Modeling and simulation of biological systems using SPICE language

Morgan Madec¹, Christophe Lallement¹, Jacques Haiech²

¹ICube, UMR7357, CNRS / Université de Strasbourg, France

²LIT, UMR 7200, CNRS / Université de Strasbourg, France

Published: August 7, 2017
doi: 10.1371/journal.pone.0182385

Abstract: The article deals with BB-SPICE (SPICE for Biochemical and Biological Systems), an extension of the famous Simulation Program with Integrated Circuit Emphasis (SPICE). BB-SPICE environment is composed of three modules: a new textual and compact description formalism for biological systems, a converter that handles this description and generates the SPICE netlist of the equivalent electronic circuit and NGSPICE which is an open-source SPICE simulator. In addition, the environment provides back and forth interfaces with SBML (System Biology Markup Language), a very common description language used in systems biology. BB-SPICE has been developed in order to bridge the gap between the simulation of biological systems on the one hand and electronics circuits on the other hand. Thus, it is suitable for applications at the interface between both domains, such as development of design tools for synthetic biology and for the virtual prototyping of biosensors and lab-on-chip. Simulation results obtained with BB-SPICE and COPASI (an open-source software used for the simulation of biochemical systems) have been compared on a benchmark of models commonly used in systems biology. Results are in accordance from a quantitative viewpoint but BB-SPICE outclasses COPASI by 1 to 3 orders of magnitude regarding the computation time. Moreover, as our software is based on NGSPICE, it could take profit of incoming updates such as the GPU implementation, of the coupling with powerful analysis and verification tools or of the integration in design automation tools (synthetic biology).

GeNeDA results from the collaboration between three laboratories:
The Laboratory of Engineering Sciences, Computer Sciences and Imaging, ICube, UMR7357, CNRS / Université de Strasbourg, France (Morgan MADEC, Yves GENDRAULT, Elise ROSATI and Christophe LALLEMENT)
The Laboratory of Therapeutic Innovation, LIT, UMR 7200, CNRS / Université de Strasbourg, France (Jacques HAIECH)
The Laboratory of Computer Sciences of Paris 6, LIP6, UMR7606, CNRS / Université Pierre et Marie Curie, Paris, France (François PECHEUX)

Relared papers has been published recently
[1] M. Madec, F. Pêcheux, Y. Gendrault, E. Rosati, C. Lallement and J. Haiech, "GeNeDA: An Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics", Journal of Computational Biology, June 2016. doi:10.1089/cmb.2015.0229.
[2] M. Madec et al., "Reuse of Microelectronics Software for Gene Regulatory Networks Design Automation", 1st international conference of the GDB BioSynSys, Paris (FR), Sept. 2016.
[3] M. Madec et al., "EDA inspired Open-source Framework for Synthetic Biology", IEEE 2013 BioCAS Conference, Rotterdam (NL), Nov. 2013.