Section: New Software and Platforms

OpenAleaLab

Keywords: Bioinformatics - Biology - Workflow - Modelling Environment

Functional Description

OpenAleaLab is an integrated modelling environment (IME) designed for scientists based on IPython and on OpenAlea components. 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). 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. Several dedicated extensions (TissueLab, PlantLab) have been developed or are in development.

• Participants: Christophe Pradal, Guillaume Baty, Julien Coste, Christophe Godin.

• Contact: Christophe Pradal, Christophe Godin

• URL: http://virtualplants.github.io/