Transcript Interactive Software for Biochemistry Using Java, Chime, and Virtual

JavaLab.chem.virginia.edu
Charles M. Grisham
University of Virginia
Interactive Biochemistry
Guidelines for Good Software
• Software should do what books cannot
• Should focus on teaching/learning problem areas
• Should be easy to use – essentially transparent to
the user
• Should be “available anytime/anywhere”
Interactive Biochemistry
What software should be….
“We look at it and do not see it.”
Lao-tzu, 6th century B.C.
Interactive Biochemistry
Another version….
“It takes a lot of money to make me
look this cheap.”
Dolly Parton, 20th century A.D.
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Our Projects
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Java-XML learning tools
3D Virtual Laboratory
Wireless networks
Hand-held devices – PDAs and cell phones
small Java Virtual Machines (VMs) are here
Interactive Biochemistry
Java – Portable Code
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Java is cross-platform and object-oriented
Applications or Applets (latter in browser)
Compiler produces “bytecode”
A platform-dependent interpreter interprets
the platform-independent bytecode
• Java can bring dynamic behavior and
interactivity to the Web environment
Interactive Biochemistry
Java in Interactive Biochemistry
• Applets can be designed for specific tasks
• Applets are small and load quickly
• Examples
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Amino acids
Enzyme kinetics and mechanisms
Sugar, nucleotide structures
Helical wheel
Coenzymes
Metabolic Map Database
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Enzyme Mechanism Tutorials
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Effective teaching/learning devices
27 tutorials in Interactive Biochemistry
But each one is a separate Java applet
Hundreds remain to be done
Programming costs would be prohibitive
This is a job for XML
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XML – Portable Data
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XML = Extensible Markup Language
XML is HTML on steroids
XML can describe any collection of data
“Tags” identify different kinds of data
<Animal>Dinosaur</Animal>
<Name>Barney</Name>
<Color>Purple</Color>
Interactive Biochemistry
Better Organized XML
<Animal>
<Name>Barney</Name>
<Color>Purple</Color></Animal>
• Tagging organizes data
• Tagged data can be parsed (read) and
utilized by a program
Interactive Biochemistry
An XML-Based Mechanism Tool
• Two parts:
– A Mechanism Design Tool (written in Java)
– A Mechanism Player (written in Java)
• The design tool is menu-driven and can be
used (without knowledge of Java or XML)
to create mechanism tutorials
• The mechanism player reads the XML file
and runs the tutorial for the student
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XML is the Data Interface
Design Tool
XML file
Mechanism
Player
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Tutorial
Exercise
A Mechanism Step from the XML File
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More Information
• Check this site for a project description:
• http://javalab.chem.virginia.edu/Java-XML/
Interactive Biochemistry
The 3D Virtual Laboratory
• Uses Java 3D to create real 3D environment
• Provides controls (not shown) to manipulate
all objects in the environment
• Permits the user to do anything they choose
in the laboratory
• Keeps track of all materials, solutions made,
instruments used, and data collected
• Allows the user to design and execute any
experiment
Interactive Biochemistry
Interactive Biochemistry
Amino Acid Titrations
• 3D scene created with Java3D
• Apparatus created in 3DS Max and added to
scene with a VRML loader
• Swing interface
• Chemistry handled by Thiago Ize’s classes
• All the parts work and integration is nearly
complete
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lab3D titration
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Thiago’s simulation:
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pH
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Volume
real titration
Real data from
Georgetown University:
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pH
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Volume
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The Isotrak II 6-DOF Digitizing and Tracking Device
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6-DOF Tracking
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The Isotrak works in Hyperterminal
Java classes for data collection are available
(See http://www.cyber.koganei.tokyo.jp/vr/)
Need only to debug and implement the
Isotrak device in our 3D scenes
• Isotrak sensor could be used on any
laboratory apparatus
Interactive Biochemistry
More Information
• Check this site for a project description:
• http://javalab.chem.virginia.edu/
Interactive Biochemistry
Java on PDAs and Cell Phones
• Uses the Java Wireless Toolkit, based on the
Mobile Information Device Protocol
• aka MIDP
• http://java.sun.com/products/j2mewtoolkit/i
ndex.html
• You create Midlets and use a Converter
utility to convert midlets to .prc files
Interactive Biochemistry
Java Midlets are converted to .prc files and downloaded to a PDA:
Interactive Biochemistry
There is an event model to handle user input, as well as internet
and database classes for PDAs and cell phones.
Interactive Biochemistry
Nonlinear Least Squares Data Fitting
• Marquardt matrix algorithm combining a
grid search with a gradient search
• Can be rapidly adapted to any equation with
any number of parameters
• Runs fast
• Uses Java 2D for plotting
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Data with initial
estimates for Km and
Vmax
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1 pass through
fitting routine
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5 passes through
fitting routine
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“No more good must be attempted
than the people can bear.”
Thomas Jefferson
Interactive Biochemistry