Transactions on computational systems biology VIII

✍ Scribed by Priami, Corrado(Editor)

• Publisher: Springer
• Year: 2007
• Tongue: English
• Leaves: 109
• Series: Lecture notes in computer science 4780
• 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. It 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. The six papers selected for this special issue cover a broad range of topics.

✦ Table of Contents

Title page......Page 2
Preface......Page 5
Organization......Page 6
Table of Contents......Page 7
Introduction......Page 8
Need for Network-Centric Control......Page 10
An Excursion to Nature - Cellular Signaling Pathways......Page 11
Data-Centric Operation......Page 13
Specific Reaction on Received Data......Page 14
Case Studies......Page 15
Discussion......Page 17
Conclusion......Page 18
References......Page 19
Introduction......Page 21
Related Works......Page 23
Analytical Model: Ligand-Protein Docking......Page 24
Rotation of the Ligand Axis with Respect to Protein A......Page 26
Finding $\theta_{avg}$......Page 27
Computing $\theta_{avg}$ Using a 3-D Coordinate System......Page 32
Calculating $pb$......Page 33
Time Taken for the Ligand to Collide with the Binding Site of the Protein Molecule with Enough Activation Energy for Successful Docking......Page 36
Finding the Average Time for Rotation of Ligand Axis......Page 37
Problems in Validation of Our Model......Page 39
Numerical Results......Page 40
Limitations of Our Model......Page 44
Biological Implications......Page 45
References......Page 46
Introduction......Page 49
A Conceptual Framework: Internet as an Ecosystem Analogy......Page 51
Internet Ecology......Page 52
Types of Population Interactions......Page 53
Evaluation Parameters......Page 55
Predator-Prey Approach: Congestion Control Using Predator-Prey Model......Page 56
Illustrative Example......Page 57
Hybrid Approach: Congestion Control Using Combination of Competition and Predator-Prey Models......Page 61
Illustrative Example......Page 62
Implementation Issues......Page 65
How Does System Biology Benefit from This Contribution?......Page 66
References......Page 67
Introduction......Page 70
Abstracting Biological Systems......Page 72
The $beta$ Workbench......Page 76
Potentials......Page 80
Conclusions......Page 81
Introduction......Page 84
Data Management......Page 85
Software Engineering Tools......Page 86
Model Repositories......Page 87
Architecture Description......Page 88
Web Tools......Page 89
Model Run Manager......Page 90
Model Service......Page 92
Parameter Service......Page 93
Model Execution......Page 94
Composite Modelling......Page 95
Modelling Use Cases......Page 96
References......Page 97
Introduction......Page 99
Preliminaries......Page 101
Stability Under Projection......Page 102
Disjoint Stable Subspaces and Positive Circuits......Page 104
Dynamic Cycles and Negative Circuits......Page 106
References......Page 107
Author Index......Page 109