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Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.
MyGenBank is a set of OpenSource software for managing a local copy of GenBank (www.ncbi.nih.gov/Genbank). It is implemented using Perl, MySQL, and Linux so that you can manage a complete or partial copy of GenBank on a computer as small as a laptop.
It moves by itself inside networks like virus infection & plagues, it is being written to solve computer virus problem drastically and responsibly. It is legal, free and open for public domain to improve W3 ICT Security.
Sight provides a friendly interface to create and connect agents for bioinformatics. The workflow supports multiple responses to a single request, structure transforms, filters and request history access.Can talk with ordinary http servers (get and post)
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Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.
Mister Model is a code generation system. It takes a UML model expressed as XMI
and generates sourcecode specifically designed to work in a cross-platform web service environment. It fixes the legendary 'Serialization Failed' messages in web services
FM100 is a computer simulation of the Farnsworth-Munsel 100 hue colour (color) vision test. The results of the test can be used to assess the user's colour vision.
Pymerase is a tool intended to generate a python object model, relational database, and an object-relational model connecting the two. However it has been extended to also output webpages and can be easily extended to output whatever else you might like.
openevo is a project started to find out about behaviour of evolutionary generated machine code. It implements a certain set of CPU instruction codes and a few interrupts for interaction with the runtime environment.
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Sequence studio main package provides classes and interfaces for various kinds of sequence alignment. Differently from regular expressions it computes similarity with two initially unknown strings. Project page provides code generating applet.
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.
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.
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
The Molecular Modeling Templates, MMT is a C++ class library for molecular simulation applications. MMT serves as a code basis that can be easily extended and modified to perform Monte Carlo and molecular dynamics simulations.
Virtual machine/emulator; "holding pen" for self-replicating programs written in custom RISC assembly-like language, evolving via random point mutations and periodic fitness-based cullings. Inspired (like Avida) by Thomas Ray's alife simulator, Tierra
Distributed Genetic Programming SRVM
(Simple Risc Virtual Machine)
Distributed function approximator of nonlinear functions with automatic induction of machine code.
Python program devoted to study the relationship between cells during inmune response. It is based on a 3D periodic boundary conditions grid where cells see each other and react according to certain movement, growth and interaction rules.
A software framework to support distributed evolutionary software development. It dynamically creates a network of nodes that can run a pre-distributed sourcecode (e.g. artificial lifeforms). The results of the calculation will be sent back to the maste
Code repository for the Laboratory for Genome Bioinformatics at Texas A&M. The LGB project was initiated primarily to support biologists at Texas A&M needing help with bioinformatics in order to use new genomic technologies.
** IMPORTANT NOTICE ** 10 Feb 2006 Code is being moved to the SMI subversion repository (http://smi-protege.stanford.edu/svn/owl/trunk/) Project will continue to be open source. ProtegeOWL info at: http://protege.stanford.edu/overview/protege-owl.html