Biological

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

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

BioMail is a small web-based application for medical researchers, biologists, and anyone who wants to know the latest information about a disease or a biological phenomenon. It is written to automate searching for recent scientific papers in the PubMed Medline database.Periodically BioMail does a... Platforms: *nix, Perl, BSD

Revised from Dr. Wang Lihong's MCML. Tested ok on windowsXP+Matlab7.0. Performes about 30% to 40% faster than MCML.Beta version 1.01.qiang.2@osu.edu Platforms: Matlab

Dynamic Bayesian networks (DBN) are widely applied in modeling various biological networks, including the gene regulatory network. Due to several NP-hardness results on learning static Bayesian network, most methods for learning DBN are heuristic, that employ either local search such as greedy... Platforms: Matlab

JSimLife is an advanced Biological Life simulation, written in Java. In JSimLife every life form is a cell. Every cell is a Sprite and it has a Brain Object (not yet implemented) and a Dna object. Every Cell's aspect are stored in a Dna (Dna is a Vector of parameters). Cells are able to riproduce... 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

wEMBOSS is a web interface for the EMBOSS software package for biological sequence analysis. Under wEMBOSS each user has a private workspace where he can organize his work by creating projects and save results for later easy recovery and review. Platforms: *nix

ProteoConnections is a bioinformatics platform tailored to address the pressing needs of proteomic analyses. Organise identifications, evaluate the the acquired dataset and accelerate biological interpretation using bioinformatics applications. Platforms: *nix

Metaboflux is a generic approach for predicting flux distribution in metabolic networks under multiple and various constraints deducted from the experiments, to increase the biological relevance of the model. Features . Muti-objective and multi-criteria analysis . Flux analysis .... Platforms: *nix

nebseq is a Python module for basic biological sequence manipulations. Import as usual >>> import nebseq Reverse complements The only note here is that revcomp does not check the input sequence to see if it looks like DNA or RNA. >>> nebseq.revcomp('ACGT') 'ACGT' >>>... Platforms: *nix