Transactions on Computational Systems Biology IX

✍ Scribed by Corrado Priami

• Publisher: Springer
• Year: 2008
• Tongue: English
• Leaves: 159
• Series: Lecture notes in bioinformatics 5121
• Edition: 1st ed
• Category: Library

✦ Synopsis

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena.

This issue contains four highly detailed papers. The first paper focuses on quantitative aspects of the bgl operon for E.coli. The second contribution deals with ecosystem transitions affecting phenotype expressions and selection mechanisms. The third paper presents the Stochastic Calculus of Looping Sequences (SCLS) suitable for the description of microbiological systems, such as cellular pathways, and their evolution. The final contribution describes the use of biological transactions to make atomic sequences of interactions in the BlenX language.

✦ Table of Contents

The Operational Semantics......Page 7
Introduction......Page 1
Model Equations......Page 5
A Cognitive Paradigm for Gene Expression......Page 11
The BlenX Language with Biological Transactions......Page 14
Syntax......Page 15
Simulation Results......Page 16
Modelling Quorum Sensing......Page 18
Mutations in $bglG$ and $bglF$ Make the Expression of bgl Operon Constitutive......Page 19
Semantics......Page 20
Examples......Page 29
Related Works......Page 3
The Syntax......Page 4
Immune Cognition......Page 10
Dynamic Manifolds......Page 17
Rates......Page 22
The Basic Idea......Page 24
Phosphorylation of p53 at Serine 15 by Two Enzymes......Page 30
Second Order Theory: Farming a Coevolutionary System......Page 34
Generalized Stochastic Resonance: Many Baldwin Effects......Page 38
Discussion and Conclusions......Page 42
The Shannon-McMillan Theorem......Page 45
The Rate Distortion Theorem......Page 47
Morse Theory......Page 49
The Mean Field Model......Page 50
References......Page 92
The Calculus of Looping Sequences......Page 2
Modelling Guidelines......Page 6
The Stochastic Calculus of Looping Sequences......Page 8
The Stochastic Algorithm......Page 13
Observation......Page 23
References......Page 120
Example: System with a Three-Reactant One-Product Reaction (Continued)......Page 25
Some Definitions......Page 26
Properties......Page 27
The Citric Acid Cycle......Page 32
Discussion and Conclusion......Page 36