Computational Models

Integrative and Multiscale Modelling Special Issue: Call for Papers

in silico Plants is calling for papers for a special issue on integrative and multiscale modelling. This special issue will aim to publish research describing improved and newly developed multiscale models and tools.
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Optimization of model representations at the level of photosynthesis, the canopy, or the root system, have already led to improvements at the plant and field level. Examples include a 25% reduction in water loss in the field-grown model crop tobacco (via PsbS overexpression), a 15% (via accelerated response to natural shading events) and 24% increase in field-grown tobacco biomass (more efficient photorespiratory pathways), and a 40% in greenhouse-grown wheat yield (via increased SBPase activity).

To continue this progress, it is not only necessary for models to take advantage of the rapid developments in high-throughput phenotyping, machine learning, genomics, metabolomics, and high-performance computing, they must also be integrative to include the underlying mechanisms of response, reaching from gene networks and metabolic pathways through to cellular organization, tissue and organ development, and resource capture in dynamic competitive environments and ecosystems.

Models that span across biological levels through integrative, multiscale modeling have the potential to further accelerate directed engineering and breeding for crop ideotypes that will result in enhanced crop production and sustainability under challenging future environmental conditions.

A banner reading "Special issue: Integrative and Multiscale Modeling"

For this reason, in silico Plants is calling for papers for a special issue on integrative and multiscale modelling. This special issue will aim to publish research describing improved and newly developed multiscale models and tools.

The scope of the Integrative and Multiscale Modelling Special Issue includes:

  • Multiscale models that include metabolic regulation across biological scales including transcriptional, post-transcriptional, translational, and post-translational regulation and the connection between microscale (cellular) and macroscale (organ and/or ecosystem), and
  • Computational tools and resources for developing multiscale models include frameworks, engines, and languages.
Dr. Amy Marshall-Colón against some golden plants.

The Guest Editor for this special issue will be Dr. Amy Marshall-Colón, Associate Professor of Plant Biology at the University of Illinois and founding Editor of in silico Plants. All article types – Original Articles (which includes research & development, theory, methods, software and computational tools), Technical Advances, Reviews, Opinions, Editorials, Letters to the Editor, and Commentaries – are welcome and will be undergo the full peer-review process of in silico Plants.

If you would like to submit a manuscript for inclusion in the Special Issue, please email office@insilicoplants.org with your list of authors, title, and key message to indicate your interest and reserve your spot. The deadline for manuscript submission is 30th October 2022.

The Special Issue will be edited in conjunction with the 6th annual Crops in silico Symposium & Hackathon to be held virtually May 11-13, 2022 through the National Center for Supercomputing Applications (NCSA) at the University of Illinois Urbana-Champaign. The Symposium program includes talks, discussions, and interactive poster presentations about mathematical modeling and associated software/ computational tools. The Hackathon will feature interactive tutorials for 5 models and modelling frameworks and tools:

Advertisement for the 6th annual crops in silico symposium and hackathon to be held virtually via the University of Iliois May 11-13, 2022. The Twitter hashtag is #2022CIS. The website is cropsinsilico.org
  • BioCro IIA semi-mechanistic dynamic crop growth model framework.
  • OpenSimRootA 3D structural functional model which simulates root growth, architecture and resource acquisition.
  • HeliosA 3D plant and environmental modeling framework.
  • CPlantBox– A 3D structural functional model focusing on root architecture and root–soil interaction.
  • OpenAleaA multi-paradigm modeling environment for plants.

More information about the special issue is available here.

The Special Issue Editor and Conference Organizers look forward to your contributions to the Special Issue and to welcoming you to participate in the 6th annual Crops in silico Symposium & Hackathon.


Read more about multiscale modelling

Bedrich Benes, Kaiyu Guan, Meagan Lang, Stephen P. Long, Jonathan P. Lynch, Amy Marshall-Colón, Bin Peng, James Schnable, Lee J. Sweetlove, Matthew J. Turk (2020), Multiscale computational models can guide experimentation and targeted measurements for crop improvement. The Plant Journal, 103: 21-31. https://doi.org/10.1111/tpj.14722

Megan L. Matthews, Amy Marshall-Colón (2021) Multiscale plant modeling: from genome to phenome and beyond. Emerging Topics in Life Sciences, 5 (2): 231–237. https://doi.org/10.1042/ETLS20200276

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