The 2020 Multiscale Microbial Dynamics Modeling course was a virtual course hosted by the Environmental Molecular Sciences Laboratory (EMSL) and Pacific Northwest National Laboratory (PNNL) Subsurface Biogeochemical Research group, and featured experts from the Joint Genome Institute and KBase.

Materials from this course cover how to incorporate microbial metagenomic and environmental metabolite data from watershed ecosystems into metabolic and community modeling using computational frameworks, such as KBase and PFLOTRAN. The curriculum includes lectures and software and data analysis tutorials. All of these materials are freely accessible to the community as part of the 2020 Microbial Dynamics Summer School Organization in KBase. Create a KBase account and request to join the KBase Org to get started today!


Workflow diagram of Multiscale Microbial Dynamics Modeling from samples through layers of modeling to environment-scale simulations. (Figure by Ellen Dow, KBase)

Course Elements

Course Elements

Overview and Objectives

Welcome to the Multiscale Microbial Dynamics Modeling course. Organizers Drs. Tim Scheibe and Nancy Hess introduce the goals and present an overview of the course modules.

1.1 Introduction

Tim Scheibe & Nancy Hess PNNL

video | presentation


1. Metagenomics

Introduction to the WHONDRS consortium and background information on the data used during the course. Learning concepts include an introduction to metagenomics and applied metagenomics research, with a demonstration of the KBase platform used for many of the analyses.

1.2 WHONDRS Introduction

Amy Goldman & James Stegen PNNL

video | presentation

1.3 Metagenomics 101

Kelly Wrighton Colorado State University

video | presentation | supplementary readings | example hands-on Narrative

1.4 KBase Orientation

Elisha Wood-Charlson LBNL

video | presentation | demo Narrative

1.5 Inferring Biogeochemical Function from Genomes (with DRAM tutorial)

Kayla Borton & Mike Shaffer Colorado State University

video | presentation | supplementary readings | example hands-on Narrative

1.7 Connecting Genes to Function: Trait-based approach

Eoin Brodie, Ulas Karaoz, & Gianna Marshmann LBNL

video | presentation | supplementary readings

1.8 Shared microbial functional traits underpin transferable hydrobiogeochemical processes in river corridors

Mike Shaffer et al. Colorado State University

presentation (presented at AGU 2020)

2. Environmental Metabolomics

Exploratory dive into the metabolomics of rivers. This section covers analysis pipelines and approaches to researching metabolomics, as the metabolic inputs and outputs from bacteria, and instruments that identify metabolites.

2.1 Metabolomics in River Corridors

James Stegen & Vanessa Garayburu-Caruso PNNL

video | presentation | supplementary readings

2.2 Metabolomics Analysis Pipeline

Bob Danczak PNNL

video | presentation | supplementary readings | ICR Tutorial (GitHub)

2.3 Connecting Metabolites to Function

Hyun-Seob Song University of Nebraska, Lincoln

video | presentation | supplementary readings | Narrative (DOI: 10.25982/65526.69/1755438) | example hands-on Narrative

2.4 High-resolution Mass Spectrometry (EMSL FTICR-MS Lab)

Will Kew PNNL

presentation | supplementary readings

3. Microbial Metabolism Modeling

Applied section that demonstrates how to create models. The instructors explore the complexities of modeling microbial communities and how to develop metabolic models using KBase.

3.1 Metabolic Modeling Landscape

Hyun-Seob Song University of Nebraska, Lincoln

video | presentation | supplementary readings

3.2 FluxOmics Tools for Metabolic Modeling

Mark Borkum PNNL

video | presentation | supplementary readings

3.3 Building and Using Metabolic Models in KBase

Janaka Edirisinghe ANL

video | presentation part 1 | presentation part 2 | Narrative | example hands-on Narrative

3.4 Integrating Metabolomic Data in Metabolic Models

Chris Henry ANL

video | presentation

3.5 Metabolic Network Modeling and Metabolomics Integration for Comparative Analysis of Biogeochemical Reactions in Multiple River Systems

Aimee Kessel, et al. University of Nebraska, Lincoln

presentation (presented at AGU 2020)

4. Reactive Transport Modeling

Additional context describing how to scale models from communities to ecosystems using reactive transport models (RTMs) to model environment dynamics. Tutorials explain how to develop RTMs and tie together the concepts of metagenomics and metabolomics for current applications to use RTMs in different riverine systems.

4.1 Incorporating Microbial Processes in RTMs

Tim Scheibe PNNL

video | presentation

4.2 Reactive Transport Modeling Tutorial #1

Kewei Chen PNNL

video | presentation

4.3 ML/AI Methods for Metabolic Modeling in RTMs

Hyun-Seob Song University of Nebraska, Lincoln

video | presentation | supplementary readings

4.4 Reactive Transport Modeling Tutorial #2

Roelof Versteeg & Rebecca Rubenstein Subsurface Insights

video | presentation

4.5 Using R for Hydrologic Data

Michelle Newcomer LBNL

video | presentation

4.6 Omics informed RTM in Marine and Lacustrine System

Christof Meile University of Georgia

video | presentation

4.7 Omics informed RTM in Watershed System

Xingyuan Chen PNNL

video | presentation | supplementary readings

4.8 Omics informed RTM in Wetland Systems

Pamela Weisenhorn ANL

video | presentation

4.9 Opportunities for Science Advancements using WHONDRS in RTM

Tim Scheibe and James Stegen PNNL

video | presentation

U.S. Department of Energy, Biological and Environmental Research (BER) Facilities and Resources

The final section covers U.S. DOE user research facilities and their available resources.

Biological and Environmental Research (BER) Facilities and Resources Overview


Joint Genome Institute (JGI)

Rekha Seshadri & Rex Malmstrom

video | presentation part 1 | presentation part 2 | presentation part 3

Environmental Molecular Sciences Laboratory (EMSL)

Will Kew PNNL



  EMSL,  the Environmental Molecular Sciences Laboratory 
 PNNL, Pacific Northwest National Laboratory
US Department of Energy | Office of Science DOE, US Department of Energy
 JGI, Joint Genome Institute
KBase KBase, DOE Systems Biology Knowledgebase
 Subsurface Insights
 WHONDRS, Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems
 SBR, Subsurface Biogeochemical Research
 ESS-DIVE, Deep Insight for Earth Science Data

Appdev maintenance Apr 9-12

The data center that hosts appdev.kbase.us will be performing power maintenance starting Friday, April 9, 2021 till Monday, April 12, 2021.  We will be shutting down appdev by noon PDT on April 9, and will bring appdev back up on April 12 as soon as we are able.