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.

Germany’s RWTH Aachen University and AMO launch joint Aachen Graphene & 2D-Materials Center

RWTH Aachen University and AMO GmbH in Germany have launched a new joint research center with a focus on efficiently bridging the gap between fundamental science and applications within graphene and related materials-based electronics and photonics.

Sharing the vision of bringing graphene and related materials research from the lab into applications, the five founding principal investigators of the Aachen Graphene and 2D-Materials Center (who are also all members of the EU-funded Graphene Flagship project) are professor Christoph Stampfer (of RWTH, and spokesman for the center), professor Max Lemme (of AMO and RWTH), professor Markus Morgenstern (of RWTH), professor Renato Negra (of RWTH) and Dr Daniel Neumaier (of AMO).

“The center will help to turn the exciting properties of graphene and 2D [two-dimensional] materials into true functions, making these materials not only fascinating for scientists but also serving society,” said Christoph Stampfer following the center’s kick-off meeting on 24 July. “With the Aachen Graphene and 2D-Material Center, we aim at increasing the visibility of Aachen as an excellent place to undertake graphene and 2D material research with both a fundamental and applied focus.”

The center enables the integration of the already ongoing work from RWTH Aachen University and AMO under a legal framework that allows for full collaboration between the groups. In particular, the center will focus on addressing the challenges of future technology including high-frequency electronics, flexible electronics, energy-efficient sensing, photonics as well as spintronics and valleytronics with graphene and related materials and their heterostructures.

Founding Members of the Aachen Graphene and 2D Materials Center:

• Prof. Christoph Stampfer, RWTH Aachen University (Spokesman)
• Prof. Max Lemme, RWTH Aachen University/AMO GmbH
• Prof. Markus Morgenstern , RWTH Aachen University
• Prof. Renato Negra, RWTH Aachen University
• Dr. Daniel Neumaier, AMO GmbH

Performance Assessment of A Novel Vertical Dielectrically Modulated TFET-Based Biosensor - IEEE Xplore #paper https://t.co/jRvJS3MUTs

Performance Assessment of A Novel Vertical Dielectrically Modulated TFET-Based Biosensor - IEEE Xplore #paper https://t.co/jRvJS3MUTs

— Wladek Grabinski (@wladek60) August 19, 2017

from Twitter https://twitter.com/wladek60

August 19, 2017 at 10:11AM
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A Threshold Voltage #Model of Tri-Gate Junctionless Field-Effect Transistors Including Substrate Bias Effects https://t.co/sEviQXJbB3

A Threshold Voltage #Model of Tri-Gate Junctionless Field-Effect Transistors Including Substrate Bias Effects https://t.co/sEviQXJbB3

— Wladek Grabinski (@wladek60) August 18, 2017

from Twitter https://twitter.com/wladek60

August 18, 2017 at 01:42PM
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[paper] Improvements to a compact MOSFET model for design by hand

Improvements to a compact MOSFET model for design by hand

A. de Jesus Costa, F. Martins Cardoso, E. Pinto Santana and A. I. Araújo Cunha

15th IEEE NEWCAS

Strasbourg, France, 2017, pp. 225-228

doi: 10.1109/NEWCAS.2017.8010146

Abstract: In this work, an improved version of the basic structure of a compact MOSFET model and the respective parameters extraction methodology are proposed. The aim of this approach is to increase accuracy in hand calculations for analog circuit design without significantly increasing its complexity. The influences of both inversion level and channel length are considered in the modeling of a few features such as mobility, threshold voltage and onset of saturation. Simple design examples of current sinks and sources are accomplished to compare the basic and the improved models [read more...]

[mos-ak] [Workshop Program] 15th MOS-AK ESSDERC/ESSCIRC Workshop in Leuven Sept.11 2017

15th MOS-AK ESSDERC/ESSCIRC Compact Modeling Workshop

Leuven; Monday Sept.11, 2017 (8:30-17:00)

Workshop Program online http://www.mos-ak.org/leuven_2017/ 

Together with International MOS-AK Board of R&D Advisers: Larry Nagel, Omega Enterprises Consulting (USA), Andrei Vladimirescu, UCB (USA); ISEP (FR) and Jean-Michel Sallese, EPFL (CH), Daniel Tomaszewski, ITE (PL), MOS-AK Technical Program Coordinators as well as all the Extended MOS-AK TPC Members, we have pleasure to invite to the 15th consecutive MOS-AK workshop organized as an integral part of the ESSDERC/ESSCIRC Conferences in Leuven on Sept.11, 2017. The MOS-AK workshop is organized with aims to strengthen a network and discussion forum among experts in the field, enhance open platform for information exchange related to the compact/SPICE modeling and its Verilog-A standardization, bring people in the compact modeling field together, as well as obtain feedback from technology developers, circuit designers, and CAD/EDA tool developers and vendors. 

Final Program of 15th MOS-AK ESSDERC/ESSCIC Workshop is available online:

http://www.mos-ak.org/leuven_2017/

Venue: 

KU LEUVEN Campus of Social Sciences 

(Parkstraat 45, 3000 Leuven) 

room AV 91.12

Online MOS-AK/Leuven Workshop Registration:

http://www.esscirc-essderc2017.org/howtoregister

(any related inquiries can be sent to register@mos-ak.org)

The MOS-AK workshop will be followed by four session of the ESSDERC Track4 "Device and Circuit Compact Modeling". These four lecture sessions include one invited and 14 pear reviewed papers in the compact/SPICE modeling and Verilog-A standardization domain:

Tuesday September 12, 2017 (11:00-12:20)

Cross-Domain Compact Modeling  

Chair: Wladek Grabinski - MOS-AK; Cristell Maneux - U-Bordeaux;

Tuesday September 12, 2017 (14:00-15:20)

Parameter Extraction  

Chair: Thierry Poiroux - CEA

Tuesday September 12, 2017 (16:40-18:00)

Modeling of Emerging Devices  

Chair: Jean-Michel Sallese - EPFL; Daniel Tomaszewski - ITE;

Wednesday September 13, 2017 (14:20-15:40)

Traps and Noise  

Chair: Benjamin Iniguez - URV; Sadayuki Yoshitomi - Toshiba;

MOS-AK Postworkshop Publications:

Selected best MOS-AK technical presentation will be recommended for further publication

in a special issue of the International Journal of High Speed Electronics and Systems 

Extended MOS-AK Committee

WG170817

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Review of commercial SiC MOSFET models: Topologies and equations - IEEE Xplore #paper https://t.co/LS090HojeE

Review of commercial SiC MOSFET models: Topologies and equations - IEEE Xplore #paper https://t.co/LS090HojeE

— Wladek Grabinski (@wladek60) August 16, 2017

from Twitter https://twitter.com/wladek60

August 16, 2017 at 11:22AM
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