EMSL Summer School: Multi-omics Modeling of Biochemical Pathways

Summer School webinar recordings
Copy and paste in your browser if having issues accessing: https://www.emsl.pnnl.gov/learn/summer-school

8:30 am - Virtual Registration: Check-in/verify Zoom connection. Engage via Discord

9:00 am - Orientation: Scott Baker and Lee Ann McCue, PNNL
Welcome, introductions, overview of the agenda, and logistics.

9:15 am - Introduction to the Agile BioFoundry (ABF): Jon Magnuson and Kristin Burnum-Johnson, PNNL
We will discuss the organization and goals of the Agile BioFoundry (ABF), and the design, build, test, learn approach used by the ABF for bioproduct development. We will also introduce the experiment and the data that we will use throughout the week in the tutorials.

10:00 pm - Introduction to DOE User Facilities: Scott Baker, PNNL

10:30 am - Break

11:00 am - Experimental Design: Nathalie Munoz and Lisa Bramer, PNNL
In this session, we will discuss choosing which data types will address the goals of an experiment (e.g. targeted vs untargeted approaches, labeled metabolites for flux or other types of modeling). Followed by an overview of how to design a robust experiment given the goals of the experiment, data types to be generated, and experimental constraints (e.g. replicates, multiple data types and the variance in data).

12:00 pm - Extended Break

1:00 pm - 3:00 pm - Breakout Groups
(Breakout groups is closed to the public. Post-doctoral researchers and advanced PhD students submitted applications by April 2nd to attend smaller breakout classes with summer school instructors each day from 1:30-3:00 pm.)

8:30 am - Introduction into Proteomics: Kristin Burnum-Johnson, PNNL
This talk will cover a general overview of proteomics. Topics will include the fundamentals of proteomics and an overview of the most popular techniques and applications.

9:15 am - Mass Spectrometry (MS) based Proteomics: Yuqian Gao, PNNL
Mass spectrometry (MS) -based proteomics is the method of choice for studying proteins in complex mixtures. This talk will cover how proteins can be identified and quantified through various techniques of MS-based proteomics, including discovery proteomics and targeted proteomics, as well as how post-translational modifications can be identified in MS-based proteomics.

10:00 am - Break

10:30 am - Proteomics Analysis Pipelines, Part 1: Yuqian Gao, PNNL
This talk will give an overview of the discovery proteomics analysis pipeline involving instrument analysis, database searches and data filtering, and the targeted proteomics analysis pipeline involving selection of peptides, assay development, instrument analysis and data analysis.

11:15 am - Proteomics Analysis Pipelines, Part 2: Aivett Bilbao, PNNL
This talk will cover data-independent acquisition and multidimensional pipelines with ion mobility spectrometry for proteomics.

12:00 pm - Extended Break

1:00 pm - 3:00 pm - Breakout Groups
(Closed session for the 25 students competitively selected via application process.)

8:30 am - Introduction to Metabolomics: Nathalie Munoz, PNNL
In this talk we will give an overview of metabolomics. We will discuss a general background of metabolomics, what are challenges found in this particular omics, what are the most common analytical platforms used when doing metabolomics studies and its applications.

9:15 am - Mass Spectrometry based Metabolomics: Young-Mo Kim, PNNL
This lecture will cover fundamentals of chromatographic separation of metabolites, basics of metabolite measurement by various mass spectrometers, and application to biological systems with discovery (global) metabolomics and targeted metabolomics approaches.

10:00 am - Break

10:30 am - Nuclear Magnetic Resonance (NMR) based Metabolomics: Robert Young, PNNL
This section will introduce some of the basics of NMR measurement, spectral features, and types of experiments. A brief walkthrough of a typical solution-state NMR metabolomics workflow, from sample preparation to data analysis, will then be presented. Finally, applications of NMR in metabolomics research will be highlighted with select examples from recent literature.

11:15 am - Break

11:30 am - Metabolomics Data Processing Pipelines: William Kew , PNNL
This talk will integrate the information discussed in previous sessions with an overview of data analysis strategies for metabolomics. The talk will cover general data analysis considerations, and then highlight some key aspects of NMR, GC-MS, and LC-MS data analysis pipelines. Discussion of key software platforms and how they relate to targeted and untargeted pipelines will be included.

12:15 pm - Extended Break

1:15 pm - 3:00 pm - Breakout Groups
(Closed session for the 25 students competitively selected via application process.)

8:30 am - Data Preprocessing: Kelly Stratton and David Degnan, PNNL
In the first talk today, we will present an introduction to methods for preparing untargeted metabolomics and proteomics data for statistical analysis. This includes topics such as available tools, data formatting, quality control/filtering, and normalization.

10:00 am - Break

10:30 am - Data Analysis: Lisa Bramer, PNNL
The second talk will focus on introducing common methods for determining qualitative and quantitative differences between experimental groups.

11:30 pm - Extended Break

12:30 pm - Data Integration Methods & Visualization: Lisa Bramer and Rachel Richardson, PNNL
The third talk will provide an introduction to implementing statistical and biological methods for integrating data. In addition, we will provide some examples for visualizing, sorting, and filtering the results.

1:30 pm -3:00 pm - Breakout Groups
(Closed session for the 25 students competitively selected via application process.)

8:30 am - Cell Factory Design Introduction: Jeremy Zucker, PNNL
This live demo will introduce the ABCs of cell factory design using a simple model. Concepts covered include flux balance analysis, elementary modes, flux variability analysis, growth-coupled design, evolutionarily stable solutions and the production envelope.

10:00 am - Break

10:30 am - Building and Using Metabolic Models in KBase: Janaka Edirisinghe, ANL
A general metabolic modeling overview and metabolic modeling in KBase (https://www.kbase.us/). We will cover accessing public RefSeq genomes via KBase reference data, construction of draft metabolic models for bacterial and fungal, run FBA, explore the synthesis of biofuel products in Yeast, upload omics data (transcriptomics and metabolomics) into the system, and visualize fluxes and omics data in pathway-based maps.

11:15 am - Integrating Metabolomic Data in Metabolic Models: Chris Henry, ANL
In this talk, we will discuss tools and workflows that have been integrated into the DOE Systems-biology Knowledgebase (KBase) to permit the combination of metabolomic and genomic data to present mechanistic explanations for the presence of species and metabolites in an industrial, environmental, or lab setting of interest. For example, we will show how exometabolite data from an isolate of Pseudomonas led to an explanation for a widely conserved correlation observed between betaine and pseudomonas in many environments. We will also explore how these tools are leading to improved annotations of metabolomic data, improved understanding of spontaneous chemistry, and overall a dramatically improved capacity to produce mechanistic explanations for the metabolites observed in biological systems ranging from the JCVI minimal genome to large-scale soil microbiomes.

12:00 pm - Extended Break

12:30 pm - FluxOmics: Jeremy Zucker, PNNL

1:30 pm - 3:00 pm - Breakout Groups
(Closed session for the 25 students competitively selected via application process.)