by Lambda Systems Ltd.
Contact Info: info@lamsys.com
URL: http://www.lamsys.com/bm.html
Load Time: Fast
Source Code Included: No
Author's Description: An implementation of Richard Dawkin's Biomorphs, mentioned in the book The Blind Watchmaker.
Spend some time with this applet (about fifteen thoughtful clicks will do it) and you'll appreciate its seemingly simplistic premise-the gene in the center parents all the rest, and you can click something in the outside ring to make it the parent of the next generation. The more fantastic looking genes you select, the weirder its children will become.
by Gregg Helt
Contact Info: gregg@fruitfly.berkeley.edu
URL: http://flybane.berkeley.edu/gregg/ProtoBrowser.html
Load Time: Fast
Source Code Included: No
Author's Description: A prototype of the genome map applet we are developing in order to present biologists with a flexible interface to genomic databases. Check back often-we are constantly updating!
This applet is a boon to biologists and other scientists studying DNA-you can move up and down the strand of fruit fly DNA, select a section to view the base pairs, and perform other detailed examinations. Also see JaMBW (this section), which is the entire collection that this applet is but one small part of, and Physical Mapping Calculators (this section).
by Luca Toldo
Contact Info: TOLDO@EMBL-HEIDELBERG.DE
URL: http://www.embl-heidelberg.de/~toldo/JaMBW.html
Load Time: Medium Fast
Source Code Included: No
Author's Description: Molecular biology is now highly dependent on appropriate computer tools in order to design and interpret experiments. Of the many operations that a molecular biologist performs with the help of a computer, many of them do not need highly powerful computers and generally are meant to be a mostly "speed-up" to typical "back-of-the-envelope" operations.
This page houses links to the JaMBW collection of biology-related applets, a total of fourteen as of this writing, produced by an international team of scientists. They all relate to the study of and experimentation with DNA, including the Genome Browser Prototype (this section) but none of the links have the source code available.
by Yuri Pryadkin
Contact Info: yuri@aludra.usc.edu
URL: http://www-hbp.usc.edu/HBP/groups/cortex/form.html
Load Time: Medium Fast
Source Code Included: No
Author's Description: Using this applet you can plot PET (positron emission topography) activity over an array of human brain slices.
This is another applet on the Gamelan directory dealing with similar subject matter-read as: brain slices-as the Whole Brain Atlas Navigator. For comparison, also check out the PickTest2 applet (Programming: User Interfaces)-read as: esophageal slices.
by Andre Grigoriev
Contact Info: andy@rag3.rz-berlin.mpg.de
URL: http://www.mpimg-berlin-dahlem.mpg.de/~andy/calc/mapcalc.html
Load Time: Fast
Source Code Included: No
Author's Description: These are calculators for predicting the experimental progress of various physical mapping projects.
There are two calculator applets accessible from this page for studying DNA results and/or genetics in general: Random Probe and Random Fingerprinting. Another useful collection of similar applets is JaMBW. Also check out the Genome Browser Prototype (both in this section).
by Adam Freeman
Contact Info: raptor@cse.ucsc.edu
URL: http://www.cse.ucsc.edu/~raptor
Load Time: Fast
Source Code Included: No
Author's Description: A realistic radiosity rendered shark swims after a school of .gif fish across the Web page. Looks cool! I used a hack to get rid of the image flickering.
Pause to admire the shark and fish chase, but don't think this is the predator-prey applet-at the bottom of the page, click the applet field in the left corner and begin a customizable simulation involving populations of rabbits and fox. The applet cycles through the number of generations you establish and draws the results on a corresponding graph.
by Simon Dennis
Contact Info: mav@psy.uq.edu.au
URL: http://psy.uq.edu.au/~mav/java/Necker.html
Load Time: Fast
Source Code Included: Yes
Author's Description: A tutorial on the Boltzmann Machine neural network using the Necker cube as an example.
A simple, straightforward Java treatment of this subject. Source code and ample documentation are available. Other resources on the Gamelan directory related to neural networks include Hopfield Neural Network (Education: Computer Science), and The HTML Neural Networks (JavaScript:Other JavaScript Resources).
by Jeff Milton, Brent Thomas, and David Yaron
Contact Info: milton@chem.cmu.edu
URL: http://www.chem.cmu.edu/milton.Spec
Load Time: Very Fast
Source Code Included: Yes
Author's Description: This is a chemical education site that is scheduled to be used in three chemistry classes (so far) at Carnegie Mellon University. Currently, applets include spectroscopic and statistical analysis simulators as well as data fitting resource applets for chemical data analysis (straight line, least squares fits). Source is available upon request (currently being documented).
This applet functions optimally on the page, not in a floating window, though you'll have to scroll around to see all the graphs in action. And it helps to have some knowledge of the subject matter-there's virtually no layperson's explanation of how to use this applet or what it does.
by Horst Vollhardt
Contact Info: horstv@pc.chemie.th-darmstadt.de
URL: http://www.pc.chemie.th-darmstadt.de/java
Load Time: Fast
Source Code Included: No
Author's Description: The applet performs a molecular dynamics simulation in real time with a hydrocarbon molecule. The molecule is rendered with double buffering and depth cueing. A VRML snapshot can be prepared and visualized with any VRML browser.
