In Silico

In Silico

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

1st Edition - June 16, 2008

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  • Authors: Jason Sharpe, Charles Lumsden, Nicholas Woolridge
  • eBook ISBN: 9780080879253

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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

Table of Contents

  • 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

Product details

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

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

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