Biological

A powerful and user-friendly graphical software designed to conduct large scale exploration of biological sequence databanks and related information (functional, taxonomy, pathways, mutations, etc). KoriBlast can be used for a wide range of applications in genomics and proteomics, such as: full... Platforms: Mac

Clotho is a comprehensive and reliable software for developing and managing synthetic biological systems. It also provides a mechanism to begin the process of creating standardized data, algorithms, and methodologies for synthetic biology. This tool allows for the development of independent... Platforms: Windows

BioJava is a tool that includes objects for manipulating biological sequences and file parsers. It also features a DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic... Platforms: Windows

TinkerCell is a Computer-Aided Design (CAD) tool for synthetic biology. Since synthetic biology is a rapidly evolving field, here are the issues which were taken into consideration when designing TinkerCell: -modeling techniques in biology are still at a developmental stage -experimental... Platforms: Windows

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded... Platforms: Mac, Linux

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

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

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

IISA - Intelligent Interface to Sequence Analysis is an expert system for biological sequence analysis using Bioperl and Prolog. 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

KYM is a GNU Octave set of functions that implements a wavelet based automated procedure of quantification and characterization of biological signals, in particular thought for the oscillatory component of calcium cytosolic concentration time course. Platforms: Windows, Mac, Linux

Easy install web server for Genetic and Molecular Biological Laboratory so that PI can update lab homepage himself. Also serve as Lab database server that store DNAStrider plasmid , order tracking and mouse colony database. Platforms: Windows, Mac, Linux

The project is for developing libraries for visualizing biological sequence data on the web. The libraries are written in C and currently use a language (lex/yacc) based front end for presenting features on genomes, contigs, or any type of sequence. Platforms: Mac, BSD, Linux

Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments. Platforms: Windows, Mac, Linux