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A brand new digital modeling setting for plant fashions

A brand new mission makes an attempt to tame the plant mannequin wilderness by making a devoted modeling platform that helps collaborative and distributed mannequin design, reproducibility, and dissemination.

Throughout the previous few a long time, siloed groups have developed fashions utilizing completely different programming languages, with completely different levels of modularity and inter-operability. As plant scientists rush to satisfy rising yield calls for within the face of local weather change, superior applied sciences in molecular biology, biochemistry and high-performance computing present an unprecedented alternative to create fashions that information fast advances in plant breeding. Progress can even require analysis to maneuver past modelling at single-scales to integrative multiscale modeling to realize integrative, multiscale modelling that takes full benefit of our understanding of molecular mechanisms and the wealth of genome-wide information that has been generated over the past three a long time. Nonetheless, the power to construct integrative multiscale fashions is at present impeded by the problem in exchanging, re-using and mixing fashions and simulation instruments between groups (and even inside a crew) regardless of the existence of devoted modelling platforms created for this goal.

Devoted modelling platforms have been in existence for the final 25 years, permitting customers to create, execute, and work together with fashions and visualize their output (e.g., V-Laby, GroIMP, L-Py, AmapSim, AMAPmod, Capsis). Newer platforms additionally facilitate the mixing and interoperability of heterogeneous fashions and information buildings (e.g., OpenAlea and Yggdrasil).

In a brand new paper revealed by Dr. Frédéric Boudon, Researcher in Plant Modelling and Pc Science at UMR AGAP Institut on the College of Montpellier and colleagues current a brand new user-friendly digital modeling setting utilizing Jupyter notebooks. Their distinctive strategy tackles a number of issues generally encountered by plant modelers together with reproducibility, reuse, modularity, collaboration, and upkeep.

In line with Boudon, “the usage of Jupyter pocket book makes our platform distinctive as a result of its means to create modelling narratives makes it attainable to present customers entry to the completely different steps of the modelling pipeline in a transparent, documented and shareable manner. We additionally use a regular illustration of multidimensional arrays to characterize plant properties, which improves the effectivity of modeling and the coding course of as a result of it doesn’t require customized codes to extract, rework and visualize information. These options are supplied out-of-the-box by the Python scientific stack, minimizing the upkeep burden.”

The Jupyter-based modeling setting makes reproducible, reusable, collaborative and distributed mannequin design attainable. The pocket book format helps clear specification of processes and documentation to create the simulation narrative of a modeling situation. This format permits hypotheses of the mannequin and precise parameter values to be clearly specified, making the data accessible to future customers. This enables collaborators and customers to check and modify a mannequin. The inclusion of the conda package deal administration system make it attainable to obviously specify software program dependencies. As well as, the setting permits the event of fashions remotely so it doesn’t require customers to have in depth computational assets. This additional facilitates collaborative and distributed mannequin design and implementation.

Rising mannequin modularity is feasible because of the inclusion of xarray-simlab, a Python library for organizing and executing simulations. The library supplies a framework to compose complicated computational fashions from units of reusable sub/fashions or modules. A group of sub/fashions will be mixed to kind a mannequin, and their computational ordering is totally deduced from course of dependencies. This modularity lets customers run simulations for a subset of processes solely and even outline different processes to exchange predefined ones.

As an example the usage of the brand new modelling setting, the authors redesigned V-Mango, an current mannequin of mango tree growth and fruit manufacturing, and reorganized its code.

3D rendering of mango trees
3D rendering of a tree at chosen simulation steps throughout a number of successive rising cycles utilizing vmango-lab. Simulation steps are from leftmost within the again to rightmost within the entrance.

“We selected V-Mango as a result of it was a posh mannequin that might profit from redesign and reorganization of code. The mannequin was composed of processes applied as easy features or L-system guidelines with no technique to distinguish them from one another. As well as, the interplay between sub-models was restricted by use of various language applied sciences,” explains Boudon.

The performance of xarray-simlab within the Jupyter setting allowed the authors to simply redesign V-mango and reorganize its code. This consisted of defining processes and their inputs/outputs and assigning corresponding mannequin logic (see outdated vs. new workflow).

The V-mango mannequin was formalized because the units of processes utilizing Jupyter pocket book digital modelling setting.

Upkeep issues are lowered with the Jupyter platform as a result of options are supplied out-of-the-box by the Python scientific stack. This reduces the necessity for troublesome to keep up customized codes, to extract, rework and visualize information.

The authors encourage others to check out the open-source platform themselves.


Jan Vaillant, Isabelle Grechi, Frédéric Normand, Frédéric Boudon, In the direction of digital modeling environments for practical structural plant fashions primarily based on Jupyter notebooks: Utility to the modeling of mango tree development and growth, in silico Crops, 2021;, diab040,

This manuscript is a part of in silico Plant’s Purposeful Structural Plant Mannequin particular challenge.

pgljupyter is obtainable at and vmango-lab at with directions for the set up course of. All examples within the part 3 can be found as notebooks in a demo repository at and will be inspected with nbviewer and reproduced both regionally or on a binder occasion. The notebooks described in part 4 can be found at



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