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Section: New Software and Platforms
Gnomon
Keywords: 4D - Modelization and numerical simulations - Finite element modelling - Computational biology - Data visualization
Scientific Description: Gnomon is a user-friendly computer platform developed by the Mosaic team for seamless simulation of form development in silico. It is intended to be a major tool for the team members to develop, integrate and share their models, algorithms and tools. In Gnomon, a developing form is represented at any time by a central data-structure that contains topological, geometric, genetic and physiological information and that represents the state of the growing form. Flexible components (plugins) make it possible to up-load or to create such data-structures, to program their development, to analyze, visualize them and interact with them in 3D+time.
Functional Description: Gnomon is developed based on the past experience of the team with the OpenAlea platform, but moving towards a more scalable software engineering solution based on the dtk kernel developed by the group of software engineers (SED) from the Sophia-Antipolis Inria Center. Gnomon development uses extensively an agile methodology and emphasizes three main aspects:
Deployable and extensible software architecture. The Gnomon platform is intended to become a perennial common resource for the members of the team as well as a tool to easily diffuse our methods to collaborators. It is a plugin-based architecture, relying on the dtk meta-platform developed by the SED at Inria Sophia-Antipolis. dtk eases the conception of a high-level C++ environment inside which added-value components are injected autonomously by the team members as Python plugins wrapping our scientific libraries. A significant effort is put on the packaging and deployability of this software (using conda), adding up unit testing, continuous integration and cross-platform installation.
Exploration of forms. The environment will provide tools to create and visualize forms, and explore them in space and time. Building on the algorithmic resources developed by the team for image sequences of multicellular tissues, user-friendly interfaces are being designed for the exploration of such structures. This gives the user the possibility to reconstruct computational representations from experimental data in an intuitive way, and to explore these spatio-temporal data in an interactive and visual manner.
Integrated form simulation framework. Within a general framework for the modeling of dynamical systems that the team is developing, a core component is the mechanical simulation engine that will handle the resolution of physical equations controlling form development. We want the simulation framework to be integrated within the Gnomon platform in a nearly transparent way for the user. To achieve this, we develop a high-level interface for a generic differential equation solver based on the fenics FEM library. Mapping the general concepts of morphogenesis modeling to this engine will allow the user to specify behavior rules of the system at high-level and easily design simulation scenarios directly in the Gnomon application.
Gnomon project organization:
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Plugin coordinators: Jonathan Legrand (TimageTK), treex (Romain Azais), Olivier Ali (Mechanics), Frédéric Boudon (L-Systems).
This work is part of the Gnomon ADT project supported by the Inria centers of Grenoble Rhône-Alpes and Sophia-Antipolis Méditerranée.
Release Functional Description: A first, fully functional, prototype of the Gnomon software platform, dedicated to the modeling and simulation of plant and animal morphogenesis, was developed during a series of intensive coding sessions in Lyon and Sophia-Antipolis. This new concept of platform dedicated to the study of morphogenesis was presented in November 2018 to a panel of modelers and biologists at the RDP lab, who will contribute next year to the further testing and refining the platform. This prototype is a clear milestone and results from a strong collaboration between the Inria software engineering group from Sophia-Antipolis (who provides the software architecture kernel - DTK)) and the Mosaic team and is supported by Inria (Action de Developpement Tecnologique, ADT).
News Of The Year: A first, fully functional, prototype of the Gnomon software platform, dedicated to the modeling and simulation of plant and animal morphogenesis, was developed during a series of intensive coding sessions in Lyon and Sophia-Antipolis. This new concept of platform dedicated to the study of morphogenesis was presented in November 2018 to a panel of modelers and biologists at the RDP lab, who will contribute next year to the further testing and refining the platform. This prototype is a clear milestone and results from a strong collaboration between the Inria software engineering group from Sophia-Antipolis (who provides the software architecture kernel - DTK)) and the Mosaic team and is supported by Inria (Action de Developpement Tecnologique, ADT).