Interactive Software for Biochemistry Using Java_ Chime_ and

Document Sample
Interactive Software for Biochemistry Using Java_ Chime_ and Powered By Docstoc
					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.




            Interactive Biochemistry
               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



                  Interactive Biochemistry
        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
                 Interactive Biochemistry
 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
                   Interactive Biochemistry
    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

                   Interactive Biochemistry
          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
•   <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
                  Interactive Biochemistry
       XML is the Data Interface

Design Tool         XML file




                  Mechanism               Tutorial
                   Player                 Exercise


               Interactive Biochemistry
A Mechanism Step from the XML File




            Interactive Biochemistry
          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
                 Interactive Biochemistry
 Thiago’s simulation:




Real data from
Georgetown University:




                         Interactive Biochemistry
The Isotrak II 6-DOF Digitizing and Tracking Device




                     Interactive Biochemistry
            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
                  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


                 Interactive Biochemistry
   Data with initial
   estimates for Km and
   Vmax




Interactive Biochemistry
       1 pass through
       fitting routine




Interactive Biochemistry
       5 passes through
       fitting routine




Interactive Biochemistry
“No more good must be attempted
   than the people can bear.”


       Thomas Jefferson



         Interactive Biochemistry
x.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


                 Interactive Biochemistry
  Data with initial
  estimates for Km and
  Vmax




Interactive Biochemistry
       1 pass through
       fitting routine




Interactive Biochemistry
       5 passes through
       fitting routine




Interactive Biochemistry
“No more good must be attempted
   than the people can bear.”


       Thomas Jefferson



         Interactive Biochemistry

				
DOCUMENT INFO
Shared By:
Categories:
Tags:
Stats:
views:17
posted:5/9/2011
language:English
pages:29