Management of data structures generated during simulations of the evolution of multicellular systems

Abstract

One major interest in tissue engineering is to model and simulate tissue growth (the auto-organization of cells into tissues) in order to optimize tissue engineering procedures. Therefore, we have developed a computational modeling tool, called SIMMMC, which allows simulating the behaviour of various multicellular systems in the vicinity of biomaterials. SIMMMC relies on the Metropolis Monte Carlo algorithm, taking into account different geometric and energetic input parameters. For a better organization and analysis of the data structures obtained by running SIMMMC and for a secure data storage, we created a cloud app, called SIMMMC Management Tool. Through this app, for each simulation, the model parameters and the output files that contain the new configurations of the biological systems are stored on the cloud. The user can search for specific simulations that are characterized by certain model parameters, visualize the data, download all the associated files on a local computer, or delete unnecessary simulations. Moreover, the SIMMMC Management Tool is convenient for data sharing: it can be accessed by any researcher who is interested in the results of SIMMMC simulations and has received an authentication code. In this work, we present the architecture of the SIMMMC information system, the functionalities and the architecture of the SIMMMC Management Tool, the implementation of the application, the design of the database, the workflow of the tasks and the user interface. SIMMMC simulations of multicellular systems generate a wealth of data, making it difficult to retrieve the information of interest. Therefore, the SIMMMC Management Tool is a useful instrument for accessing and for analyzing the big variety of simulation data, helping the optimization of in vitro tissue structure creation.