures on how to best engage your research community to utilize metabolomics services.