Computational methods in systems biology : 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings / David Gilbert, Monika Heiner (eds.).

By: (10th : CMSB (Conference) (10th : 2012 : London, England)
Contributor(s): Gilbert, David, Dr | Heiner, Monika, 1954-
Material type: TextTextSeries: SerienbezeichnungLecture notes in computer science: 7605.; Lecture notes in computer science: ; LNCS sublibrary: Publisher: Berlin ; New York : Springer, ©2012Description: 1 online resourceContent type: text Media type: computer Carrier type: online resourceISBN: 9783642336362; 3642336361; 3642336353; 9783642336355Other title: CMSB 2012Subject(s): Computational biology -- Congresses | Systems Biology -- methods | Models, Biological | Models, Genetic | Informatique | Computational biology | Computer science | Software engineering | Computer simulation | Bioinformatics | Computational Biology/Bioinformatics | Computation by Abstract Devices | Computer Appl. in Life Sciences | Symbolic and Algebraic ManipulationGenre/Form: Congress. | Electronic books. | Conference papers and proceedings. Additional physical formats: Print version:: Computational methods in systems biology.DDC classification: 570.285 LOC classification: QH324.2 | .C57 2012Online resources: Click here to access online
Contents:
Differential and Integral Views of Gene-Phenotype Relations: A Systems Biological Insight / Denis Noble -- Resolving the Three-Dimensional Histology of the Heart / Matthew Gibb, Rebecca A.B. Burton, Christian Bollensdorff, Carlos Afonso and Tahir Mansoori, et al. -- Bimodal Protein Distributions in Heterogeneous Oscillating Systems / Maciej Dobrzyński, Dirk Fey, Lan K. Nguyen and Boris N. Kholodenko -- Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics / Paolo Ballarini, Jarno Mäkelä and Andre S. Ribeiro -- Symmetry-Based Model Reduction for Approximate Stochastic Analysis / Kirill Batmanov, Celine Kuttler, Francois Lemaire, Cédric Lhoussaine and Cristian Versari -- Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum / Laura Bennett, Artem Lysenko, Lazaros G. Papageorgiou, Martin Urban and Kim Hammond-Kosack, et al. -- Predicting Phenotype from Genotype through Automatically Composed Petri Nets / Mary Ann Blätke, Monika Heiner and Wolfgang Marwan.
A Simple Model to Control Growth Rate of Synthetic E. coli during the Exponential Phase: Model Analysis and Parameter Estimation / Alfonso Carta, Madalena Chaves and Jean-Luc Gouzé -- Multi-objective Optimisation, Sensitivity and Robustness Analysis in FBA Modelling / Jole Costanza, Giovanni Carapezza, Claudio Angione, Pietro Liò and Giuseppe Nicosia -- Analysis of Modular Organisation of Interaction Networks Based on Asymptotic Dynamics / Franck Delaplace, Hanna Klaudel, Tarek Melliti and Sylvain Sené -- Concretizing the Process Hitting into Biological Regulatory Networks / Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin and Olivier Roux -- Abstraction of Graph-Based Models of Bio-molecular Reaction Systems for Efficient Simulation / Ibuki Kawamata, Nathanael Aubert, Masahiro Hamano and Masami Hagiya -- Parameter Identification and Model Ranking of Thomas Networks / Hannes Klarner, Adam Streck, David Šafránek, Juraj Kolčák and Heike Siebert.
Investigating Co-infection Dynamics through Evolution of Bio-PEPA Model Parameters: A Combined Process Algebra and Evolutionary Computing Approach / David Marco, Erin Scott, David Cairns, Andrea Graham and Judi Allen, et al. -- Population Dynamics P Systems on CUDA / Miguel A. Martínez-del-Amor, Ignacio Pérez-Hurtado, Adolfo Gastalver-Rubio, Anne C. Elster and Mario J. Pérez-Jiménez -- Approximate Bisimulations for Sodium Channel Dynamics / Abhishek Murthy, Md. Ariful Islam, Ezio Bartocci, Elizabeth M. Cherry and Flavio H. Fenton, et al. -- Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control / Aurélien Naldi, Pedro T. Monteiro and Claudine Chaouiya -- Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks / Ilya Potapov, Jarno Mäkelä, Olli Yli-Harja and Andre Ribeiro -- Simulating Insulin Infusion Pump Risks by In-Silico Modeling of the Insulin-Glucose Regulatory System / Sriram Sankaranarayanan and Georgios Fainekos.
Revisiting the Training of Logic Models of Protein Signaling Networks with ASP / Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele and Niels Grabe, et al. -- JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept / Mary Ann Blätke, Anna Dittrich, Monika Heiner, Fred Schaper and Wolfgang Marwan -- ManyCell: A Multiscale Simulator for Cellular Systems / Joseph O. Dada and Pedro Mendes -- Inferring Reaction Models from ODEs / François Fages, Steven Gay and Sylvain Soliman -- Modelling Trafficking of Proteins within the Mammalian Cell Using Bio-PEPA / Vashti Galpin -- Models of Tet-On System with Epigenetic Effects / Russ Harmer, Jean Krivine, Élise Laruelle, Cédric Lhoussaine and Guillaume Madelaine, et al. -- GeneFuncster: A Web Tool for Gene Functional Enrichment Analysis and Visualisation / Asta Laiho, András Király and Attila Gyenesei -- Effects of Molecular Noise on the Multistability in a Synthetic Genetic Oscillator / Ilya Potapov and Evgenii Volkov -- Towards an Ontology of Biomodelling / Larisa Soldatova, Qian Gao and David Gilbert.
Summary: This book constitutes the thoroughly refereed conference proceedings of the 10th International Conference on Computational Methods in Systems Biology, CMSB 2012, held in London, UK, during October 3-5, 2012. The 17 revised full papers and 8 flash posters presented together with the summaries of 3 invited papers were carefully reviewed and selected from 62 submissions. The papers cover the analysis of biological systems, networks, and data ranging from intercellular to multiscale. Topics included high-performance computing, and for the first time papers on synthetic biology.
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Differential and Integral Views of Gene-Phenotype Relations: A Systems Biological Insight / Denis Noble -- Resolving the Three-Dimensional Histology of the Heart / Matthew Gibb, Rebecca A.B. Burton, Christian Bollensdorff, Carlos Afonso and Tahir Mansoori, et al. -- Bimodal Protein Distributions in Heterogeneous Oscillating Systems / Maciej Dobrzyński, Dirk Fey, Lan K. Nguyen and Boris N. Kholodenko -- Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics / Paolo Ballarini, Jarno Mäkelä and Andre S. Ribeiro -- Symmetry-Based Model Reduction for Approximate Stochastic Analysis / Kirill Batmanov, Celine Kuttler, Francois Lemaire, Cédric Lhoussaine and Cristian Versari -- Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum / Laura Bennett, Artem Lysenko, Lazaros G. Papageorgiou, Martin Urban and Kim Hammond-Kosack, et al. -- Predicting Phenotype from Genotype through Automatically Composed Petri Nets / Mary Ann Blätke, Monika Heiner and Wolfgang Marwan.

