Multi-scale modeling

Today is the multi-scale modeling workshop at PlantBiology 2022!

Here are some recommended reading for further information on multi-scale modeling in plant biology.

Introduction to modeling

First, if you want some background on different modeling approaches, their application at different scales in plant biology, developing and collaboration, check out our review from last year. https://doi.org/10.3389/fpls.2021.687652

Introduction to multi-scale modeling for general audience

If you are more on the biology and experimental side of things, I highly recommend this article. It’s written in a more colloquial style, and takes you through the development of some classic models (Lotka-Volterra, Turing patterns), ultimately motivating mutli-scale models. DOI: 10.1511/2007.64.134

More biological and mathematical details

For those interested in digging in more to both the biology and the math, take a look at this review article. It discusses modeling techniques and their application at different scales of life, integrating this more technical information with deeper biological considerations. doi:10.1146/annurev-bioeng-071811-150104.

Multi-scale models at all levels of plant biology

Crop models are perhaps the most popular multi-scale models in plant biology, but there’s great work being done at all scales. For a wide variety of plant biology applications across all scales of life, check out this review. https://doi.org/10.1016/j.pbi.2018.07.001

Multi-scale modeling background for modelers

For a more technical, mathematical take on multi-scale modeling, I highly recommend this review. There’s discussion of more specific features to be considered, such as heterogeneity and overcoming computational challenges. ¡doi:10.1016/j.pbiomolbio.2011.06.004

Machine learning and multi-scale modeling

Machine learning is one potential solution to the problem of multi-scale modeling – the increasing number of parameters. This article discusses the intersection of machine learning and multi-scale modeling, and the usefulness of leveraging both. A more technical

Coding practices

With multi-scale modeling comes coding. Check out this paper to start thinking about good organizational and note-taking practices. https://doi.org/10.1371/journal.pcbi.1005510

New: multi-scale crop modeling and the microbiome

At the workshop, a question was asked about integrating microbiome data into large-scale crop models. Courtesy of our crop modeling expert Mary-Francis, here is a link to the recording of a workshop that discusses genomic prediction using microbiome metagenomic data: https://www.ag2pi.org/workshops-and-activities/field-day-2021-12-15/