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Oleson, Björn Edwin: Integrative simulation framework for modeling dynamic cellular phenomena in 3D over time. 2008
Inhalt
1 Introduction
1.1 Motivation
1.2 Objectives
1.3 Structure
2 Dynamics in Systems Biology
2.1 Modeling and Simulation
2.1.1 Biology as a Model Featurer
2.1.2 Computation as a Model Solver
2.2 Cellular Calcium Models
2.2.1 Calcium Signaling
2.2.2 Two Pool Model
3 Related Approaches and Tools
3.1 Database and Information Retrieval
3.2 Modeling and Simulation Software
3.2.1 Deterministic
3.2.2 Stochastic
3.2.3 Frameworks
3.2.4 Comparison
4 Definitions and Implementation
4.1 General Overview
4.1.1 Survey of Integral Parts
4.1.2 Function Classes
4.1.3 Use-Case Descriptions
4.1.4 Program Dynamics
4.2 Considerations and Definitions
4.2.1 Geometry Model
4.2.2 Activity Description
4.2.3 Algorithm Handling
4.2.4 User Interfaces
4.3 Application Details
4.3.1 User Interfaces
4.3.2 Applicability
4.3.3 Complexity Considerations
4.3.4 Availability
5 Applications, Results, and Analysis
5.1 Application Development
5.1.1 Plug-Ins
5.1.2 Programming Languages
5.2 Modeling and Simulation
5.2.1 Simple Diffusion Simulation
5.2.2 Applying Diffusion-Reaction Systems
5.3 Comparing Tools
5.3.1 Comparison Criteria
5.3.2 Comparing Related Works
5.3.3 In Comparison to 4DiCeS
5.4 Related Work
6 Conclusions
6.1 Design Decisions
6.2 Related Attempts
6.3 Challenges and Accomplishment
6.3.1 Model Complexity
6.3.2 Performance Evaluation
6.4 Outlook
A Algorithms in Detail
A.1 Reaction Algorithms
A.1.1 Runge-Kutta Method
A.1.2 Dynamic MC Algorithms
A.2 Diffusion Algorithm
A.2.1 Discrete Lévy Process
B Backus-Naur Form
C Unified Modeling Language
C.1 Use-Case Diagrams
C.2 Class Diagrams
C.3 Sequence Diagrams
C.4 Component Diagrams
List of Abbreviations
List of Figures
List of Tables
Bibliography