Microbiological Modeling with Reactive Transport

Under a recent DOE SBIR (SBIR Award DE-SC0019619) Subsurface Insights, in collaboration with Colorado State University (Dr. Kelly Wrighton) and Argonne National Lab (Dr. Chris Henry) has been working on developing a pipeline which can semi automatically generate reactive transport models based on genomics. Results of this work were (presented at the 2019 AGU Meeting.

One of the core requirements for such a pipeline is a robust computational infrastructure. Among other things, such an infrastructure should allow users to run and parameterize the reactive transport models generated by such a pipeline programmatically. Subsurface Insights has developed such an infrastructure.

In addition to models being exposed through an API we also provide visual interfaces which allow users to run models and get results in real time. In order to demonstrate both the value of such an interface and the ease of use we provide this interface for the two nitrification models discussed in Dr. Rubinstein’s talk. A copy of this talk can be downloaded here.

This interface allows users to vary some of the model parameters, and then run the model. Once the Run Model button is pressed the model will be submitted to one of our compute engines for execution. The model should just take a few seconds to run, and once it is completed interface elements will show up which allow users to graph model output. Users which run into issues with this interface should contact us. Also please feel free to reach out to us with any questions, comments or suggestions on improvements or modifications.

Click here to go to the Web-based PFLOTRAN Model Interface


Funding for this effort was provided under SBIR Award DE-SC0019619 (program manager Paul Bayer) from the DOE Biological and Environmental Research program.

Hanford site data processing and analysis were performed using EMSL (grid.436923.9), a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research.

Sample sequencing was performed by JGI

Field sample data was collected by James Stegen and Emily Graham at PNNL

The Wrighton Lab:Garret Smith and Pengfei Liu provided metabolic expertise for model curation and Lindsey Solden worked with Kayla Borton on genome reconstruction and multi-omics analysis.

The KBase team

Tasya Rodzianko, Doug Johnson, Erek Alper at Subsurface Insights