Abstract
Simbiotics is a spatially explicit multiscale modeling platform for the design, simulation and analysis of bacterial populations. Systems ranging from planktonic cells and colonies, to biofilm formation and development may be modeled. Representation of biological systems in Simbiotics is flexible, and user-defined processes may be in a variety of forms depending on desired model abstraction. Simbiotics provides a library of modules such as cell geometries, physical force dynamics, genetic circuits, metabolic pathways, chemical diffusion and cell interactions. Model defined processes are integrated and scheduled for parallel multithread and multi-CPU execution. A virtual lab provides the modeler with analysis modules and some simulated lab equipment, enabling automation of sample interaction and data collection. An extendable and modular framework allows for the platform to be updated as novel models of bacteria are developed, coupled with an intuitive user interface to allow for model definitions with minimal programming experience. Simbiotics can integrate existing standards such as SBML, and process microscopy images to initialize the 3D spatial configuration of bacteria consortia. Two case studies, used to illustrate the platform flexibility, focus on the physical properties of the biosystems modeled. These pilot case studies demonstrate Simbiotics versatility in modeling and analysis of natural systems and as a CAD tool for synthetic biology.
Highlights
Bacterial colonies are networks of interacting cells that coordinate their behavior to produce system level organization.[1−3] As an additional layer of organization, bacteria may form biofilms, i.e., complex communities of cells often of mixed consortia that adapt to their environment and coordinate their individual behavior.[4−6] Bacterial colonies and biofilms are relevant in many disciplines ranging from microbiology and medicine to biotechnology such as synthetic biology.[7]
We present Simbiotics, a multicellular bacterial simulator which represents cells as individual physical entities embedded in chemical gradients, each cell may have modeler-defined dynamics and may interact with its environment and with other cells
We present a spatially explicit modeling platform, Simbiotics, which allows for the design, simulation and analysis of synthetic bacterial populations
Summary
Java with feedback between microprocesses such as gene regulation and metabolism, and macroprocesses such as spatial organization and differentiation.[15,16] Second, each cell has stochastic behavior that may change significantly based on its local environment,[17] understanding population behavior requires an in-depth knowledge of how its constituent parts behave. We present Simbiotics, a multicellular bacterial simulator which represents cells as individual physical entities embedded in chemical gradients, each cell may have modeler-defined dynamics and may interact with its environment and with other cells. Simbiotics is developed in Java; it utilizes the spatial representation, multithreaded and multi-CPU parallelized execution, and the 3D rendering as implemented in the Cortex3D platform.[27] The platform is designed with a modular architecture, allowing for model features to be represented as discrete components that can be readily added, removed and modified for the specific modeling application. The modeling library contains a collection of modules, which are discrete submodels describing specific model behavior These range from physical law integrators and chemical diffusionreaction solvers, to bacterial geometries, cellular dynamics and boundary conditions.
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