Software

  • Simuscale



    • Ode, Simulation, Multiscale, Multi-agent


    • SiMuScale is a C++ simulation framework that models both intra- and extra-cellular processes at different time scales. Its decoupled architecture allows for an easy and parsimonious extension of the model with e.g. a new kind of intra-cellular formalism.


    • Simuscale is a multiscale, individual-based modelling platform written in C++ for performing numerical simulations of heterogeneous populations of individual cells evolving in time and interacting physically and biochemically. Models are described at two levels: cellular level and population level. The cellular level describes the dynamics of single cells, as defined by the modeller. Cells have an internal state that includes default properties such as cell size and position, and may also include any other cell-specific state, such as gene or protein expression. The population level describes the mechanical constraints and biochemical interactions between cells. Cells evolve in bounded 3D domain, and can divide or die. Simuscale implements the physical simulator that manages the simulations at the population level. It delegates the details of cellular dynamics to each cell. This makes Simuscale modular, as it can accommodate any number of cell models with the same simulation, including models with different modelling formalisms. Biochemical interactions occur between cells that are in contact with each other, through intercellular signals. Intercellular signals can be known to all or to a subset of the cells only. Simuscale expects an input file describing the initial cell population and numerical options, it runs a simulation over a specified time interval, updating the cell population at given time steps, and generates an output file containing the state of each cell at each time step, and the tree of cell divisions and deaths.



      • Thi Nhu Thao Nguyen, Madge Martin, C Arpin, Samuel Bernard, Olivier Gandrillon, et al.. In silico modelling of CD8 T cell immune response links genetic regulation to population dynamics. 2024. ⟨hal-04489553⟩
      • Samuel Bernard, Fabien Crauste, Olivier Gandrillon, Carole Knibbe, David Parsons. Simuscale: A Modular Framework for Multiscale Single-Cell Modelling. RT-0520, Inria Lyon. 2024, pp.18. ⟨hal-04400510⟩



    • Carole Knibbe (carole.knibbe@inria.fr), David Parsons (david.parsons@inria.fr), Fabien Crauste (fabien.crauste@inria.fr), Olivier Gandrillon (olivier.gandrillon@inria.fr), Raphael Bournhonesque (raphael.bournhonesque@inria.fr), Samuel Bernard (samuel.bernard@inria.fr)


    • CNRS, UCBL Lyon 1


    • Samuel Bernard (samuel.bernard@inria.fr)


    • https://gitlab.inria.fr/bernard1/simuscale
  • CelDyn



    • Modeling, Bioinformatics, Biology



    • Software "Celdyn" is developed in order to model cell population dynamics for biological applications. Cells are represented either as soft spheres or they can have more complex structure. Cells can divide, move, interact with each other or with the surrounding medium. Different cell types can be introduced. When cells divide, the types of daughter cells are specified. A user interface is developed.





    • Alen Tosenberger, Laurent Pujo-Menjouet (laurent.pujo-menjouet@inria.fr), Nikolai Bessonov, Vitaly Volpert (vitaly.volpert@inria.fr)



    • Vitaly Volpert (vitaly.volpert@inria.fr)



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