Team, Visitors, External Collaborators
Overall Objectives
Research Program
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
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Section: New Software and Platforms


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 a plugin-based computational platform for the analysis and simulation of morphogenesis. It relies on a scalable software architecture based on the dtk kernel developed by the group of software engineers (SED) from the Sophia-Antipolis Inria Center. The development of Gnomon aims at answering four main challenges:

* Provide an easily accessible computational tool for the exploration of morphogenesis, by focusing on the deployability of the software (using conda), on the ergonomics of the user interface and the availability of the documentation.

* Give access to powerful tools for the exploration of dynamical forms, through an interactive visualization framework allowing the exploration in space in time and the access to algorithmic resources developed by the team for image sequences of multicellular tissues or collections of branching forms.

* Ensure the interoperability of computational libraries within the platform and its extensibility by a generalized plugin-based architecture (facilitated by the dtk framework) for algorithms, visualizations and data structures, enabling the members of the team and future users to feed the platform with their own C++ and Python libraries.

* Bridge the gap between experimental data and computational simulations by offering the possibility to go from one to the other in the same platform in a nearly transparent way, thanks to a common dynamical system framework integrated to the core of the platform.

Gnomon project organization: * Project leader: Christophe Godin * Software development coordinator: Guillaume Cerutti * DTK coordinators: Julien Wintz, Thibaud Kloczko * Plugin coordinators: Jonathan Legrand, Romain Azais, Olivier Ali, Frédéric Boudon. * Diffusion coordinator: Teva Vernoux

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 major technical update has been carried out on the Gnomon platform with the switch of the platform core to dtk2, implying an upgrade of all involved Python code to python 3.6+. The newer version 0.13 displays a clearer and more customizable interface and all functionalities from the version 0.9. In terms of functionalities, a major effort has been put on recovering former applications of the team (LPy and PlantGL) and including them in a robust way in the scope of the platform. A release of the version 1.0 is planned for early 2020 including validated algorithms for the quantitative analysis of 3D images of tissue, a much more robust user interface and an extensive user and developer documentation made available online.