In Silico: 3D Animation and Simulation of Cell Biology with Maya and MEL
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Table of contents
- Contentsv
- Prefacexiii
- Who is this book for?xiv
- Why Maya?xiv
- What the book offersxv
- Computer hardware and softwarexxi
- About the authorsxxii
- Acknowledgmentsxxiii
- Part 1 Setting the Stage1
- Chapter 01 Introduction3
- The challenge4
- Wetware for seeing5
- Visualization in science6
- Organizational hierarchy: Keys to biology in vivo and in silico8
- Enter Maya13
- Endless possibilities19
- References19
- Chapter 02 Computers and the Organism21
- Introduction22
- Information and process22
- Language and program23
- High and low26
- Interpret or compile?27
- The Backus watershed28
- Stored programs30
- Conditional control33
- The computed organism35
- The computational organism36
- OOPs and agents39
- Summary41
- References43
- Chapter 03 Animating biology45
- Introduction46
- Animation and film perception46
- The animator's workflow49
- The three-stage workflow51
- Putting it all together67
- References67
- Part 2 A Foundation in Maya69
- Chapter 04 Maya Basics71
- Getting started72
- How Maya works (briefly)78
- Maya's UI82
- Summary99
- Chapter 05 Modeling Geometry101
- Introduction102
- NURBS modeling103
- Polygonal modeling107
- Tutorial 05.01: NURBS primitive modeling109
- Tutorial 05.02: Deform the sphere using components117
- Tutorial 05.03: Make and deform a polygon primitive119
- Tutorial 05.04: Construction history122
- Tutorial 05.05: Create a NURBS "fiber"129
- Summary134
- References135
- Chapter 06 Animation137
- Introduction138
- Animation138
- Tutorial 06.01: A keyframe animation145
- Animation nodes in the Hypergraph and Attribute Editor151
- Tutorial 06.02: A simple procedural animation151
- Summary154
- Chapter 07 Dynamics157
- Introduction158
- The Dynamics module160
- Tutorial 07.01: Rigid body dynamics166
- Tutorial 07.02: Particles in a container173
- Tutorial 07.03: Create a playblast184
- Summary185
- Chapter 08 Shading187
- Introduction188
- The Render menu set190
- Shading191
- Tutorial 08.01: Shading203
- Summary214
- References214
- Chapter 09 Cameras215
- Maya Cameras217
- Tutorial 09.01: A camera on hemoglobin222
- Summary230
- Chapter 10 Lighting231
- Lighting232
- Tutorial 10.01: Lighting the hemoglobin scene235
- Summary241
- Chapter 11 Action! Maya Rendering243
- Rendering244
- Advanced rendering techniques with the mental ray for Maya renderer249
- Tutorial 11.01: Batch rendering252
- Tutorial 11.02: Playback using fCheck257
- Summary259
- Chapter 12 MEL Scripting261
- Introduction262
- The origins of MEL263
- In a word: Scripting264
- Getting started266
- MEL syntax269
- Values270
- Variables271
- Mathematical and logical expressions277
- The MEL command280
- Attributes in MEL286
- Conditional statements288
- Loops289
- Procedures291
- Animation expressions292
- Putting it all together: The MEL script301
- Tutorial 12.01: Building a MEL script302
- Debugging your scripts306
- Random number generation in Maya308
- Summary309
- Chapter 13 Data Input/Output311
- Introduction312
- Translators313
- Reading and writing files with MEL315
- Tutorial 13.01: Visualizing cell migration322
- Summary337
- Part 3 Biology in Silico„Maya in Action339
- Chapter 14 Building a Protein341
- Introduction342
- Problem overview346
- Methods: Algorithm design354
- Methods: Encoding the algorithm354
- Results: Running the script368
- Results: Rendering your molecule372
- Summary380
- References381
- Chapter 15 Self-assembly383
- Introduction384
- Problem overview385
- Methods: Actin geometry394
- Methods: Diffusion and reaction events399
- Methods: Reaction rates and probabilities403
- Methods: Algorithm design409
- Methods: Encoding the algorithm412
- Results: Running your simulation437
- Summary441
- References442
- Chapter 16 Modeling a Mobile Cell443
- Introduction444
- Problem overview445
- Model definition449
- Methods: Generating pseudopods451
- Methods: Algorithm design453
- Methods: A cell locomotion engine454
- Methods: Encoding the algorithm466
- Methods: Loading the script475
- Results: Running the script476
- Summary477
- References477
- Chapter 17 Growing an ECM Scaffold479
- Introduction480
- Problem overview481
- Model definition483
- Methods: Algorithm design486
- Methods: Encoding the algorithm494
- Methods: Grow your scaffold!512
- Results: Parameter effects516
- Summary517
- References517
- Chapter 18 Scaffold invasions: Modeling 3D Populations of Mobile Cells519
- Introduction520
- Problem overview521
- Model definition525
- Methods: Model design528
- Methods: Encoding the algorithm538
- Methods: Running the simulation565
- Results: Data output572
- Summary573
- References573
- Chapter 19 Conclusion: A New Kind of Seeing575
- Explanations, simulations, speculations576
- Maya's role578
- The path so far578
- The future579
- References582
- Further reading585
- Glossary593
- A594
- B595
- C595
- D597
- E597
- F598
- G598
- H599
- I600
- K600
- L600
- M601
- N601
- P602
- R603
- S604
- T604
- V605
- W605
- Index607
- A607
- B608
- C608
- D610
- E611
- F612
- G612
- H612
- I613
- J613
- K613
- L613
- M614
- N615
- O616
- P616
- Q617
- R618
- S619
- T621
- U621
- V622
- W622
- X622
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
*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