Computational methods in systems biology : International Conference CMSB 2004, Paris, France, May 26-28, 2004 : revised selected papers /
The Computational Methods in Systems Biology (CMSB) workshop series was established in 2003 by Corrado Priami. The purpose of the workshop series is to help catalyze the convergence between computer scientists interested in language design, concurrency theory, software engineering or program verific...
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| Format: | Conference Proceeding Book |
| Language: | English |
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Berlin :
Springer,
c2005
Berlin : Springer ©2005 Berlin ; New York : Springer-Verlag, c2005 Berlin ; New York : ©2005 Berlin ; New York, NY : c2005 |
| Series: | Lecture notes in computer science ;
3082 Lecture notes in computer science Lecture notes in bioinformatics. Lecture notes in computer science 3082 |
| Subjects: |
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| 111 | 2 | |a CMSB (Conference) |n (2nd : |d 2004 : |c Paris, France) |1 http://viaf.org/viaf/172975150 | |
| 111 | 2 | |a CMSB (Conference) |n (2nd : |d 2004 : |c Paris, France) | |
| 245 | 1 | 0 | |a Computational methods in systems biology : |b International Conference CMSB 2004, Paris, France, May 26-28, 2004 : revised selected papers / |c Vincent Danos, Vincent Schachter (eds.) |
| 246 | 3 | 0 | |a CMSB 2004 |
| 260 | |a Berlin : |b Springer, |c c2005 | ||
| 260 | |a Berlin : |b Springer, |c ©2005 | ||
| 260 | |a Berlin ; |a New York : |b Springer |c c2005 | ||
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| 260 | |a Berlin ; |a New York, NY : |b Springer-Verlag, |c c2005 | ||
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| 490 | 1 | |a Lecture notes in computer science, |x 0302-9743 ; |v 3082 |a Lecture notes in bioinformatics | |
| 504 | |a Includes bibliographical references and index | ||
| 505 | 0 | |a Long Papers -- An Explicit Upper Bound for the Approximation Ratio of the Maximum Gene Regulatory Network Problem -- Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis -- Beta Binders for Biological Interactions -- Biomimetic in Silico Devices -- Building and Analysing an Integrative Model of HIV-1 RNA Alternative Splicing -- Graph-Based Modeling of Biological Regulatory Networks: Introduction of Singular States -- IMGT-Choreography: Processing of Complex Immunogenetics Knowledge -- Model Checking Biological Systems Described Using Ambient Calculus -- Modeling the Molecular Network Controlling Adhesion Between Human Endothelial Cells: Inference and Simulation Using Constraint Logic Programming -- Modelling Metabolic Pathways Using Stochastic Logic Programs-Based Ensemble Methods -- Projective Brane Calculus -- Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data -- Spatial Modeling and Simulation of Diffusion in Nuclei of Living Cells -- The Biochemical Abstract Machine BIOCHAM -- Towards Reusing Model Components in Systems Biology -- VICE: A VIrtual CEll -- Short Papers -- Biological Domain Identification Based in Codon Usage by Means of Rule and Tree Induction -- Black Box Checking for Biochemical Networks -- CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems -- Combining State-Based and Scenario-Based Approaches in Modeling Biological Systems -- Developing SBML Beyond Level 2: Proposals for Development -- General Stochastic Hybrid Method for the Simulation of Chemical Reaction Processes in Cells -- The Biodegradation Network, a New Scenario for Computational Systems Biology Research -- Invited Contributions -- Brane Calculi | |
