Advanced Visualisation

1
Advanced Visualisation Implementation
Techniques with Java 1.6, OpenGL GLSL for
Biological Data Visualisation Analysis

• Thanasis Theocharidis
• BSc in Mathematics
• MSc in Interactive Multimedia
• MSc in Artificial Intelligence
• 28th April 2009

(Web site www.biolayout.org)
2

• Background in Mathematics Software
  Engineering, previous roles included producing
  high-end AI graphics engines in Java 1.6 C
• Games company co-founder (www.dotredgames.com)
• Joined Toms group in January 2008 back in DPM
• Role consisted of taking over the RD of
  BioLayout Express 3D
• Framework originally started by Anton
  Enrights group, Tom and others in Sanger/Human
  Genome Campus
• Work of more than 5 years (non-continuous),
  originally a 2D-only application
• Innovative way of visualisation data
  analysis of biological data in both 2D/3D,
  proof-of-concept fully working
• BioLayout framework at that time (version RC1)
  
• Used obsolete slow Java 1.4 JVM syntax
• Old-fashioned slow Data Structures
• No use of Generics/Templates, hard-to-read
  code
• Slow execution because of all the above
• Many-many bugs throughout the framework
• Source at 600kb

3

• Ongoing Development Stages / Roadmap from
  January 2008 until now
• Migration from old-fashioned syntax of Java
  1.4 to current Java 1.6 standards
• Full use of Generics and advanced Data
  Structures, easier-to-read code, big speed
  upgrade
• Framework Object Oriented (OO) updates, many
  general libraries added
• Graphml generics XML parser for pathway
  modeling with yEd
• Implementation of very fast OpenGL 2D
  renderer, substituting the old Java2D slow
  renderer
• Full update of both 2D 3D renderers using
  hierarchical modeling in display lists (30k
  graphs)
• Fixed many problems throughout the framework
  along with countless feature GUI additions
  optimisations, source now at 1.7Mb from original
  600Kb
• Design implementation of the BioLayout web
  site (www.biolayout.org) and officially releasing
  version 3.0 last year with frequent updates.
  Online datasets also available through the
  WebStart technology

4

• OpenGL What the heck is it all about ?!?
• Industry-leading Application Programming
  Interface (API) in C, pioneered by Silicon
  Graphics, Silicon Valley, in beginning of 1990s
• Hollywood movies graphical effects use it
  (Pixar, Dreamworks, etc)
• Huge usage push from the games industry (ID
  Software/Quake 1-2-3/HalfLife, etc)
• All major CAD applications for rendering
  (AutoDesks 3D Studio Max, AutoCAD, etc)
• Industry standard nowadays, centrally
  controlled by the Khronos Group
• THE standard for OS-independent, graphics
  hardware acceleration
• (Windows, Linux, MacOS, Sony Playstation 3,
  PlayStation Portable, iPhone)

5

• OpenGL Whats under the hood
• Usage of mathematical Euclidean 3D Vector
  Spaces, Matrix Theory Linear Algebra for 3D
  graphics (see whiteboard for details, no scary
  mathematical formulas shown here!)
• Usage of homogeneous 4D coordinates for 3D
  spaces in 4x4 matrices
• VERY processor-intensive calculations
• Hardware implemented on ASIC (specific tasks)
  chips for 10x-100x speed increase!
• Nowadays graphic chips evolved to generic
  parallelised CPUs, called GPUs, very complex even
  compared to recent QuadCore Intel/AMD chips
• High-end NVidia graphics cards on teams Dell
  Vostros, Geforce Generation 8, have 512Mb Video
  RAM (VRAM) onboard 112 parallel microcores. New
  NVidia Geforce Generation X has 2Gb VRAM 480
  microcores! These cards are termed the current
  499 super computers

6

• OpenGL A C-based API from the 90s
• C-based, no Object Oriented-ness (OO),
  old-fashioned C-style coding
• Sun finally introduced it to the Java platform
  at the end of 2005 through their Game Team Group
  Java OpenGL (JOGL)
• Merges high-end OO Java code with fast
  industry-standard hardware acceleration in C
• BioLayout Express 3D uses this API for very
  impressive results
• The OpenGL 2D renderer achieved a 10x-20x
  speed increase when replacing Java2D
• Both OpenGL 2D/3D renderers highly interactive
  giving very impressive visual results
• Can load HUGE maps compared to Java graphics
  (currently at 30k range)

7

• OpenGL Implementation tricks
• 3 main transformations translate, rotate,
  scale. See board for simple 2D examples
• Matrix Theory fully used underneath (singular,
  inversed transposed matrices)
• Caveat Order DOES matter, matrices
  non-commutative!
• M RTM NOT EQUALS TO M TRM
• glTranslate() then glRotate() different with
• glRotate() then glTranslate()
• Full usage of double Display Lists using
  Hierarchical Modeling as an extra optimisation
  technique
• BioLayout Express 3D uses all the above for
  user-navigation
• with the mouse for both 2D/3D renderers

8

• BioLayout Express 3D Presenting navigating
  the application
• (please follow interactive demo)

9

• BioLayout Express 3D Presenting navigating
  through the web site
• (www.biolayout.org)

10

• Current future plans (Roadmap)
• OpenGL fast 2D renderer for the plot in the
  Class Viewer, sample-to-sample graphs (scheduled
  for Update 7)
• Parallelism (grid computing) experiments
  through custom code (multi-core renderers in
  Update 6) GL Shader Language (GLSL) utilising
  the extreme microparallelism on current graphics
  cards (watch on-screen demo for a
  proof-of-concept). Upcoming updates will be fully
  using the standard
• Parallelism becomes THE norm in summer 2009
  the Khronos Group new standard, OpenCL, for
  future generic parallel programming executed on
  CPU/GPU hardware
• January 2010 Suns (now Oracles) Java 1.7
  hits the road. Parallelism again a major
  milestone for the Java world through
  hardware-independent implementations

11

• Innovative Navigation
• Who said Data Analysis with BioLayout Express 3D
  is not fun ?
• Usage of cheap of-the-shelf commercial
  navigation tools Nintendo Wii remote controller
  with BioLayout Express 3D!
• (please follow interactive demo)

12

• Many Thanks
• The rest of the BioLayout Express 3D team
• Dr. Tom Freeman
• Dr. Anton Enright
• Dr. Stjin Van Dongen
• PhD students for their beta testing time user
  insights
• Sobia Raza
• Neil McDerment
• GLSL implementation insights
• Michael Kargas
• Thanks for your time patience!