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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


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


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.


No. of pages:
© Morgan Kaufmann 2007
16th June 2008
Morgan Kaufmann
eBook ISBN:

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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