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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:
• Background in Mathematics & Software Engineering, previous roles included
producing high-end AI & graphics engines in Java 1.6 & C
Games company co-founder (
• Joined Tom’s group in January 2008 back in DPM
• Role consisted of taking over the R&D of BioLayout Express 3D
• Framework originally started by Anton Enright’s 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
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 ( and officially releasing version 3.0 last year
with frequent updates. Online datasets also available through the WebStart technology
• Now at Update 6 celebrating 1 year after first release!
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 1990’s
• 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 (AutoDesk’s 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)
OpenGL: What’s 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 team’s 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’
OpenGL: A C-based API from the 90’s
• 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)
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
• glTranslate() then glRotate() different with:
• glRotate() then glTranslate()
• Full usage of double Display Lists using Hierarchical Modeling as an extra optimisation
BioLayout Express 3D uses all the above for user-navigation
with the mouse for both 2D/3D renderers
BioLayout Express 3D: Presenting & navigating the application
(please follow interactive demo)
BioLayout Express 3D: Presenting & navigating through the web site
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: Sun’s (now Oracle’s) Java 1.7 hits the road. Parallelism again a major
milestone for the Java world through hardware-independent implementations
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)
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!