Biology

Researchers in quantitative systems biology make use of a large number of different software packages for modeling, analysis, visualization, and general data manipulation. The Systems Biology Workbench (SBW), is a software framework that allows heterogeneous application components-written in...

The Systems Biology Workbench(SBW) is a simple framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32.

The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.


Platforms: Windows, Mac, 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

TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological 'parts'. Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.


Platforms: Windows, Mac, Linux

StrBio is a set of Java classes and libraries useful for development of software for computational structural biology research. They are licenced under the LGPL. he strbio.org classes are the basis for several published research projects, including the Pred2ary secondary structure prediction...


Platforms: *nix

Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry. It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling...


Platforms: *nix

Geneious is a useful, unique and easy-to-use software system which has been designed to greatly speed up and simplify the research in molecular biology and biochemistry. Geneious is a cross-platform research engine for the retrieval, organization and analysis of biomolecular data that allows...


Platforms: Windows

Geneious is a useful, unique and easy-to-use software system which has been designed to greatly speed up and simplify the research in molecular biology and biochemistry. Geneious is a cross-platform research engine for the retrieval, organization and analysis of biomolecular data that allows...


Platforms: Windows

exploRase was specially designed as an Open Source R-based instrument for the exploratory multivariate analysis of Systems Biology data. It provides a GUI on top of the analysis functionality provided by R and the Bioconductor project. exploRase is designed to be accessible to biologists...


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

SBSI or Systems Biology Software Infrastructure is a handy suite of software tools specially designed for systems biology. It includes parallelized numerical algorithms, and a client application for visualizing results, running simulations, and integrating SBML based plugins. SBSI is a suite of...


Platforms: Windows

EMBOSS is "The European Molecular Biology Open Software Suite", it is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of...


Platforms: Most OSs

Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the...


Platforms: Mac

Thyroid hormones play an essential role for metabolism, growth and differentiation. Therefore, exact regulation of thyroid hormone levels is vital for most organisms. Although the principles of thyrotropic feedback control have been described decades ago we still have not yet gained comprehensive...


Platforms: Mac

An award winning, integrated on-line learning environment where users experience the world of biology through discovery-based learning. GDL was developed as a series of curriculum-aligned and integrated games, modules, and interactive simulations covering an array of topics in biology. To meet...


Platforms: Mac

A Molecular Biology software that provides tools with an intuitive interface to assists you in DNA cloning, sequence analysis and visualization. Serial Cloner 2.1 handles Features/Annotations and now allows to define, import and export, customized lists of Features. User can annotate any sequence...


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

The project aims to extend the PHP scripting language to enable PHP developers to write bioinformatics applications more rapidly than if they had to start from scratch using 'vanilla php'.


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