Biological

ORFer reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. ORFprimer is an extended software package for high throughput PCR primer design for biological sequences Platforms: Windows, Mac, BSD, Solaris, Linux

PyCogent: A toolkit for making sense from sequence. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for 3rd party applications. Platforms: Windows, Mac, Linux

This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps... Platforms: Windows, Mac, 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

XMLPipeDB is a suite of tools for building relational databases from XML sources with minimal manual processing of the data. While the applicability is general, our motivation was to facilitate the management of biological data from different sources. Platforms: Windows, Mac, Linux

The phpLabDB Project is a community-supported open source project. Built around independent modules that interact with each other, phpLabDB manages a variety of day-to-day useful laboratory information. It is also a high powered and highly customisable open-source laboratory database project.... Platforms: Windows, Mac, *nix, PHP, BSD Solaris

The BioPHP Project is a non-profit, open source software project that aims to extend the PHP scripting language so it can be used to develop bioinformatics applications. BioPHP is NOT a bioinformatics application. Rather, it is a collection of tools to help PHP developers write bioinformatics... Platforms: Windows, Mac, *nix, PHP, BSD Solaris

The Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and... Platforms: Windows, Mac, *nix, Python, BSD Solaris

Evolutionary optimization methods, inspired from natural processes, have shown good performance in solving complex optimization problems. For example, genetic algorithms (inspired from biological evolution of human and other species), ant colony optimization (based on ants effort to find optimal... Platforms: Matlab

These files are the MATLAB code for "Imperialist Competitive Algorithm (ICA)" which in some papers is referred by "Colonial Competitive Algorithm CCA".Evolutionary optimization methods, inspired from natural processes, have shown good performance in solving complex optimization problems. For... Platforms: Matlab

How do bacteria find their way to the food ? many biological systems use the chemo-taxis algorithm to improve their conditions and hence, their chance to survive. Chemo-taxis in general refers to movement influenced by chemical properties of the medium. In this model, we have a group of... Platforms: Matlab

This software has been realized at the CNS Technology Lab at Boston University - http://techlab.bu.edu. The main author of this software is Chaitanya Sai ( http://techlab.bu.edu/members/sai/ ).CONFIGR (CONtour FIgure GRound) is a computational model based on principles of biological vision that... Platforms: Matlab

Blast2GO?*A* is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Main Application Features are: Easy start up and low maintenance. Make sure you have JAVA, download Blast2GO from this site and start using the application. Updates are... Platforms: Mac

Seqlib is a Python module and application package for population genetics (and more). It allows processing, analyzing and simulating biological sequences. It is specifically designed for automated large-scale sequence analysis. Main features: * Fasta-centered input and output, format... Platforms: Mac

This handcrafted package contains Python wrappers for Berkeley DB, the Open Source embedded database system. Berkeley DB is a programmatic toolkit that provides high-performance built-in database support for desktop and server applications. The Berkeley DB access methods include B+tree, Extended... Platforms: Mac

ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists... Platforms: Mac

massXpert is about mass spectrometry. This is software that runs on MS-Windows, Apple-Mac-OS-X, GNU-Linux, and almost all variants of the UNIX system. With massXpert you actually have four programs in one : 1. With the XpertDef module you define brand new polymer chemistries (what are the... Platforms: Mac

Colombia Radio Stations is a simple script shamelessly recopied for Amarok 2. It offers you some Colombian radio streams. Platforms: *nix

BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources. Features . 3D rendering of biological images . image processing and analysis . segmentation with ITK .... Platforms: *nix

segtools is a Python library designed to put genomic segmentations back in the context of the genome! Using R for graphics, segtools provides a number of modules to analyze a segmentation in various ways and help you interpret its biological relevance. Segmentations should be in BED format, with... Platforms: *nix