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In Silico
3D Animation and Simulation of Cell Biology with Maya and MEL
1st Edition - June 16, 2008
Authors: Jason Sharpe, Charles John Lumsden, Nicholas Woolridge
eBook ISBN:9780080879253
9 7 8 - 0 - 0 8 - 0 8 7 9 2 5 - 3
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… Read more
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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.
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
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
No. of pages: 656
Language: English
Edition: 1
Published: June 16, 2008
Imprint: Morgan Kaufmann
eBook ISBN: 9780080879253
JS
Jason Sharpe
Affiliations and expertise
AXS Biomedical Animation Studio and Institute of Medical Science, University of Toronto, Canada
CL
Charles John Lumsden
Affiliations and expertise
Department of Medicine, University of Toronto, Canada
NW
Nicholas Woolridge
Affiliations and expertise
Institute of Medical Science, University of Toronto, Canada