| 505 | 0 | 0 | |a note: |t explicit upper bound for the approximation ratio of the maximum gene regulatory network problem / |r Sergio Pozzi / |r Giancarlo Mauri / |r Gianluca Della Vedova -- |t Autonomous mobile robot control based on white blood cell chemotaxis / |r Matthew D. Onsum / |r Adam P. Arkin -- |t Beta binders for biological interactions / |r Corrado Priami / |r Paola Quaglia -- |t Biomimetic in silico devices / |r C. Anthony Hunt / |r Glen E. P. Ropella / |r Michael S. Roberts / |r Li Yan -- |t Building and analysing an integrative model of HIV-1 RNA alternative splicing / |r A. Bockmayr / |r A. Courtois / |r D. Eveillard / |r M. Vezain -- |t Graph-based modeling of biological regulatory networks : introduction of singular states / |r Adrien Richard / |r Jean-Paul Comet / |r Gilles Bernot -- |t IMGT-choreography : processing of complex immunogenetics knowledge / |r Denys Chaume / |r Veronique Giudicelli / |r Kora Combres / |r Chantal Ginestoux / |r Marie-Paule Lefranc -- |t Model checking biological systems described using ambient calculus / |r Radu Mardare / |r Corrado Priami / |r Paola Quaglia / |r Oleksandr Vagin -- |t Modeling the molecular network controlling adhesion between human endothelial cells : inference and simulation using constraint logic programming / |r Eric Fanchon / |r Fabien Corblin / |r Laurent Trilling / |r Bastien Hermant / |r Danielle Gulino -- |t Modelling metabolic pathways using stochastic logic programs-based ensemble methods / |r Huma Lodhi / |r Stephen Muggleton -- |t Projective brane calculus / |r Vincent Danos / |r Sylvain Pradalier -- |t Residual bootstrapping and median filtering for robust estimation of gene networks from microarray data / |r Seiya Imoto / |r Tomoyuki Higuchi / |r SunYong Kim / |r Euna Jeong / |r Satoru Miyano -- |t Spatial modeling and simulation of diffusion in nuclei of living cells / |r Dietmar Volz / |r Martin Eigel / |r Chaitanya Athale / |r Peter Bastian / |r Harald Hermann / |r Constantin Kappel / |r Roland Eils -- |t biochemical abstract machine BIOCHAM / |r Nathalie Chabrier-Rivier / |r Francois Fages / |r Sylvain Soliman -- |t Towards reusing model components in systems biology / |r Adelinde M. Uhrmacher / |r Daniela Degenring / |r Jens Lemcke / |r Mario Krahmer -- |t VICE : a virtual CEll / |r D. Chiarugi / |r M. Curti / |r P. Degano / |r R. Marangoni -- |t Biological domain identification based in codon usage by means of rule and tree induction / |r Antonio Neme / |r Pedro Miramontes -- |t Black box checking for biochemical networks / |r Dragan Bosnacki -- |t CMBSlib : a library for comparing formalisms and models of biological systems / |r Sylvain Soliman / |r Francois Fages -- |t Combining state-based and scenario-based approaches in modeling biological systems / |r Jasmin Fisher / |r David Harel / |r E. Jane Albert Hubbard / |r Nir Piterman / |r Michael J. Stern / |r Naamah Swerdlin -- |t Developing SBML beyond level 2 : proposals for development / |r Andrew Finney -- |t General stochastic hybrid method for the simulation of chemical reaction processes in cells / |r Martin Bentele / |r Roland Eils -- |t biodegradation network, a new scenario for computational systems biology research / |r Florencio Pazos / |r David Guijas / |r Manuel J. Gomez / |r Almudena Trigo / |r Victor de Lorenzo / |r Alfonso Valencia |
| 505 | 0 | 0 | |t An explicit upper bound for the approximation ratio of the maximum gene regulatory network problem / |r Sergio Pozzi, Gianluca Della Vedova and Giancarlo Mauri -- |t Autonomous mobile robot control based on white blood cell chemotaxis / |r Matthew D. Onsum and Adam P. Arkin -- |t Beta binders for biological interactions / |r Corrado Priami and Paola Quaglia -- |t Biomimetic in silico devices / |r C. Anthony Hunt, Glen E. P. Ropella, Michael S. Roberts and Li Yan -- |t Building and analysing an integrative model of HIV-1 RNA alternative splicing / |r A. Bockmayr, A. Courtois, D. Eveillard and M. Vezain -- |t Graph-based modeling of biological regulatory networks : introduction of singular states / |r Adrien Richard, Jean-Paul Comet and Gilles Bernot -- |t IMGT-choreography : processing of complex immunogenetics knowledge / |r Denys Chaume, Veronique Giudicelli, Kora Combres, Chantal Ginestoux and Marie-Paule Lefranc -- |t Model checking biological systems described using ambient calculus / |r Radu Mardare, Corrado Priami, Paola Quaglia and Oleksandr Vagin -- |t Modeling the molecular network controlling adhesion between human endothelial cells : inference and simulation using constraint logic programming / |r Eric Fanchon, Fabien