TY - JOUR
T1 - Cell studio
T2 - A platform for interactive, 3D graphical simulation of immunological processes
AU - Liberman, Asaf
AU - Kario, Danny
AU - Mussel, Matan
AU - Brill, Jacob
AU - Buetow, Kenneth
AU - Efroni, Sol
AU - Nevo, Uri
N1 - Publisher Copyright:
© 2018 Author(s).
PY - 2018/6/1
Y1 - 2018/6/1
N2 - The field of computer modeling and simulation of biological systems is rapidly advancing, backed by significant progress in the fields of experimentation techniques, computer hardware, and programming software. The result of a simulation may be delivered in several ways, from numerical results, through graphs of the simulated run, to a visualization of the simulation. The vision of an in-silico experiment mimicking an in-vitro or in-vivo experiment as it is viewed under a microscope is appealing but technically demanding and computationally intensive. Here, we report "Cell Studio," a generic, hybrid platform to simulate an immune microenvironment with biological and biophysical rules. We use game engines - generic programs for game creation which offer ready-made assets and tools - to create a visualized, interactive 3D simulation. We also utilize a scalable architecture that delegates the computational load to a server. The user may view the simulation, move the "camera" around, stop, fast-forward, and rewind it and inject soluble molecules into the extracellular medium at any point in time. During simulation, graphs are created in real time for a broad view of system-wide processes. The model is parametrized using a user-friendly Graphical User Interface (GUI). We show a simple validation simulation and compare its results with those from a "classical" simulation, validated against a "wet" experiment. We believe that interactive, real-time 3D visualization may aid in generating insights from the model and encourage intuition about the immunological scenario.
AB - The field of computer modeling and simulation of biological systems is rapidly advancing, backed by significant progress in the fields of experimentation techniques, computer hardware, and programming software. The result of a simulation may be delivered in several ways, from numerical results, through graphs of the simulated run, to a visualization of the simulation. The vision of an in-silico experiment mimicking an in-vitro or in-vivo experiment as it is viewed under a microscope is appealing but technically demanding and computationally intensive. Here, we report "Cell Studio," a generic, hybrid platform to simulate an immune microenvironment with biological and biophysical rules. We use game engines - generic programs for game creation which offer ready-made assets and tools - to create a visualized, interactive 3D simulation. We also utilize a scalable architecture that delegates the computational load to a server. The user may view the simulation, move the "camera" around, stop, fast-forward, and rewind it and inject soluble molecules into the extracellular medium at any point in time. During simulation, graphs are created in real time for a broad view of system-wide processes. The model is parametrized using a user-friendly Graphical User Interface (GUI). We show a simple validation simulation and compare its results with those from a "classical" simulation, validated against a "wet" experiment. We believe that interactive, real-time 3D visualization may aid in generating insights from the model and encourage intuition about the immunological scenario.
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U2 - 10.1063/1.5039473
DO - 10.1063/1.5039473
M3 - Article
AN - SCOPUS:85076174412
SN - 2473-2877
VL - 2
JO - APL Bioengineering
JF - APL Bioengineering
IS - 2
M1 - 026107
ER -