Biological Evolution

BioDOM is a JAVA library for easy creation of XML files according to simple XML schemas for describing biological data. It can also be used to convert other commonly used biological (possibly non-)XML data into these new formats. Platforms: Windows, Mac, Linux

A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case. Platforms: Windows, Mac, Linux

BiOrbit is a small Biological information project -- scripts and other useful stuff for the IT & Biology world. Platforms: Windows, Mac, Linux

A Collection of classes related to biological and bioinformatical topics. Platforms: Windows, Mac, Linux

Cellontro models and simulates cells, other biological entities, and biochemical networks. Specify your models using XML and Java, or SBML. Cellontro is now completely contained within the Xholon sourceforge project. Platforms: Windows, Mac, Linux

Dogwood is an ontology-aware Distributed Annotation System (DAS) server framework for the integration of biological, biomedical and clinical data. Platforms: Windows, Mac, Linux

dub manages databasemodifications (schema-evolution) during the development process/maintenance. It centralizes the changes, in order to execute them to the target database, and will keep an overview of all exising changes (new, current and past). Platforms: Windows, Mac, Linux

The Edinburgh Pathway Editor (EPE) is a tool and framework that allows the drawing and manipulation of Biological Networks, such as signalling or matabolic pathways. The editor supports several notations including SBGN and Cytoscape notations. Platforms: Windows, Mac

The Evolutionary Environment (EvENet) provides a P2P Network for guiding the evolution of Software Services and Service Compositions over time. This evolution is based on knowledge sharing and optimised using GA and Agent Systems. It is part of the DBE. Platforms: Windows, Mac, Linux

The evTools package provides tools to manipulate and display output from the binary stellar-evolution code ev (also known as STARS and TWIN). Platforms: Mac, BSD, Linux

The FAKE GAME tool uses natural evolution to evolve Data Mining models. It incorporates several preprocessing, optimization and visualization methods aimed to streamline the Knowledge Discovery process. Knowledge Extraction from data is being automated! Platforms: Windows, Mac, Linux

GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more. Platforms: Windows, Mac, Linux

GenomePixelizer is a program for comparative genomics, detection of duplication events in genomes, tracking the 'footprints' of evolution. It may be considered as a drawing tool that generates custom images of genomes out of the given set of genes. Platforms: Windows, Mac, BSD, Linux

GenX is a scientific program to refine x-ray refelcetivity, neutron reflectivity and surface x-ray diffraction data using the differential evolution algorithm. GenX is very modular and highly extensible and can be used as a general fitting program. Platforms: Windows, Mac, Linux

Gnubert will be a system to use the power of many computers across the internet to solve problems using evolutionary techniques. Any user may define a problem and the system will attempt to solve it. Platforms: Windows, Mac, Linux

Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Platforms: Windows, Mac, Linux

IISA - Intelligent Interface to Sequence Analysis is an expert system for biological sequence analysis using Bioperl and Prolog. Platforms: Windows, Mac, Linux

The interverse is the evolution and combination of the web, chat, IM, and voice communication. It is not just a graphical user interface (GUI), but an immersive user interface (IUI). This project will develop the clients and content used in the interverse Platforms: Windows, Mac, Linux

JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model. Platforms: Windows, Mac, Linux

JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of... Platforms: Mac