Biological Rhythms

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

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.

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

MBAS -- Macro-Biological Analysis System -- provides a set of interoperable tools for aid in the analysis of biological data. The backing database is currently PostgreSQL and the primary language is C, though some data entry tools are written in Java.


Platforms: Windows, Mac, BSD, Linux

NetBuilder' is a tool for building, visualizing, and simulating multi-layered biological networks, structured as hierarchical Petri-nets. It has a built-in stochastic simulator, but also provides easy access to other simulation and analysis.


Platforms: Windows, Mac, Linux

OpenCryobank is an attempt to develop a simple, free and open database system for frozen samples inventory in biological laboratories. It is mainly aimed at semen and embryo cryobanks, but it can be used for any kind of biological sample.


Platforms: Windows, Mac, Linux

A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout.


Platforms: Windows, Mac

A python library for handling and analyzing biological sequence annotations as described in GFF files (General Feature Format). The library is intended to be a complete framework for this file format.


Platforms: Windows, Mac, Linux

Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes.


Platforms: Mac, BSD, Linux

Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.


Platforms: Windows, Mac, BSD, Linux

Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.


Platforms: Windows, Mac, Linux

This tool is a platform-independent software to create individual pathways and to examine biological networks of distributed, heterogeneous data sources, e.g. KEGG, BRENDA.


Platforms: Windows, Mac, Linux

BlastViewer provides an interactive graphical user interface for the analysis of the reports produced by the BLAST sequence database search system. BlastViewer is an easy to use software designed for everyday biological sequence analysis relying on BLAST. It allows an easy visualisation and...


Platforms: Mac, Java 1.5 or later

Record your voice, your fridge, your neighbour's dog or let your computer speak and make loops and rhythms out of the sounds immediately. RealBeat concentrates on simplicity and fast results. No steep learning curve or cluttered screens! Get creative in an instant! RealBeat is a sampler...


Platforms: Mac

Features a broad array of funky, uncluttered rhythms that work well in rap, hip-hop and cross-genre environments. A solid foundation for building sophisticated hip-hop grooves. Product Details: 39 (39.4mb) grooves for the ultimate Hip Hop experience. For the Techies: Source material was...


Platforms: Mac

HASAS (HydroAcoustic Signal Analysis System) is a modular system for passive sonar signal analysis. It can be used for biological research or surveillance, for example. The soundcard is used as input device, and it currently includes all the very basic fu


Platforms: *nix, C/C++, BSD