Corblin, Laurent Trilling, Bastien Hermant and Danielle Gulino -- |t Modelling metabolic pathways using stochastic logic programs-based ensemble methods / |r Huma Lodhi and Stephen Muggleton -- |t Projective brane calculus / |r Vincent Danos and Sylvain Pradalier -- |t Residual bootstrapping and median filtering for robust estimation of gene networks from microarray data / |r Seiya Imoto, Tomoyuki Higuchi, SunYong Kim, Euna Jeong and Satoru Miyano -- |t Spatial modeling and simulation of diffusion in nuclei of living cells / |r Dietmar Volz, Martin Eigel, Chaitanya Athale, Peter Bastian, Harald Hermann, Constantin Kappel and Roland Eils -- |t The biochemical abstract machine BIOCHAM / |r Nathalie Chabrier-Rivier, Francois Fages and Sylvain Soliman -- |
| 505 | 8 | 0 | |t Towards reusing model components in systems biology / |r Adelinde M. Uhrmacher, Daniela Degenring, Jens Lemcke and Mario Krahmer -- |t VICE : a virtual CEll / |r D. Chiarugi, M. Curti, P. Degano and R. Marangoni -- |t Biological domain identification based in codon usage by means of rule and tree induction / |r Antonio Neme and Pedro Miramontes -- |t Black box checking for biochemical networks / |r Dragan Bosnacki -- |t CMBSlib : a library for comparing formalisms and models of biological systems / |r Sylvain Soliman and Francois Fages -- |t Combining state-based and scenario-based approaches in modeling biological systems / |r Jasmin Fisher, David Harel, E. Jane Albert Hubbard, Nir Piterman, Michael J. Stern and Naamah Swerdlin -- |t Developing SBML beyond level 2 : proposals for development / |r Andrew Finney -- |t General stochastic hybrid method for the simulation of chemical reaction processes in cells / |r Martin Bentele and Roland Eils -- |t The biodegradation network, a new scenario for computational systems biology research / |r Florencio Pazos, David Guijas, Manuel J. Gomez, Almudena Trigo, Victor de Lorenzo and Alfonso Valencia -- |t Brane calculi, interactions of biological membranes / |r Luca Cardelli |
| 520 | |a The Computational Methods in Systems Biology (CMSB) workshop series was established in 2003 by Corrado Priami. The purpose of the workshop series is to help catalyze the convergence between computer scientists interested in language design, concurrency theory, software engineering or program verification, and physicists, mathematicians and biologists interested in the systems-level understanding of cellular processes. Systems biology was perceived as being increasingly in search of sophisticated modeling frameworks whether for representing and processing syst- level dynamics or for model analysis, comparison and refinement. One has here a clear-cut case of a must-explore field of application for the formal methods developed in computer science in the last decade. This proceedings consists of papers from the CMSB 2003 workshop. A good third of the 24 papers published here have a distinct formal methods origin; we take this as a confirmation that a synergy is building that will help solidify CMSB as a forum for cross-community exchange, thereby opening new theoretical avenues and making the field less of a potential application and more of a real one. Publication in Springer's new Lecture Notes in Bioinformatics (LNBI) offers particular visibility and impact, which we gratefully acknowledge. Our keynote speakers, Alfonso Valencia and Trey Ideker, gave challenging and somewhat humbling lectures: they made it clear that strong applications to systems biology are still some way ahead. We thank them all the more for accepting the invitation to speak and for the clarity and excitement they brought to the conference | ||
| 530 | |a Also available on the World Wide Web | ||
| 530 | |a Also available online via the World Wide Web; access restricted to licensed sites/users | ||
| 530 | |a Also issued online | ||
| 588 | 0 | |a Print version record | |
| 590 | |a *vhl 20060131 | ||
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| 590 | |a SpringerLink |b Springer Lecture Notes in Computer Science | ||
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