The Virtual Plant Laboratory
The Virtual Plant Laboratory is in an early developmental stage and it is released for the purposes of early testing and user feedback. Please contact me if you intend to use it for research or commercial purposes at this stage.
Introduction
The Virtual Plant Laboratory (VPL) is a Julia package that aids in the construction, simulation and visualization of functional-structural plant models (FSPM). VPL is not a standalone solution to all the computational problems relevant to FSPM, but rather it focuses on those algorithms that are specific to FSPM and for which there are no good solutions in the Julia package ecosystem. Furthermore, VPL is 100% written in Julia and therefore VPL will work in any platform and with any code editor where Julia works. Finally, VPL does not offer a domain specific language for FSPM but rather it allows building FSP models by creating user-defined data types and methods.
There is no standard definition of what an FSPM is (though these models will always involve some combination of plant structure and function) so VPL may not be useful with every possible FSPM. Instead, VPL focuses on models that represent indivudual plants as graphs of elements (usually organs) that interact with each other and with the environment. In a typical VPL model, each plant is represented by its own graph which can change dynamically through the iterative application of graph rewriting rules. Based on this goal, what VPL offers are data structures and algorithms that allow modelling the dynamic evolution of graphs that represent plants as collections of organs or other morphological elements and modelling the the interaction between plants and their environment by generating 3D structures and simulating capture of different resources (e.g. light).
In terms of design, VPL gives priority to performance and simple interfaces as opposed to complex layers of abstraction. This implies that models in VPL may be more verbose and procedural (as opposed to descriptive) than in other FSPM software, though may also make them more transparent and easier to follow.
Installation
VPL requires using Julia version 1.7 or higher. The installation of VPL is as easy as running the following code:
using Pkg
Pkg.add(PackageSpec(url = "https://github.com/AleMorales/VPL.git", rev = "master"))This requires an Internet connection such that Julia will download the source code of the VPL package and install it in the local machine.
The VPLverse
The package VPL contains all the basic functionality to build FSP models but, as indicated earlier, the emphasis is on minimal, simple and transparent interfaces. In order to facilitate the construction of non-trivial FSP models, an ecosystem of packages built around VPL provide additional support to the modeller by offering reusable modules that can be reused in new models.
The packages currently planned for VPLverse are:
Ecophys - Algorithms and data structures to simulate ecophysiological processes including photosynthesis, transpiration, leaf energy balance, phenology or respiration.
Sky - Algorithms to simulate different sky conditions in terms of the intensity of solar radiation and its spatial distribution.
In addition, all the tutorials on this website can be found at the VPLTutorials package.
Documentation
Documentation for VPL is provided in this website in four formats:
- User manual
- Tutorials and examples
- API
- Technical notes
The documentation for packages from the VPLverse are included in their respective sections.
New users are expected to start with the tutorials and consult the user manual to understand better the different concepts used in VPL and get an overview of the different options available. The API documentation describes each individual function and data type, with an emphasis on inputs and outputs and (in addition to this website) it can be accessed from within Julia with ? (see the section Accessing Documentation in the Julia manual). The technical notes are useful for people who want to understand the internal details of VPL and how different algorithms are implemented (i.e. the technical notes should be seen as a supplementary to the source code of VPL).