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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.
Plos One
|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.
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.
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