A Simple Model to Control Growth Rate of Synthetic E. coli during the Exponential Phase: Model Analysis and Parameter Estimation / Alfonso Carta, Madalena Chaves and Jean-Luc Gouzé -- Multi-objective Optimisation, Sensitivity and Robustness Analysis in FBA Modelling / Jole Costanza, Giovanni Carapezza, Claudio Angione, Pietro Liò and Giuseppe Nicosia -- Analysis of Modular Organisation of Interaction Networks Based on Asymptotic Dynamics / Franck Delaplace, Hanna Klaudel, Tarek Melliti and Sylvain Sené -- Concretizing the Process Hitting into Biological Regulatory Networks / Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin and Olivier Roux -- Abstraction of Graph-Based Models of Bio-molecular Reaction Systems for Efficient Simulation / Ibuki Kawamata, Nathanael Aubert, Masahiro Hamano and Masami Hagiya -- Parameter Identification and Model Ranking of Thomas Networks / Hannes Klarner, Adam Streck, David Šafránek, Juraj Kolčák and Heike Siebert.

Investigating Co-infection Dynamics through Evolution of Bio-PEPA Model Parameters: A Combined Process Algebra and Evolutionary Computing Approach / David Marco, Erin Scott, David Cairns, Andrea Graham and Judi Allen, et al. -- Population Dynamics P Systems on CUDA / Miguel A. Martínez-del-Amor, Ignacio Pérez-Hurtado, Adolfo Gastalver-Rubio, Anne C. Elster and Mario J. Pérez-Jiménez -- Approximate Bisimulations for Sodium Channel Dynamics / Abhishek Murthy, Md. Ariful Islam, Ezio Bartocci, Elizabeth M. Cherry and Flavio H. Fenton, et al. -- Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control / Aurélien Naldi, Pedro T. Monteiro and Claudine Chaouiya -- Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks / Ilya Potapov, Jarno Mäkelä, Olli Yli-Harja and Andre Ribeiro -- Simulating Insulin Infusion Pump Risks by In-Silico Modeling of the Insulin-Glucose Regulatory System / Sriram Sankaranarayanan and Georgios Fainekos.

Revisiting the Training of Logic Models of Protein Signaling Networks with ASP / Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele and Niels Grabe, et al. -- JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept / Mary Ann Blätke, Anna Dittrich, Monika Heiner, Fred Schaper and Wolfgang Marwan -- ManyCell: A Multiscale Simulator for Cellular Systems / Joseph O. Dada and Pedro Mendes -- Inferring Reaction Models from ODEs / François Fages, Steven Gay and Sylvain Soliman -- Modelling Trafficking of Proteins within the Mammalian Cell Using Bio-PEPA / Vashti Galpin -- Models of Tet-On System with Epigenetic Effects / Russ Harmer, Jean Krivine, Élise Laruelle, Cédric Lhoussaine and Guillaume Madelaine, et al. -- GeneFuncster: A Web Tool for Gene Functional Enrichment Analysis and Visualisation / Asta Laiho, András Király and Attila Gyenesei -- Effects of Molecular Noise on the Multistability in a Synthetic Genetic Oscillator / Ilya Potapov and Evgenii Volkov -- Towards an Ontology of Biomodelling / Larisa Soldatova, Qian Gao and David Gilbert.

Includes bibliographical references and author index.

This book constitutes the thoroughly refereed conference proceedings of the 10th International Conference on Computational Methods in Systems Biology, CMSB 2012, held in London, UK, during October 3-5, 2012. The 17 revised full papers and 8 flash posters presented together with the summaries of 3 invited papers were carefully reviewed and selected from 62 submissions. The papers cover the analysis of biological systems, networks, and data ranging from intercellular to multiscale. Topics included high-performance computing, and for the first time papers on synthetic biology.

English.

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