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3D Modeling of Dendritic Spines with Synaptic Plasticity

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Modeling and simulation of biological systems using SPICE language.

Morgan Madec¹, Christophe Lallement¹, Jacques Haiech¹

¹Laboratory of Engineering Sciences, Computer Sciences and Imaging (ICube, University of Strasbourg / National Center for Scientific Research), Solid and Systems Electronic Department, Strasbourg, France.

|August 9, 2017

Summary

BB-SPICE simulates biological systems using electronic circuit principles, offering faster computation than existing tools. This approach aids synthetic biology and biosensor design.

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Area of Science:

Biotechnology
Computational Biology
Electronic Engineering

Background:

Traditional biological system simulation lacks integration with electronic circuit design methodologies.
Existing tools for systems biology simulation can be computationally intensive.
Bridging the gap between biological and electronic system modeling is crucial for emerging fields.

Purpose of the Study:

To introduce BB-SPICE, a novel environment extending SPICE for biochemical and biological systems.
To provide a unified platform for simulating biological systems using electronic circuit principles.
To enhance the efficiency and applicability of biological system simulations.

Main Methods:

Developed BB-SPICE with three modules: a description formalism, a converter to SPICE netlists, and the NGSPICE simulator.
Implemented interfaces for System Biology Markup Language (SBML) compatibility.
Compared BB-SPICE performance against COPASI using benchmark models in systems biology.

Main Results:

BB-SPICE accurately simulates biological systems, yielding quantitative results consistent with COPASI.
BB-SPICE demonstrates a 1 to 3 orders of magnitude improvement in computation time compared to COPASI.
The NGSPICE foundation allows BB-SPICE to benefit from future advancements like GPU implementation and integration with design automation tools.

Conclusions:

BB-SPICE offers a significant computational advantage for simulating biological systems.
The environment is well-suited for applications at the intersection of biology and electronics, including synthetic biology and biosensor development.
BB-SPICE represents a powerful new tool for computational systems biology and bio-electronic design.