Algebraic and Numeric Biology
4th International Conference, ANB 2010, Hagenberg, Austria, July 31-August 2, 2010, Revised Selected Papers
Published on 13. January 2012
IX, 185 pages
978-3-642-28067-2 (ISBN)
Description
This book constitutes the refereed proceedings of the 4th International Conference on Algebraic Biology, ANB 2010, held at the Castle of Hagenberg, Austria in July/August 2010. The conference is a follow up of the AB Conference.
The 10 papers were carefully reviewed and selected from numerous submissions. The papers are organized in topical sections on mathematical modeling, system analysis and design, genomics, molecular structure analysis, automata theory, artificial intelligence, sequence analysis, automated reasoning, formal language and hybrid symbolic numerical methods.
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Katsuhisa Horimoto | Masahiko Nakatsui | Nikolaj Popov
Algebraic and Numeric Biology
4th International Conference, ANB 2010, Hagenberg, Austria, July 31-August 2, 2010, Revised Selected Papers
Book
02/2012
1st Edition
Springer
€53.49
Shipment within 7-9 days
Content
- Title
- Preface
- Conference Organization
- Table of Contents
- P$_0$-Matrix Products of Matrices
- Introduction
- Some Properties of P-Type Matrices
- The Main Question
- Notation and Definitions
- Main Results
- Preliminary Results
- Qualitative Classes and Related Ideas
- Compatibility of all Matrices in a Qualitative Class
- Compatibility of a Matrix with its Qualitative Class
- Matrices with Diagonal Factors
- Discussion and Conclusions
- References
- A Formal Model for Databases in DNA
- Introduction
- Related Work
- The Sticker-Complex Data Model
- Operations on Complexes
- Data Representation
- Implementation in DNA
- DNAQL
- Simulation of the Relational Algebra
- Concluding Remarks
- References
- Efficient and Accurate Haplotype Inference by Combining Parsimony and Pedigree Information
- Introduction
- Haplotype Inference
- Minimum Recombinant Haplotype Configuration
- Haplotype Inference by Pure Parsimony
- The PedRPoly Model
- Improving Efficiency
- Lower Bounds
- Sorting Genotypes
- Symmetries
- Experimental Evaluation
- Efficiency
- Accuracy
- Conclusions
- References
- MABSys: Modeling and Analysis of Biological Systems
- Introduction
- Related Works
- Main Structure of MABSys
- Description of Biochemical Reaction Networks
- Modeling by Means of ODEs
- Exact Symbolic Simplifications
- Qualitative Analysis
- Tyson's Negative Feedback Oscillator
- Symbolic Simplification
- Discussion
- Installation of MABSys
- Conclusion and Perspectives
- References
- Models of Stochastic Gene Expression and Weyl Algebra
- Introduction
- The Classical Theory
- Chemical Reactions Systems
- Stochastic Petri Nets
- Markov Chain of the Temporisation and Master Equation
- The Schrödinger Equation Analog
- Reformulation in the Weyl Algebra
- The Algorithm
- Model Reduction, Model Restriction and Conservation Laws
- Model Reduction
- Model Restriction
- A Combined Formula for Differentiating and Evaluating
- Order of a Chemical Reaction System
- Examples
- First Order Systems
- Second Order Systems
- Conclusion
- References
- Reconciling Competing Models: A Case Study of Wine Fermentation Kinetics
- Introduction
- Methods
- Results
- Conclusions and Discussion
- References
- Computational Modeling and Verification of Signaling Pathways in Cancer
- Introduction
- Statistical Model Checking
- Bounded Linear Temporal Logic
- Bayesian Statistical Model Checking
- Crosstalk Model of HMGB1
- Motivations
- Model Formulation
- Simulation Models
- Simulation Results
- Verification of the HMBG1 Pathway
- Discussion
- References
- Composability: Perspectives in Ecological Modeling
- Introduction
- The BlenX Language
- Composability as a Modeling Aid
- Composability and Language Design
- Discussion
- References
- A General Procedure for Accurate Parameter Estimation in Dynamic Systems Using New Estimation Errors
- Introduction
- Procedure
- Overview of Present Procedure
- Example
- Differential Elimination
- Simplification
- Introduction of Constraints
- Optimization Algorithm
- Results
- Discussion
- References
- Analyzing Pathways Using ASP-Based Approaches
- Introduction
- Answer Set Programming
- Symbolic Systems Biology
- Reaction Networks
- Equilibrium States
- Maximal Solutions
- Preferred Solutions
- ASP Computation of Maximal and Preferred Solutions
- Related Work
- Conclusion
- References
- Author Index
