Biological Rhythms

VitaPad is a small, easy to use, Java based application, specially designed to offer you a program to help you visualize and analyze pathways. You can use this software not only to visualize biological pathways but also to map experimental data to them. for WindowsAll Platforms: Windows

IsTa is a small, simple application that will help you find closed frequent item sets by intersecting transactions, which is based on the insight that an item set is closed if it is the intersection of all transactions that contain it. Such an approach can be highly competitive in special... Platforms: Windows

Carpenter is a handy, easy to use application specially designed to help you find closed frequent item sets with the carpenter algorithm, which enumerates transaction sets, in contrast to many other frequent item set mining algorithms, which enumerate item sets. Such an approach can be highly... Platforms: Windows

CWC Simulator is a C++ implementation of CWC (Calculus of Wrapped Compartments). This package is basically a rewriting-based calculus for the representation and simulation of biological systems. Platforms: Windows

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

With CatchDad you can catch 4 different sounds with just the click of a button and instantly start to program rhythms with the built in step sequensers. The plugin is capable of building advanced rhythmic patterns with the different sequencer speed settings. The plugin is quite straightforward,... 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

Get complete picture of your biorhythms by seeing a total of 15 built-in rhythms: Primary, I-Ching, Secondary, and Intuitive Patterns, as well as user-defined rhythms, by visualizing them like never before with 9 fully customizable and interactive views, including: Graph, Table, Calendar,... Platforms: Windows, Edition 2005,Edition 2005

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