In Silico (eBook)

Cover 
1 
Contents 
6 
Preface 14
Who is this book for? 15
Why Maya? 15
What the book offers 16
Computer hardware and software 22
About the authors 23
Acknowledgments 24
Part 1 Setting the Stage 28
Chapter 01 Introduction 
30 
The challenge 31
Wetware for seeing 32
Visualization in science 33
Organizational hierarchy: Keys to biology in vivo and in silico 35
Enter Maya 40
Endless possibilities 46
References 46
Chapter 02 Computers and the Organism 48
Introduction 49
Information and process 49
Language and program 50
High and low 53
Interpret or compile? 54
The Backus watershed 55
Stored programs 57
Conditional control 60
The computed organism 62
The computational organism 63
OOPs and agents 66
Summary 68
References 70
Chapter 03 Animating biology 72
Introduction 73
Animation and film perception 73
The animator's workflow 76
The three-stage workflow 78
Putting it all together 94
References 94
Part 2 A Foundation in Maya 96
Chapter 04 Maya Basics 98
Getting started 99
How Maya works (briefly) 105
Maya's UI 109
Summary 126
Chapter 05 Modeling Geometry 128
Introduction 129
NURBS modeling 130
Polygonal modeling 134
Tutorial 05.01: NURBS primitive modeling 136
Tutorial 05.02: Deform the sphere using components 144
Tutorial 05.03: Make and deform a polygon primitive 146
Tutorial 05.04: Construction history 149
Tutorial 05.05: Create a NURBS "fiber" 156
Summary 161
References 162
Chapter 06 Animation 164
Introduction 165
Animation 165
Tutorial 06.01: A keyframe animation 172
Animation nodes in the Hypergraph and Attribute Editor 178
Tutorial 06.02: A simple procedural animation 178
Summary 181
Chapter 07 Dynamics 184
Introduction 185
The Dynamics module 187
Tutorial 07.01: Rigid body dynamics 193
Tutorial 07.02: Particles in a container 200
Tutorial 07.03: Create a playblast 211
Summary 212
Chapter 08 Shading 214
Introduction 215
The Render menu set 217
Shading 218
Tutorial 08.01: Shading 230
Summary 241
References 241
Chapter 09 Cameras 242
Maya Cameras 244
Tutorial 09.01: A camera on hemoglobin 249
Summary 257
Chapter 10 Lighting 258
Lighting 259
Tutorial 10.01: Lighting the hemoglobin scene 262
Summary 268
Chapter 11 Action! Maya Rendering 270
Rendering 271
Advanced rendering techniques with the mental ray for Maya renderer 276
Tutorial 11.01: Batch rendering 279
Tutorial 11.02: Playback using fCheck 284
Summary 286
Chapter 12 MEL Scripting 288
Introduction 289
The origins of MEL 290
In a word: Scripting 291
Getting started 293
MEL syntax 296
Values 297
Variables 298
Mathematical and logical expressions 304
The MEL command 307
Attributes in MEL 313
Conditional statements 315
Loops 316
Procedures 318
Animation expressions 319
Putting it all together: The MEL script 328
Tutorial 12.01: Building a MEL script 329
Debugging your scripts 333
Random number generation in Maya 335
Summary 336
Chapter 13 Data Input/Output 338
Introduction 339
Translators 340
Reading and writing files with MEL 342
Tutorial 13.01: Visualizing cell migration 349
Summary 364
Part 3 Biology in Silico„Maya in Action 366
Chapter 14 Building a Protein 368
Introduction 369
Problem overview 373
Methods: Algorithm design 381
Methods: Encoding the algorithm 381
Results: Running the script 395
Results: Rendering your molecule 399
Summary 407
References 408
Chapter 15 Self-assembly 410
Introduction 411
Problem overview 412
Methods: Actin geometry 421
Methods: Diffusion and reaction events 426
Methods: Reaction rates and probabilities 430
Methods: Algorithm design 436
Methods: Encoding the algorithm 439
Results: Running your simulation 464
Summary 468
References 469
Chapter 16 Modeling a Mobile Cell 470
Introduction 471
Problem overview 472
Model definition 476
Methods: Generating pseudopods 478
Methods: Algorithm design 480
Methods: A cell locomotion engine 481
Methods: Encoding the algorithm 493
Methods: Loading the script 502
Results: Running the script 503
Summary 504
References 504
Chapter 17 Growing an ECM Scaffold 506
Introduction 507
Problem overview 508
Model definition 510
Methods: Algorithm design 513
Methods: Encoding the algorithm 521
Methods: Grow your scaffold! 539
Results: Parameter effects 543
Summary 544
References 544
Chapter 18 Scaffold invasions: Modeling 3D Populations of Mobile Cells 546
Introduction 547
Problem overview 548
Model definition 552
Methods: Model design 555
Methods: Encoding the algorithm 565
Methods: Running the simulation 592
Results: Data output 599
Summary 600
References 600
Chapter 19 Conclusion: A New Kind of Seeing 602
Explanations, simulations, speculations 603
Maya's role 605
The path so far 605
The future 606
References 609
Further reading 612
Glossary 620
A 621
B 622
C 622
D 624
E 624
F 625
G 625
H 626
I 627
K 627
L 627
M 628
N 628
P 629
R 630
S 631
T 631
V 632
W 632
Index 
634 
A 634
B 635
C 635
D 637
E 638
F 639
G 639
H 639
I 640
J 640
K 640
L 640
M 641
N 642
O 643
P 643
Q 644
R 645
S 646
T 648
U 648
V 649
W 649
X 649