Article

Executable biology

Authors:

Thomas A. HenzingerAuthors Info & Claims

WSC '06: Proceedings of the 38th conference on Winter simulation

Pages 1675 - 1682

Published: 03 December 2006 Publication History

Abstract

Computational modeling of biological systems is becoming increasingly common as scientists attempt to understand biological phenomena in their full complexity. Here we distinguish between two types of biological models --- mathematical and computational--- according to their different representations of biological phenomena and their diverse potential. We call the approach of constructing computational models of biological systems Executable Biology, as it focuses on the design of executable computer algorithms that mimic biological phenomena. We give an overview of the main modeling efforts in this direction, and discuss some of the new challenges that executable biology poses for computer science and biology. We argue that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research, driving biology towards a more precise engineering discipline.

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Cited By

Olarte CChiarugi DFalaschi MHermith D(2016)A proof theoretic view of spatial and temporal dependencies in biochemical systemsTheoretical Computer Science10.1016/j.tcs.2016.03.029641:C(25-42)Online publication date: 16-Aug-2016
https://dl.acm.org/doi/10.1016/j.tcs.2016.03.029
Demir AErman BHenkel J(2013)Simulation of temporal stochastic phenomena in electronic and biological systemsProceedings of the International Conference on Computer-Aided Design10.5555/2561828.2561983(811-818)Online publication date: 18-Nov-2013
https://dl.acm.org/doi/10.5555/2561828.2561983
Cook BFisher JKrepska EPiterman N(2011)Proving stabilization of biological systemsProceedings of the 12th international conference on Verification, model checking, and abstract interpretation10.5555/1946284.1946295(134-149)Online publication date: 23-Jan-2011
https://dl.acm.org/doi/10.5555/1946284.1946295
Show More Cited By

Executable biology
1. Applied computing
  1. Life and medical sciences
2. Computing methodologies
  1. Modeling and simulation
    1. Model development and analysis

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Information & Contributors

Information

Published In

cover image ACM Conferences

WSC '06: Proceedings of the 38th conference on Winter simulation

December 2006

2429 pages

ISBN:1424405017

Editors:
L. Felipe Perrone
Bucknell University
,
Barry G. Lawson
University of Richmond
,
Jason Liu
Colorado School of Mines
,
Frederick P. Wieland
Sensis Corporation
,
General Chair:
David Nicol
University of Illinois, Urbana-Champaign
,
Program Chair:
Richard Fujimoto
College of Computing, Georgia Tech

Sponsors

IIE: Institute of Industrial Engineers
ASA: American Statistical Association
IEICE ESS: Institute of Electronics, Information and Communication Engineers, Engineering Sciences Society
IEEE-CS\DATC: The IEEE Computer Society
SIGSIM: ACM Special Interest Group on Simulation and Modeling
NIST: National Institute of Standards and Technology
(SCS): The Society for Modeling and Simulation International
INFORMS-CS: Institute for Operations Research and the Management Sciences-College on Simulation

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Winter Simulation Conference

Publication History

Published: 03 December 2006

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WSC06

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IIE
ASA
IEICE ESS
IEEE-CS\DATC
SIGSIM
NIST
(SCS)
INFORMS-CS

WSC06: Winter Simulation Conference 2006

December 3 - 6, 2006

California, Monterey

Acceptance Rates

WSC '06 Paper Acceptance Rate 177 of 252 submissions, 70%;

Overall Acceptance Rate 3,413 of 5,075 submissions, 67%

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Cited By

Olarte CChiarugi DFalaschi MHermith D(2016)A proof theoretic view of spatial and temporal dependencies in biochemical systemsTheoretical Computer Science10.1016/j.tcs.2016.03.029641:C(25-42)Online publication date: 16-Aug-2016
https://dl.acm.org/doi/10.1016/j.tcs.2016.03.029
Demir AErman BHenkel J(2013)Simulation of temporal stochastic phenomena in electronic and biological systemsProceedings of the International Conference on Computer-Aided Design10.5555/2561828.2561983(811-818)Online publication date: 18-Nov-2013
https://dl.acm.org/doi/10.5555/2561828.2561983
Cook BFisher JKrepska EPiterman N(2011)Proving stabilization of biological systemsProceedings of the 12th international conference on Verification, model checking, and abstract interpretation10.5555/1946284.1946295(134-149)Online publication date: 23-Jan-2011
https://dl.acm.org/doi/10.5555/1946284.1946295
Casagrande APiazza CPolicriti A(2009)Discrete Semantics for Hybrid AutomataDiscrete Event Dynamic Systems10.1007/s10626-009-0082-719:4(471-493)Online publication date: 1-Dec-2009
https://dl.acm.org/doi/10.1007/s10626-009-0082-7

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