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Multiscale Microbial Dynamics Modeling Summer School
  • July 6-10, 2020
    SCIENCE CONFERENCE
    Richland, Washington
         
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Click here to view and print the agenda.

Click on the presentation titles below (those in rust color) for presentation slides. 

The summer school recorded sessions are all on EMSL's YouTube channel.  Click here for the playlist to view the sessions. (Here is the link should you need to copy and paste in your browser: https://www.youtube.com/playlist?list=PL6ecvCJPoOtmshHIV0Gpzy8ibxiJBgM94)

Agenda

Monday, July 6, 2020
Day 1: Metagenomics

8:00 am:  Virtual Registration:  Participants “check in” to the zoom room, check their audio/video connections, and are signed into the roll call.

8:30 am:  Orientation - ​Tim Scheibe and Nancy Hess (PNNL)
Instructor introductions, overview of the agenda, aims and expected outcomes of the course, guidelines and logistics

8:50 am:  Introduction to WHONDRS - Amy Goldman and James Stegen (PNNL)
Discussion of the scientific objectives of the course, including an introduction to the WHONDRS consortium and the datasets. 

9:15 am:  Metagenomics 101 – Kelly Wrighton (Colorado State University)
Introduction to metagenomics data and analysis.

9:55 am:  KBase Orientation (Tutorial-No Slides available) – Elisha Wood-Charlson (LBNL)
Introduction to the KBase platform in tutorial format.

10:15 am:  Extended Break

12:45 pm:   Inferring Biogeochemical Function from Genomes (DRAM) – Mike Shaffer and Kayla Borton (Colorado State University)

1:30 pm:  Extended Break

3:50 pm:   Introduction to Genome Application Session (No Slides) – Kelly Wrighton (Colorado State University)

3:55 pm:  Joint Genome Institute - Introduction and Capabilities (slides broken into two parts: Part 1 and Part 2) - Rekha Seshadri (LBNL)

4:25 pm:  Connecting Genes to Function: Trait-Based Microbially-Explicit Modeling of Environmental Microbial Community Dynamics - Eoin Brodie, Ulas Karaoz and Gianna Marschmann (LBNL)

5:00 pm:  Adjourn


Tuesday, July 7, 2020
Day 2: Environmental Metabolomics


8:30 am:  Metabolomics in River Corridors - James Stegen and Vanessa Garayburu-Caruso (PNNL)

9:15 am:  Metabolomics Analysis Pipeline Tutorial - Bob Danczak (PNNL)

11:15 am: 
Virtual Tour: EMSL Mass Spectrometry Laboratory - Will Kew (PNNL)

12:00 pm:  Lunch Break

12:30 pm:   Connecting Metabolites to Function: Substrate-explicit Modeling of Environmental Microbial Community Dynamics - Hyun-Seob Song (University of Nebraska, Lincoln

2:00 pm:   Extended Break

4:15 pm:   Opportunities for Scientific Advances using Numerical Experimentation Integrating WHONDRS Data with Reactive Transport Models - Tim Scheibe (PNNL)

5:00 pm:  Adjourn

 

Wednesday, July 8, 2020
Day 3: Generating Metabolic Networks and Metabolic Modeling

8:30 am:  Metabolic Modeling Landscape: A Review of Approaches and Methods - Hyun-Seob 
Song (University of Nebraska, Lincoln)

9:15 am:  Using FluxOmics Tools to Perform Metabolic Modeling - Mark Borkum (PNNL)

10:00 am:  Break

10:15 am:  Building and Using Metabolic Models in KBase (slides broken into two parts: Part 1 and Part 2)  - Janaka Edirisinghe (ANL)

11:15 am:  Integrating Metabolomic Data in Metabolic Models - Chris Henry (ANL)

12:00 pm:  Adjourn 


Thursday, July 9, 2020
Day 4: Flow and Reactive Transport Modeling

8:30 am:  Incorporating Microbial Processes in Reactive Transport Models - Tim Scheibe (PNNL)

9:15 am:  Reactive Transport Modeling Tutorial Session #1 - Kewei Chen (PNNL)

11:00 am:  Machine Learning / AI Methods for Metabolic Modeling in RTMs - Hyun-Seob Song (University of Nebraska, Lincoln)
 
11:45 am:  Lunch Break

1:00 pm:  Reactive Transport Modeling Tutorial Session #2 - Roelof Versteeg and Rebecca Rubenstein (Subsurface Insights)

2:00 pm:  Using R for Hydrologic Data
- Michelle Newcomer (LBNL)

2:45 pm:
Adjourn

 

Friday, July 10, 2020
Day 5: Synthesis and Applications

8:30 am:  Omics-Informed Reactive Transport Modeling in Marine and Lacustrine Systems - Christof Meile (University of Georgia)

9:15 am:  Omics-Informed Reactive Transport Modeling in Plant-Soil-Microbe Systems (No slides or recording available) - Marco Keiluweit (University of Massachusetts, Amherst), Steve Yabusaki, and Yilin Fang (PNNL)

10:00 am:  Break

10:15 am:  Discussion (No slides available)

Students and observers informally present ideas on how they could use these concepts in their research. Identify opportunities for collaboration and new proposal ideas.  Provide slide templates the day before for students to complete on Thursday evening.

11:30 am:  U.S. Department of Energy Resources and Opportunities
Short presentations on EMSL, JGI, FICUS, ESS-DIVE, KBase, IDEAS access mechanisms and capabilities.  Plans for special topic FICUS call?
The Joint Genome Institute is a DOE User Facility - Rex Malmstrom (JGI)

12:00 pm:  Lunch Break


12:30 pm:  Omics-Informed Reactive Transport Modeling in Watershed Systems -
Xingyuan Chen (PNNL)

1:15 pm:  Omics-Informed Reactive Transport Modeling in Wetland Systems -
Pamela 
Weisenhorn (ANL)


2:00 pm:  
Adjourn

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