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In Silico - 1st Edition - ISBN: 9780123736550, 9780080879253

In Silico

1st Edition

3D Animation and Simulation of Cell Biology with Maya and MEL

Authors: Jason Sharpe Charles Lumsden Nicholas Woolridge
eBook ISBN: 9780080879253
Imprint: Morgan Kaufmann
Published Date: 16th June 2008
Page Count: 656
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Table of Contents

Preface
Who is this book for?
Why Maya?
What the book offers
Acknowledgments
Contact us
Part 1 Setting the stage
Chapter 1 Introduction
The challenge
Wetware for seeing
Visualization in Science
Organizational hierarchy: Keys to biology in vivo and in silicoEnter Maya
Endless possibilities
References
Chapter 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
Chapter 3 Animating biology
Introduction
Animation and film perception
Part 2 A foundation in Maya
Chapter 4 Maya basics
Getting started
How Maya works (briefly)
Maya’s user interface (UI)
Summary
Chapter 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
Chapter 6 Animation
Introduction
Animation
Tutorial 06.01 A keyframe animation
Tutorial 06.02 A simple procedural animation
Chapter 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
Chapter 8 Shading
Introduction
The Render menu set
Shading 209
Tutorial 08.01 Shading
Chapter 9 Cameras
Maya cameras
Tutorial 09.01 A camera on hemoglobin
Chapter 10 Lighting
Lighting 253
Tutorial 10.01 Lighting the hemoglobin scene
Chapter 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
Chapter 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
Chapter 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
Chapter 14 Building a protein
Introduction
Problem overview
Methods: Algorithm design
Encoding the algorithm
Results: Running the script
Chapter 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
Chapter 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
Chapter 17 Growing an ECM scaffold
Introduction
Problem overview
Model definition
Methods: Algorithm design
Encoding the algorithm
Grow your scaffold!
Results: Parameter effects
Summary
References
Chapter 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
Chapter 19 Conclusion
Glossary
Further Reading
Index


Description

In Silico introduces Maya programming into one of the most fascinating application areas of 3D graphics: biological visualization. In five building-block tutorials, this book prepares animators to work with visualization problems in cell biology. The book assumes no deep knowledge of cell biology or 3D graphics programming. An accompanying DVD-ROM includes code derived from the tutorials, the working Maya computer files, and sample animated movies.

Key Features

Teaches artists and scientists to create realistic digital images of humans and nature with the popular CG program, Maya
This self-contained study guide includes background, foundations, and practice
Step-by-step example programs and end-result demonstrations help readers develop their own portfolios
Gorgeous four-color screen shots throughout

Readership

Students, educators, and professionals working in 3D visualization in biomedical science. Professionals in cell, molecular, and computational biology. Animators in education, film and games interested in more realistic depictions of biology.


Details

No. of pages:
656
Language:
English
Copyright:
© Morgan Kaufmann 2008
Published:
16th June 2008
Imprint:
Morgan Kaufmann
eBook ISBN:
9780080879253

Ratings and Reviews


About the Authors

Jason Sharpe

Affiliations and Expertise

AXS Biomedical Animation Studio and Institute of Medical Science, University of Toronto, Canada

Charles Lumsden

Affiliations and Expertise

Department of Medicine, University of Toronto, Canada

Nicholas Woolridge

Affiliations and Expertise

Institute of Medical Science, University of Toronto, Canada