OpenAleaLab: An integrated multi-paradigm modelling environment

Julien Coste , Guillaume Baty , Christophe pradal

Abstract

Highlights

We present an integrated modelling environment (IME) designed for scientists and based on IPython and OpenAlea. This open source environment is extensible via plug-ins and allows user to work with a set of diverse modelling paradigms like imperative languages (Python, R), scientific workflows (visual programming) or rule-based language (L-System). Two examples will be presented at two different scales: PlantLab (an environment for plant modelling and simulation) and TissueLab (an environment for cell tissue reconstruction and analysis using 3D+t images).

Abstract

The development of a model of plant or cell tissue structure requires the use of a modelling paradigm. This paradigm may be either i) imperative using a script or a compiled language; ii) declarative to define a set of rewriting rules like in L-systems; or iii) visual to combine existing components in a scientific workflow using a visual programming interface. All these modelling paradigms have been developed in different software platforms. But, as of today, there is no open source software environment that integrate all these applications or can be extended to provide such functionalities:

Spyder and Canopy focus on Python script development;
RStudio focuses on statistical models development in R language;
vlab/LStudio (Prusinkiewicz et al. 2007), GroIMP (Hemmerling et al. 2008) and L-Py (Boudon et al. 2012) focus on L-systems;
and OpenAlea (Pradal et al., 2008) focuses on visual programming and scientific workflows.

However, the need to develop more complex and integrated models, often assembling many sub-models, leads us to consider a modelling environment capable of supporting multiple design paradigms and models, and make them interoperable.

We will present the architecture of OpenAleaLab, a new integrated modeling environment (IME), based on IPython architecture (Pérez et al., 2007) and on OpenAlea components. This IME, built using PyQt, provides an IPython shell, a text editor, a project manager, a graphical package installer and a world, containing the objects and state variables shared by the different paradigms. The world can be graphically interpreted in 3D or 2D. Different paradigms and tools for plant modelling are available as plug-ins, such as a visual programming environment, a L-system language, a 3D viewer, and an R editor and interpreter. The plug-in system is based on setuptools entry-points and provide both functional and GUI components.

This environment is designed to be easily extensible in order to include new plant modelling paradigms in the future or to be customized for other scientific domains. Two applications (PlantLab and TissueLab) will be presented to demonstrate the extensibility and modularity of the architecture as well as the user interface. These applications share components (e.g. a 3D viewer and a visual programming environment) but have specific ones like L-Py, a L-system language for plant modelling, or Mars-Alt (Fernandez et al. 2010), a package for tissue reconstruction and lineage, based on 4D images.

OpenALeaLab GUI

References

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Fernandez, R., Das, P., Mirabet, V., Moscardi, E., Traas, J., Verdeil, J. L., ... & Godin, C. 2010. Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Nature Methods, 7(7), 547-553.
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