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Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.
Anthill is a framework to support the design, implementation and evaluation of P2P applications based on ideas such as multi-agent and evolutionary programming borrowed from the complex adaptive systems area.
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 and Smith-Waterman.
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HmmSDK is a hidden Markov model (HMM) software development kit written in Java. It consists of core library of HMM functions (Forward-backward, Viterbi, and Baum-Welch algorithms) and toolkits for application development.
Alife research platform to study the evolvability of different assembly-like computer languages. It's similar to Tierra and Avida but it's designed to be more general.
Talisman is an interpreter for a logical markup language. This language contains the content and logic of a web (or, in the future, Java Swing) based user interface, including arbitrary datatypes and processing actions.
The JPAT API is a Java API designed to provide developers with tools for calculating the results of protease digestion of proteins and ms/ms fragmentation of peptides. JPAT also contains GUI components for displaying the results. JPAT is a nice way to get
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OmniGene is a set of reausable components that have been packaged into frameworks. These frameworks are used to produce domain specific services for common bioinformatics tasks including: visualization, database access, and pipeline building.
Jeep is a modular, abstract and distributed evolutionnary programming core written in Java, allowing to grow autonomous agents as well a gene pool (as in genetic algorithms).
Jaybird is java-language based, source & xml & codebyte class inter-converting tool.
You can write your Envolvable Code with it;
You can make your computer write program itself;
You can run program without compiling time;
You can manage source as data
Cytoscape is a software platform for computational biology and
bioinformatics, useful for integrating data, and for visualizing and
performing calculations on molecular interaction networks
jrgp is a strong-typed Genetic Programming system, which features a graphical interface (gool) to setup and run GP-problems and a tool (fs-d) that greatly simplifies the definition of a GP-problem.
Surviving bots is continuous software application in Java that will guide robots to search for energy source around it, tap it and explore ahead for survival and thus evolve into much more advance system.Software is ment to be hardware independent.
Info Sapient will be an Open Source, Common License 0.5, 100% Pure Java based program that is a mechanism for the expression and execution of business rules.
The ultimate goal of this project is to create a Java based DNA viewer that is both flexible and extendable. The initial phase will involve the design and implementation of a framework that can be used either with this project or other similar projects.
A modular, database-backed system for 5 dimensional (5D) analytical biological microscopy and cell-based screening. Please note - we have moved. Please come visit us and download from our new site at http://cvs.openmicroscopy.org.uk
SPedit is a new curation environment for the Swiss-Prot and TrEMBL databases. For more information about these databases see http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/
Cooperative effort to develop a Java-XML API and architecture to manage and share health concepts and processes eficiently. Includes a framework to develop healthcare applications (from PDA reminders to hospital information systems) quickly and easily.
This project provides software resources for creating solid models of proteins that can be printed on color 3D printers. The main focus is a java program that reads in a PDB file and produces a PLY format stick representation of the protein.
A straight-forward Java implementation of a mixture model with pluggable mixture functions, e.g. a mixture of Gaussian functions. The number and dimensionality of the mixture functions is not limited. All critical calculations are performed in log-space.