Transactions on Computational Systems Biology X (Lecture Notes in Computer Science, 5410)

✍ Scribed by Corrado Priami (editor), Falko Dressler (editor), Ozgur B. Akan (editor), Alioune Ngom (editor)

• Publisher: Springer
• Year: 2008
• Tongue: English
• Leaves: 204
• Category: Library

✦ Synopsis

Technology is taking us to a world where myriads of heavily networked devices interact with the physical world in multiple ways, and at many levels, from the globalInternetdowntomicroandnanodevices. Manyofthesedevicesarehighly mobile and autonomous and must adapt to the surrounding environment in a totally unsupervised way. A fundamental research challenge is the design of robust decentralized c- puting systemsthat arecapableofoperating in changing environmentsandwith noisy input, and yet exhibit the desired behavior and response time, under c- straints such as energy consumption, size, and processing power. These systems should be able to adapt and learn how to react to unforeseen scenarios as well as to display properties comparable to social entities. The observation of nature has brought us many great and unforeseen concepts. Biological systems are able to handle many of these challenges with an elegance and e?ciency far beyond currenthumanartifacts. Basedonthisobservation,bio-inspiredapproacheshave been proposed as a means of handling the complexity of such systems. The goal is to obtain methods to engineer technical systems, which are of a stability and e?ciency comparable to those found in biological entities. This Special Issue on Biological and Biologically-inspired Communication contains the best papers from the Second International Conference on Bio- Inspired Models of Network, Information, and Computing Systems (BIONET- ICS 2007). The BIONETICS conference aims to bring together researchers and scientistsfromseveraldisciplines incomputerscienceandengineeringwhereb- inspired methods are investigated, as well as from bioinformatics, to deepen the information exchange and collaboration among the di?erent communities.

✦ Table of Contents

Title Page
Preface
Table of Contents
Biological and Biologically-Inspired Communication
Towards a Self-structured Grid: An Ant-Inspired P2P Algorithm
Introduction
Related Work
The Antares Algorithm
Pick Operation
Drop Operation
Spatial Sorting of Descriptors
Management of Peer Disconnections
Performance Evaluation
Conclusions
References
Robustness to Code and Data Deletion in Autocatalytic Quines
Introduction
Background and Related Work
Self-replicating Code
Artificial Chemistries
The Fraglet Reaction Model
Self-replication in Fralgets
Embedding Functionality
Dynamic Aspects of Self-replication
Growth
Dilution
Emergent Robustness to Code Deletion
Robust Programs Using Self-replicating Operations
Example: Arithmetic Expression
Discussion
From Robustness towards Security
Conclusions
References
A Computational Scheme Based on Random Boolean Networks
Introduction
Random Boolean Networks
Definition of RBNs
Frozen and Chaotic Phases
Attractors
Redundant Vertices
Computational Scheme Based on RBNs
Computation of Attractors
Binary Decision Diagrams
Transition Relation
Forward Reachability
Backward Reachability
Example
Simulation Results
Conclusion and Open Problems
References
On Channel Capacity and Error Compensation in Molecular Communication
Introduction
Molecular Communication Model
Molecule Delivery
An Information Theoretical Approach for Molecular Communication
Adaptive Error Compensation in the Molecular Communication
A Selection Strategy for Molecular Bit Transmission Probability
An Adaptive Molecular Error Compensation Scheme
Numerical Analysis
Effect of Environmental Factors on Molecular Communication Capacity
Effect of the Parameters Specific to TN and RN on Molecular Communication
Adaptive Molecular Error Compensation Scheme
Conclusion
References
Molecular Communication through Gap Junction Channels
Introduction
System Characteristics
System Design
Gap Junction Channels
Molecular Communication through Gap Junction Channels
Design Detail
Experimental Demonstration
Theoretical Prediction
Distance and Speed of Intercellular Ca$^{2+}$ Waves
Regenerative Intercellular Ca$^{2+}$ Waves
Repetitive Intercellular Ca$^{2+}$ Waves
Summary
Concluding Remarks
References
Clustering Time-Series Gene Expression Data with Unequal Time Intervals
Introduction
Area-Based Profile Alignment
Clustering Method for Profile Alignment
Optimizing the Number of Clusters
Experimental Results
The Serum Dataset
The Yeast Dataset
Biological Analysis
Conclusion
References
Integrating Thermodynamic and Observed-Frequency Data for Non-coding RNA Gene Search
Introduction
Covariance Models
Parameter Estimation Using Family Member Observed Frequencies Only
Parameter Estimation Including Non-family Observed Frequencies
Information in Consensus Loop Lengths and Types
Potential Use of Thermodynamic Data for Improvement of Loop Priors
Evidence That Thermodynamic Data Helps Predict Insertion Probability
Information in Consensus Nucleotides of Helix Neighbors
Conclusion
References
An Evolutionary Approach to the Non-unique Oligonucleotide Probe Selection Problem
Introduction
Non-unique Probe Selection Problem
Previous Work
Probe Selection Function
Coverage Function
Separation Function
Selection Function
Deterministic Greedy Heuristic for Non-unique Probes
Genetic Algorithm for Non-unique Probes
Representation and Fitness Function
Parent Selection Operator
Crossover Operator
Mutation Operator and Variable Mutation Rate
Heuristic Feasibility Operator
Initial Population
Replacement Strategy
The Algorithm
Computational Experiments
Data Sets
Results and Discussions
Conclusions and Future Research
References
Stochastic π-Calculus Modelling of Multisite Phosphorylation Based Signaling: The PHO Pathway in Saccharomyces Cerevisiae
Introduction
The PHO Pathway in Saccharomyces Cerevisiae
Stochastic π-Calculus Sub-models for the PHO Pathway
The Multisite Phosphorylation Model
Dynamic Regulation of the Number of Processes
The Promoter Model
The Transmembrane Transport Model
The Protein Synthesis and Degradation Model
The $Pho4$ Multisite Phosphorylation Model
The PHO Pathway MODEL
In Silico Simulations vs. Biological Data
$Pho4$ Multisite Phosphorylation Model Tuning and Validation
$In silico$ Estimation of the Average Number of $Pho4$ Phosphorylation Events Per Binding Event between $Pho4$ and the Cyclin-CDK $Pho80-Pho85$
Kinetic Analysis of $Pho4$ Phosphorylation Profiles Predicts Biological Outcomes
PHO Pathway Results
Analysis of Process Calculi Features
$In silico$ Process Calculi for Multisite Phosphorylations
Biological Modelling of Discrete and Null Events
The Problem of Explosion of the Number of Process Definition
Compositionality for Handling Systems Biology Complexity
Conclusions
References
The Stochastic π-Calculus and SPiM
The Model for the Dynamic Regulation of the Number of Processes as a Continuous-Time Markov Chain
Author Index