Freeware Listing: Biological

BiNA - Biological Network Analyzer is an easy-to-use workbench specially designed to help you visualize biological networks (regulatory, interaction, and metabolic).

This tool can easilly be used as a front-end for BN++ databases, but also as stand-alone tool.

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  • Platform: WinOther

JBioWH provides a framework for biological data integration and management which contains a relational schema for biological data integration, a java Application Programming Interface (API) and a powerful Desktop tool. This framework is designed to provide

1. Data warehouse capabilities to integrate and normalize non heterogeneous biological data
2. An extensive desktop tool for a scientist with no programming experience including an advanced SQL editor for scientist with this programming skill, and,
3. A java API to handle the integrated biological data for further development of Bioinformatics tools.

  • Publisher: jBiowh
  • Date:
  • Size: 12800 KB
  • Platform: Windows 7, Windows 8, WinOther, WinVista

A tool for modelling biological systems through boolean networks. Can represent and execute biological models..

  • Platform: WinOther

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 techniques are constantly evolving, especially automation and directed evolution methods -databases of biological components are still maturing In summary, TinkerCell is designed with the anticipation that the future of synthetic biology will be an intricate interplay between a variety of experimental techniques, databases that store results from experiments, and mathematical models explaining different aspects of the experiments.

  • Platform: WinOther

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. We work along with the Open Bioinformatics Foundation, who generously host our website, bug tracker, and mailing lists. This wiki will help you download and install Biopython, and start using the libraries and tools.

  • Platform: WinOther

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. We work along with the Open Bioinformatics Foundation, who generously host our website, bug tracker, and mailing lists. This wiki will help you download and install Biopython, and start using the libraries and tools.

  • Platform: WinOther

Biological Annotation Tool is a general-purpose high speed environment for manipulating biological sequence annotations in multiple input and output formats. A plugin-style API permits much extensibility..

  • Platform: Linux, Mac OS X, Unix

Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool..

  • Platform: Linux, Mac OS X, WinOther

BioPAX - A Data Exchange Format for Biological Pathway Information.

  • Platform: Linux, Mac OS X, WinOther

Simulation describing the electrophysiological behavior of a biological neuron (nerve cell). Two sets of membrane kinetics are included: Hodgkin-Huxley and Schwarz for unmyelinated and myelinated axons..

  • Platform: Matlab, Scripts

Large set of functions for biological records (ECG, EEG, phono), datastore, datamining and analysis (HRV, QT, RR, ST). The application is written in Java, so that it is assumed to work on all devices. It runs as a desktop or client-server application. It
BiSiDat - biological signals database License - Apache License V2.0.

  • Platform: Linux, Mac OS X, WinOther

BioCM is Biological Content Manager: a Zope/Plone/Biopython product to manage, share and publish biological annotations on the web.
Biological Content Management License - GNU General Public License (GPL).

  • Platform: WinOther

A collection of corpus and access routines for developing biological literature analysis systems.
Biological Corpus Collection License - GNU General Public License version 2.0 (GPLv2).

  • Platform: WinOther

A biological data warehouse that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies.Website:http://bioinformatics.ubc.ca/atlas
Atlas Biological Database License - GNU General Public License (GPL).

  • Platform: WinOther

BIRBU (BIological Relationship BUilder) is a Java tool for microarray gene expression data analysis. BIRBU identifies biologically significant relationship between genes using microarray data and prior knowledge on relationships between genes.
Biological Relationship Builder License - GNU General Public License (GPL).

  • Platform: WinOther

An ontology-centered framework within the Semantic Web infrastructure that aims at standardizing various knowledge involved in the biological modeling processes. Three biological cases have been developed to evaluate the implementation of this framework.
Biological Modeling Framework License - Academic Free License (AFL); GNU General Public License (GPL).

  • Platform: Linux, Mac OS X, WinOther

JBioWH Desktop Client provides users with a relational schema for biological data integration and management.

The application integrates the most important and interesting biologic data sources into a database and allows you to view the name, the URL address and status.

JBioWH (Java Biological Warehouse) Desktop Client includes features such as a SQL Editor, data warehouse capabilities and a Java API designed. The application is designed to integrate and handle biological data for further development.

The database you need to connect to includes data source types such as Taxonomy, Ontology, Gene, Enzymes, Metabolites, Reactions, Diseases and much more.

  • Platform: Windows 7, Windows 8, WinOther, WinVista

BioUtils is a handy, easy to use collection of classes specially designed for biological and bioinformatical topics.

With the help of this Java framework, you will be able to manage biological data with ease.

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  • Platform: WinOther

FunMod Network Analysis for Cytoscape is a useful and simple plugin that enables you to easily view biological pathways.

Using the plugin, you have the possibility to display molecular interaction networks, analyze the existing pathways, view gene expression profiles and more.


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  • Platform: WinOther

InBiNA, which is actually short for Integrated biological networks analyzer, was created as an Open Source analysis software for biological networks.

InBiNA is a generic application that's capable of supporting most kinds of biological networks.

InBiNA is capable of importing networks from file in the SIF, SBML level 2 version 1 and MBNF formats.

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  • Platform: WinOther

Biological: Freeware | All

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