Watch a molecule in action and rotate, translate, or scale it with mouse and key combinations, or download a VRML snapshot for a true 3-D image.
by Scott Le Grand
Contact Info: legrand@tesla.mbi.ucla.edu
URL: http://www.mbi.ucla.edu/people/legrand/pdb.html
Load Time: Fast
Source Code Included: Yes
Author's Description: PDB3D is a high-speed 3-D molecule rendering applet which has been designed specifically for viewing protein data bank (PDB) format molecular structure files within Web pages. As a benchmark, PDB3D can render an alpha carbon trace of a 3,000 residue protein at approximately 2 fps and that of a 500 residue protein at approximately 10 fps when running as interpreted Java within Netscape 2.01.
Shrink and turn the cytochrome at the top of this page using the right and left mouse buttons respectively. The author refers users to the Web page's source for the source to this applet, and provides detailed installation instructions along with a list of links to view PDB3D in action.
by Christopher Grayce
Contact Info: cgrayce@uci.edu
URL: http://www.chem.uci.edi/instruction/applets/bounce.html
Load Time: Fast
Source Code Included: No
Author's Description: The second law of thermodynamics is demonstrated by a bouncing box-gravitational potential energy turns into heat.
You have to see this cool visual intepretation of chemistry to properly appreciate it-note the rippling action of each line within the box as it relates to color/temperature changes and reaction to gravity.
by The Paradigm Exchange
Contact Info: lsmith@sunset.net
URL: http://www.tripos.com/SandF.html
Load Time: Fast
Source Code Included: No
Author's Description: An application for searches in chemical databases. A sketch applet that lets you sketch the substructure of a molecule and a search for this substructure is performed in one of three chemical databases. The molecules found are also displayed using an applet.
Click and place atoms of several compounds (choose individual substances with the pull-down menu) and click Search to find a match. The applet will search the available databases for compounds that resemble the user's drawing and display them on a subsequent page. The found molecules can be rotated, translated, and scaled, viewed in three different ways, or translated to VRML. If you're looking for freehand drawing applets, see WebDraw Applet (Network and Communications: Chat and Multiuser) and/or NINA (Multimedia: Graphics Resources).
by Michael Woodson
Contact Info: n9942097@fozzie.cc.wwu.edu
URL: http://rowlf.cc.wwu.edu/~n9942097/bt.html
Load Time: Very Fast
Source Code Included: Yes
Author's Description: This applet helps show how a binary tree works.
This page features descriptions of the tools on the toolbar, the applet source code, an information page containing some documentation, and a link to another similar applet.
by Baogang Yao and Shingang Chen
Contact Info: b-yao@cs.uiuc.edu, s-chen5@cs.uiuc.edu
URL: http://www.ncsa.uiuc.edu/People/byao/cd423/mp1/mp1.html
Load Time: Very Fast
Source Code Included: Yes
Author's Description: Comparison of routing techniques.
Despite the author's warning, all three of these applets performed well, both individually and on the group page, on both our Windows 95 and Macintosh testing platforms.
by Brandon Bachman, Scott Foster, John Hoopes, Eric Mercer, and Kathy Vamianakis
Contact Info: bbachman@facility.cs.utah.edu
URL: http://www.cs.utah.edu/~bbachman/gtutor
Load Time: Fast
Source Code Included: No
Author's Description: An interactive tutorial written in Java that teaches the fundamentals of computer graphics. Topics include perspective viewing, scan fill, line drawing, bezier curves, bezier surfaces, and so forth.
Two- and three-dimensional lessons are available on this applet page, as outlined in the main menu frame. Overviews appear in the left frame while the interactive applet demo runs on the right. You will have to scroll up and down to view the images and use the button controls, but wait till the text is complete, otherwise the time lapse just increases.
by Jeff So
Contact Info: soj3990@cs.uleth.ca
URL: http://www.uleth.ca/~soc101
Load Time: Medium Fast
Source Code Included: Yes
Author's Description: An applet that demonstrates the speed and technique between Quick Hull algorithm and Brute Force algorithm in solving the Convex Hull problem.
Click to plot points on the applet field, choose an algorithm, and click Go. Source code is included.
by Iwan van Rienen
Contact Info: ivr@bart.nl
URL: http://www.lookup.com/Homepages/96457/digsim/load.html
Loading Time: Fast
Source Code Included: Yes
Author's Description: A Digital Simulator in Java-learn how digital components work by loading an example schematic or draw your own schematic. Over 30 components available: switches, LEDs, ports, flipflops, and so forth. When running offline you can also save your own schematics. Includes over 400K of documented source code.
Some knowledge of the components is necessary to really play around successfully, but the concept is way cool. Original schematics are savable and loadable when run offline using appletviewer, and they're apparently much faster than the perfectly fast online simulations. Also see Active Schematics (Education: Engineering).
by Carla Laffra
Contact Info: carla@cs.pace.edu
URL: http://www.cs.pace.edu/~carla/graph.html
Load Time: Fast
Source Code Included: Yes
Author's Description: Draw your own graph with edges and set their weights. Or, simply modify an example graph. Then, step through an animation of Dijkstra's algorithm to determine to shortest path between points in a graph. During the animation, the applet explains each step.
If your knowledge of this subject is limited, scroll through the documentation and run the example first. The pull-down menu in the upper-left corner allows you to customize various aspects of the demo, while the buttons on the right side execute the primary functions. The source code link is provided on the first page.
by Christopher Waterson
Contact Info: waterson@eecs.umich.edu
URL: http://ai.eecs.umich.edu/people/waterson/EightPuzzle
Load Time: Fast
Source Code Included: No
Author's Descri
