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NeoBio - Bioinformatics Algorithms in Java  
NeoBio is a Java class library of computational biology algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch (global alignment) and Smith & Waterman (local alignment).
Submitted: Nov 10, 2003
JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological pairwise sequence alignment. The package is a clean and efficient implementation of the algorithm with Gotoh's improvement and a support to the affine gap penalties.
Submitted: Apr 08, 2004
Java Epidemiology  
A computer program that simulates the spread of a disease in a population. By manipulating values such as population death rates, birth rates, the length of time infected individuals are infectious, the probability of disease transmission, and initial population characteristics, and then using the simulation to see how population characteristics change through time, users of Epidemiology can investigate important questions in population biology and public health, develop a deeper understanding of fundamental population concepts, and explore issues related to public health policy.
Submitted: Nov 01, 2000
The applet that displays various molecules in 3-D.
Submitted: Sep 04, 2000
Bouncing Baby Biomorphs  
This applet draws biomorphs, plausibly lifelike forms invented by the brilliant evolutionary biologist Richard Dawkins and first presented to the world in his book The Blind Watchmaker. In this exhibit, the biomorph's DNA changes with time, and the result is continually updated in the applet's window.
Submitted: Nov 01, 2000
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
Submitted: Oct 31, 2000
Artemis is a free DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, and is available for UNIX, Macintosh or MS Windows.
Submitted: Sep 23, 2000
A Java chemistry site.
Submitted: Oct 20, 2000
The Java based Molecular Biologist's Workbench.
Submitted: Sep 05, 2000
Simulated Evolution  
This program simulates an evolution in the world of "bugs" (the small, colorful, moving squares) and their food, randomly placed stationary bacteria (the purple dots). The bugs eat their food by moving onto it, and they move strictly according to their limited genome (they have no sense organs to help them detect food). The best genome is one that keeps a bug moving mostly in straight lines, turning only occasionally; this keeps a bug constantly moving to new areas, rather than exhausting the local food supply and then slowly starving.
Submitted: Nov 01, 2000
Structure Drawing Applet 1.30  
ACD Structure Drawing Applet is a platform-independent, chemically intelligent tool for composing chemical structures and substructure queries in a Java-enabled Internet browser. The applet can be used for exporting and importing MOL files and for structure visualizations.
Submitted: Oct 24, 2000
ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as downloadable application, on any computer with a Java 1.1 or later virtual machine.
Submitted: Sep 30, 2000
The Weasel Applet  
This exhibit demonstrates the ability of evolutionary techniques to solve enormous problems rapidly. This ability is startling; at first exposure, it is every bit as counterintuitive as quantum mechanics. The applet works like this. You provide a phrase to one part of the program, the Scorer, and another part of the program (the Breeder) tries to make the Scorer happy by breeding possible solutions until it matches the supplied phrase.
Submitted: Nov 01, 2000
A freeware molecule display applet including source code, you can try rotating the molecule in various directions by dragging your mouse on the black background.
Submitted: Jan 06, 2001
GeneFisher processes aligned or unaligned sequences. GeneFisher comes with a built in alignment tool that feeds the results directly into the next step. You have the option of looking at a graphical representation of the alignments and the consensus sequence that is really useful for a variety of tasks, not just primer design. At this point you can reject the alignment and adjust the parameters to try again or you can continue to the primer design step.
Submitted: Dec 02, 2000
Java Demography  
A computer program that simulates exponential population growth. By manipulating values for mortality rates, fertility rates, and initial population characteristics, and then using the simulation to see how population characteristics change through time, users of Demography can investigate important questions in population biology, develop a deeper understanding of fundamental population concepts, and explore issues related to population policy.
Submitted: Nov 01, 2000
WebMol was designed to display and analyze structural information contained in the Protein Data Bank (PDB). It can be run as an applet or as a stand-alone application.
Submitted: Sep 16, 2000
J-Express is a java application for the analysis of gene expression data provided by microarray experiments. It is programmed for the java runtime environment 1.2, which is available for most operating systems.
Submitted: Dec 08, 2000
TheRate is an acronym for Theoretical Rates. TheRate allows thermal rate constants of unimolecular and bimolecular gas-phase reactions to be calculated directly from an ab initio and/or density functional electronic structure theory. The calculations are based on variational transition state theory augmented by several multidimensional semiclassical tunneling approximations. TheRate was designed to be an advanced research tool, as well as a teaching tool for courses in applied quantum chemistry and kinetics.
Submitted: Jan 06, 2001
ACD / Structure Drawing Applet  
ACD Structure Drawing Applet (ACD/SDA) is a complete structure drawing, editing and visualizACD Structure Drawing Applet is a chemically-intelligent applet. It understands valency and atom charges and sets them automatically as you draw your structure. If you make a mistake, the applet will show you where.ation tool written in Java that can be incorporated into HTML documents.
Submitted: Sep 04, 2000
A tool for drawing RNA secondary structures in molecular biology.
Submitted: Oct 19, 2000
Formula To Mass To Formula  
This applet has been written at Dr. H. Rzepa lab, Chemistry dept, Imperial College of Science, Medicine and Technology, by Guillaume Cottenceau.
Submitted: Sep 04, 2000
Multiple atom-picking using JavaScript.
Submitted: Sep 04, 2000
ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis. In common with Artemis, ACT is written in Java and runs on UNIX, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequence in FASTA or raw format.
Submitted: Sep 23, 2000
JavaScript-controlled CHIME demo  
Molecular Animation on the Web using Chime™ and JavaScript
Submitted: Sep 04, 2000
SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs.
Submitted: Sep 11, 2000
Chemical Markup Lanauge  
Examples of Chemical Markup Language by Peter Murray-Rust.
Submitted: Sep 04, 2000
Multi-cut is a database of restriction endonuclease buffers. It finds compatible buffers for a list of enzymes that you want to use in a multiple restriction endonuclease digest. Multi-Cut searches through activity data from the catalogs of several major restriction endonuclease manufacturers and finds buffers that will work with all of the endonucleases in the reaction.
Submitted: Sep 09, 2000
SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs. It is usable on common computer systems, including Macintosh, MS-Windows and X-Windows.
Submitted: Sep 30, 2000
ACD/I-Lab is an Internet-based service for instant access to chemical databases and property predictions programs. With I-Lab access, you can obtain NMR spectra, get systematic chemical names and predict properties such as pKa or LogP for their chemical structures from both your Internet browser and from inside ChemSketch, a powerful structure drawing tool that can be downloaded from the Web site for free.
Submitted: Sep 04, 2000
GeneKonv converts the input files from several genetic analyse programs into each other. Currently used programms are BIOSYS, GSED and Popgen.
Submitted: Nov 17, 2000

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