JavaLab.chem.virginia.edu

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JavaLab.chem.virginia.edu

• Charles M. Grisham
• University of Virginia

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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

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What software should be.
We look at it and do not see it.
Lao-tzu, 6th century B.C.
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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

• Java-XML learning tools
• 3D Virtual Laboratory
• Wireless networks
• Hand-held devices PDAs and cell phones
• small Java Virtual Machines (VMs) are here

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Java Portable Code

• 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

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Java in Interactive Biochemistry

• Applets can be designed for specific tasks
• Applets are small and load quickly
• Examples
• Amino acids
• Enzyme kinetics and mechanisms
• Sugar, nucleotide structures
• Helical wheel
• Coenzymes
• Metabolic Map Database

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Enzyme Mechanism Tutorials

• 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

• XML Extensible Markup Language
• XML is HTML on steroids
• XML can describe any collection of data
• Tags identify different kinds of data
• Dinosaur
• Barney
• Purple

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Better Organized XML

• Barney
• Purple
• Tagging organizes data
• Tagged data can be parsed (read) and utilized by
  a program

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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
Tutorial Exercise
Mechanism Player
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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/

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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

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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 Izes classes
• All the parts work and integration is nearly
  complete

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Thiagos simulation
Real data from Georgetown University
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The Isotrak II 6-DOF Digitizing and Tracking
Device
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6-DOF Tracking

• 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

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More Information

• Check this site for a project description
• http//javalab.chem.virginia.edu/

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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/index.ht
  ml
• You create Midlets and use a Converter utility to
  convert midlets to .prc files

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Java Midlets are converted to .prc files and
downloaded to a PDA
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There is an event model to handle user input, as
well as internet and database classes for PDAs
and cell phones.
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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