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Keywords
(9)
Biological Data
Differential Equation
Genetic Network
Genetic Regulatory Network
Model Checking
Modeling and Simulation
piecewise linear
Tool Support
High Throughput
Related Publications
(5)
Program Analysis as Model Checking of Abstract Interpretations
A formal basis for architectural connection
Application of formal methods to biological regulatory networks: extending Thomas’ asynchronous logical approach with temporal logic
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks
Model Checking Genetic Regulatory Networks with Parameter Uncertainty
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Model Checking Genetic Regulatory Networks Using GNA and CADP
Model Checking Genetic Regulatory Networks Using GNA and CADP,10.1007/9783540247326_12,Grégory Batt,Damien Bergamini,Hidde De Jong,Hubert Garavel,
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Model Checking Genetic Regulatory Networks Using GNA and CADP
(
Citations: 21
)
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Grégory Batt
,
Damien Bergamini
,
Hidde De Jong
,
Hubert Garavel
,
Radu Mateescu
The study of genetic regulatory networks, which underlie the functioning of living organisms, has received a major impetus from the recent development of highthroughput genomic techniques. This experimental progress calls for the development of appropriate computer tools supporting the analysis of genetic regulatory processes. We have developed a
modeling and simulation
method [5,7], based on piecewiselinear differential equations, that is welladapted to the qualitative nature of most available biological data. The method has been implemented in the tool
Genetic Network
Analyzer (GNA) [6], which produces a graph of qualitative states and transitions between qualitative states. The graph provides a discrete abstraction of the dynamics of the system.
Conference:
International Workshop on Model Checking of Software  SPIN
, pp. 158163, 2004
DOI:
10.1007/9783540247326_12
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Citation Context
(14)
...Formal verification can then be carried out enumeratively (for instance, using the tools [10], [
1
], [26]) or symbolically (see, for example, [5], [2])...
Gregor Goessler
.
ComponentBased Modeling and Reachability Analysis of Genetic Networks
...Previous versions of GNA supported the export of the FSTS to text files accepted by several model checkers [13,
41
]...
...Some modeling tools like GINSIM [27] and previous versions of GNA [
41
] are capable of exporting the model in an implicit or explicit format accepted by the model checker and the entire analysis is carried out in the modelchecking environment, without any feedback to the modeling tool...
Pedro T. Monteiro
,
et al.
A serviceoriented architecture for integrating the modeling and forma...
...Then, the account should cover the first complete application to a paradigmatic case study, the genetic toggle, where the language of lineartemporal logic is used to express the main properties of the network [
7
]...
...The toggle had already been studied by model checking [
7
]...
Giampaolo Bella
,
et al.
Formal Analysis of the Genetic Toggle
...[1,1] [1,2] [1,3] [1,
4
] [1,5] [2,1] [2,2] [2,3] [2,4] [2,5] [3,1] [3,2] [3,3] [3,4] [3,5]...
...[1,1] [1,2] [1,3] [1,4] [1,5] [2,1] [2,2] [2,3] [2,
4
] [2,5] [3,1] [3,2] [3,3] [3,4] [3,5]...
...[1,1] [1,2] [1,3] [1,4] [1,5] [2,1] [2,2] [2,3] [2,4] [2,5] [3,1] [3,2] [3,3] [3,
4
] [3,5]...
Jiri Barnat
,
et al.
Parallel Model Checking LargeScale Genetic Regulatory Networks with D...
...in boolean [33,32,16], discrete [39,
40
], stochastic [41,42] and continuous models [14,43,32]...
Franccois Fages
,
et al.
Formal Cell Biology in BIOCHAM
References
(12)
Symbolic Model Checking of Biochemical Networks
(
Citations: 67
)
Nathalie Chabrier
,
François Fages
Conference:
Computational Methods in Systems Biology  CMSB
, pp. 149162, 2003
Automated Symbolic Reachability Analysis; with Application to DeltaNotch Signaling Automata
(
Citations: 55
)
Ronojoy Ghosh
,
Ashish Tiwari
,
Claire Tomlin
Conference:
Hybrid Systems
, pp. 233248, 2003
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks
(
Citations: 92
)
Hidde De Jong
,
Johannes Geiselmann
,
Céline Hernandez
,
Michel Page
Journal:
Bioinformatics/computer Applications in The Biosciences  BIOINFORMATICS
, vol. 19, no. 3, pp. 336344, 2003
Contribution of Computational Tree Logic to Biological Regulatory Networks: Example from Pseudomonas Aeruginosa
(
Citations: 8
)
Sabine Peres
,
Jeanpaul Comet
Conference:
Computational Methods in Systems Biology  CMSB
, pp. 4756, 2003
Efficient onthefly modelchecking for regular alternationfree mucalculus
(
Citations: 109
)
Radu Mateescu
,
Mihaela Sighireanu
Journal:
Science of Computer Programming  SCP
, vol. 46, no. 3, pp. 255281, 2003
Sort by:
Citations
(21)
ComponentBased Modeling and Reachability Analysis of Genetic Networks
(
Citations: 1
)
Gregor Goessler
Journal:
IEEE/ACM Transactions on Computational Biology and Bioinformatics  TCBB
, vol. 8, no. 3, pp. 672682, 2011
A serviceoriented architecture for integrating the modeling and formal verification of genetic regulatory networks
(
Citations: 5
)
Pedro T. Monteiro
,
Estelle Dumas
,
Bruno Besson
,
Radu Mateescu
,
Michel Page
,
Ana T. Freitas
,
Hidde de Jong
Journal:
BMC Bioinformatics
, vol. 10, no. 1, pp. 45012, 2009
Formal Analysis of the Genetic Toggle
Giampaolo Bella
,
Pietro Liò
Conference:
Computational Methods in Systems Biology  CMSB
, pp. 96110, 2009
Parallel Model Checking LargeScale Genetic Regulatory Networks with DiVinE
(
Citations: 7
)
Jiri Barnat
,
Lubos Brim
,
Ivana Cerná
,
S. Drazan
,
David Safránek
Journal:
Electronic Notes in Theoretical Computer Science  ENTCS
, vol. 194, no. 3, pp. 3550, 2008
Formal Cell Biology in BIOCHAM
(
Citations: 7
)
Franccois Fages
,
Sylvain Soliman
Published in 2008.