Interactive Biochemistry

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

MechanismPlayer

TutorialExercise

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

lab3D titration

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pH

real titration

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Thiago’s simulation:

Real data fromGeorgetown 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/index.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 internetand 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