In Silico,

Preface
Who is this book for?
Why Maya?
What the book offers
Acknowledgments
Contact us

Part 1 Setting the stage
1 Introduction
The challenge
Wetware for seeing
Visualization in Science
Organizational hierarchy: Keys to biology in vivo and in silicoEnter Maya
Endless possibilities
References
2 Computers and the organism
Introduction
Information and Process
Language and Program
High and Low
Interpret or Compile?
The Backus Watershed
Stored Programs
Conditional Control
The Computed Organism
The Computational Organism
OOPS and Agents
Summary
References
3 Animating biology
Introduction
Animation and film perception

Part 2 A foundation in Maya
4 Maya basics
Getting started
How Maya works (briefly)
Maya’s user interface (UI)
Summary
5 Modeling geometry
Introduction
NURBS modeling
Tutorial 05.01 NURBS primitive modeling
Tutorial 05.02 Deform the sphere using components
Tutorial 05.03 Make and deform a polygon primitive
Tutorial 05.04 Construction history
Tutorial 02.05 Create a NURBS “fiber¿
Summary
References
6 Animation
Introduction
Animation
Tutorial 06.01 A keyframe animation
Tutorial 06.02 A simple procedural animation
7 Dynamics
Introduction
The Dynamics module
Tutorial 07.01 Rigid body dynamics
Tutorial 07.02 Particles in a container
Tutorial 07.03 Create a playblast
Summary
8 Shading
Introduction
The Render menu set
Shading 209
Tutorial 08.01 Shading
9 Cameras
Maya cameras
Tutorial 09.01 A camera on hemoglobin
10 Lighting
Lighting 253
Tutorial 10.01 Lighting the hemoglobin scene
11 Action! Maya rendering
Rendering
Advanced rendering techniques with the mental ray for Maya renderer
Tutorial 11.01 Batch rendering
Tutorial 11.02 Playback using fcheck
Summary
12 MEL Scripting
Introduction
The origins of MEL
In a word: Scripting
Getting started
MEL syntax
Values
Variables
Mathematical and logical expressions
The MEL command
Attributes in MEL
Conditional statements
Loops
Procedures
Animation expressions
Putting it all together: The MEL script
Tutorial 12.01 Building a MEL script
Debugging your scripts
Random number generation in Maya
Summary
13 Data Input/Output
Introduction
Translators
Reading and writing files with MEL
Tutorial 13.01 Visualizing cell migration
Summary

Part 3 Biology in silico-Maya in action
14 Building a protein
Introduction
Problem overview
Methods: Algorithm design
Encoding the algorithm
Results: Running the script
15 Self Assembly
Introduction
Problem overview
Methods: Actin geometry
Diffusion and reaction events
Reaction rates and probabilities
Algorithm design
Encoding the algorithm
Results: Running your simulation
Summary
References
16 Modeling a mobile cell
Introduction
Problem overview
Model definition
Methods: Generating pseudopods
Algorithm design
A cell locomotion engine
Encoding the algorithm
Loading the script
Running the script
Summary
References
17 Growing an ECM scaffold
Introduction
Problem overview
Model definition
Methods: Algorithm design
Encoding the algorithm
Grow your scaffold!
Results: Parameter effects
Summary
References
18 Scaffold invasions: Modeling 3D populations of mobile cells
Introduction
Problem overview
Model definition
Methods: Model design
Encoding the algorithm
Running the simulation
Results: Data output
Summary
References
19 Conclusion
Glossary
Further Reading
Index