| NeoBio - Bioinformatics Algorithms in Java
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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
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| JAligner
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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
Updated Jul 01, 2004
by Ahmed Moustafa
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Total Visits: 91
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| Java Epidemiology
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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
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Total Visits: 72
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| Interactive Editor for Multiple Sequence Alignments STRAP
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STRAP is an editor for multiple sequence alignments of proteins, it supports the analysis of hundreds of proteins and integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence and residue annotation.
Submitted Feb 22, 2005
by Ahmed Moustafa
Updated Feb 23, 2005
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Total Visits: 58
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| XYZApp.java
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The applet that displays various molecules in 3-D.
Submitted Sep 04, 2000
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Total Visits: 56
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| Bouncing Baby Biomorphs
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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
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Total Visits: 52
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| Jmol
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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
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Total Visits: 46
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| Artemis
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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
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Total Visits: 43
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| Pirika
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A Java chemistry site.
Submitted Oct 20, 2000
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Total Visits: 36
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| JaMBW
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The Java based Molecular Biologist's Workbench.
Submitted Sep 05, 2000
Updated Jan 06, 2001
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Total Visits: 34
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| Simulated Evolution
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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
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| Structure Drawing Applet 1.30
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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
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Total Visits: 34
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| ImageJ
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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
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Total Visits: 27
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| The Weasel Applet
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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
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Total Visits: 26
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| DisMol
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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
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Total Visits: 24
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| GeneFisher
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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
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Total Visits: 23
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| Java Demography
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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
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Total Visits: 21
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| The IrYdium Project -- Applets
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Some nice educational java applets for students.
Submitted Sep 04, 2000
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Total Visits: 21
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| WebMol
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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
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Total Visits: 20
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| J-Express
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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
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| TheRate
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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
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Total Visits: 15
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| ACD / Structure Drawing Applet
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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
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Total Visits: 13
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| loopDloop
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A tool for drawing RNA secondary structures in molecular biology.
Submitted Oct 19, 2000
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Total Visits: 11
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| Formula To Mass To Formula
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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
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Total Visits: 10
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| TOPS
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Software for generation, editing and viewing protein topology cartoons.
Submitted Sep 15, 2000
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Total Visits: 10
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| CHIME
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Multiple atom-picking using JavaScript.
Submitted Sep 04, 2000
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Total Visits: 9
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| Marvin
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Marvin Applets are made for the Web Developer who builds chemistry-related World Wide Web sites. Marvin Beans are made for the Software Developer who wants to incorporate molecule drawing or visualizing capabilities into his/her application. MarvinSketch is an application for the Chemist or anyone else who wants to draw chemical structures.
Submitted Sep 05, 2000
Updated Dec 22, 2000
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Total Visits: 9
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| ACT
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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
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Total Visits: 8
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| Vanilla
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Vanilla is a collection of command line programs written in Java to access features of PAL, a Java library for molecular evolution and phylogenetics. Vanilla includes programs to compute maximum-likelihood distances for nucleotides and amino acid data, to estimate of maximum-likelihood branch lengths on trees (incl. clock trees and dated tips), for statistical comparison of trees (e.g., Shimodaira-Hasegawa), to infer demographic parameters from trees (based on the coalescent), and also utility programs to reformat and modify alignments.
Submitted Jan 06, 2001
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| JavaScript-controlled CHIME demo
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Molecular Animation on the Web using Chime™ and JavaScript
Submitted Sep 04, 2000
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| SeqPup
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SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs.
Submitted Sep 11, 2000
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Total Visits: 5
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| Chemical Markup Lanauge
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Examples of Chemical Markup Language by Peter Murray-Rust.
Submitted Sep 04, 2000
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Total Visits: 4
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| Multi-Cut
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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
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| SeqPup
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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
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Total Visits: 4
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| ACD/I-Lab
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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
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Total Visits: 3
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| GeneKonv
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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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Total Visits: 2
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