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Bioinformatics Template Library This library focuses on the data structures and algorithms used in bioinformatics and molecular modelling, following closely the approach of the Standard Template Library (STL) to implement efficient generic programming modules using compile time mechanisms. Although the BTL was designed with biomolecular applications in mind it contains classes of more general utility: for instance, the Matrix class could be used for matrix algebra in many contexts.

Biskit Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs.

Blossoc Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input, score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation. Building the local genealogy trees is based on a number of heuristics that are not guaranteed to build true trees, but have the advantage over more sophisticated methods of being extremely fast. Blossoc can therefore handle much larger data sets than more sophisticated tools, but at the cost of sacrificing some accuracy.

CAGE A generic and fairly complete cellular automata simulation engine. CAGE is a fairy generic and complete cellular automaton simulation engine in Python. It supports both 1D and 2D automata, a variety of prepackaged rules, and the concept of "agents" which can move about independently on the map for implementing agent behavior. CAGE comes with numerous examples of fully-functional CA systems, including Conway's Game of Life, Langton's self-reproducing automaton, Langton's "vants," and 1D automata rule explorers. It also comes with simple displayers (including a curses interface for 2D automata). Also included is a unique implementation of a finite state machine (ant.py).

CT Sim Computed Tomography is the technique of estimating the interior of objects from the measurements of radiation projected through the object. That radiation can be transmitted through the object such as in X-ray computed tomography or emitted from internal radiation sources as in nuclear medicine scans. CTSim simulates the transmission of X-rays through phantom objects. These X-ray data are called projections; CTSim reconstructs the original phantom image from the projections using a variety of algorithms. The program also has a wide array of image analysis and image processing functions.

CoaSim 'CoaSim' is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro-satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.

CoaSim-gui 'CoaSim-gui' is a graphical use interface for the coalescence process simulator CoaSIm.

CvEyeTracker 'cvEyeTracker' is a toolkit for low-cost real-time eye tracking. It is intended to provide a hardware design and a set of software tools useful for the analysis of eye movement data collection using inexpensive, off-the-shelf hardware. Available tools include algorithms to measure eye movements from digital videos, techniques to calibrate the eye tracking system, and example software to facilitate real-time eye-tracking application development.

E-CELL Simulation Environment E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.

FastDNAml 'fastDNAml' estimates maximum likelihood phylogenetic trees from nucleotide sequences. It is derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). 'fastDNAml' tries to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C.

GAUL The Genetic Algorithm Utility Library (GAUL) is a programming library designed to assist in the development of code requiring genetic algorithms. The steady-state, generation based and the island model of evolution are supported, using the Darwinian, Lamarkian or Baldwininan evolutionary schemes. Standard mutation, crossover and selection operators are provided, while code hooks additionally allow custom operators. It provides data structures and functions for handling and manipulation of the data required for a genetic algorithm. Additional stochastic algorithms are provided for comparison to the genetic algorithms. Much of the functionality is also available through a simple S-Lang interface.

GENtle GENtle is bioinformatics software for everyday molecular biology tasks. It features DNA and amino acid sequence display and editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, primer design, virtual PCR, online database access, and more.

HASAS 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 functionality; beamforming, direction finding, level histogram, LOFAR/DEMON (narrowband spectrogram), wideband spectrogram, and raw audio.

Health GNU Health is a program designed for hospitals, offering the following funtionality:

• Electronic Medical Record (EMR)
• Hospital Information System (HIS)
• Health Information System

It has a strong focus on family medicine and primary care, along with socio-economic circumstances. It uses the following disease and medical procedure standards: (ICD-10 / ICD-10-PCS). There are facilities to aid in choosing medicines; prescription writing; patient, hospital finacial, and lab administration tools; a database of 4,200 disease-related genes; epidemiological reporting; and much more.

GNU Health is part of GNU Solidario, an NGO offering health and education to the underpriveledged through free software: http://www.gnusolidario.org/

NeuroScope NeuroScope is an advanced viewer for electrophysiological and behavioral data (with limited editing capabilities): it can display local field potentials (EEG), neuronal spikes, behavioral events, and the position of the animal in the environment.

Open BEAGLE Open BEAGLE is an evolutionary computation framework. It provides an Object-Oriented software environment enabling the implementation of almost any kind of evolutionary algorithm, such as genetic algorithms and genetic programming. The only necessary condition is to have a population of individuals to which a sequence of evolving operations is iteratively applied. So far, two specialized frameworks have been implemented: genetic algorithms and genetic programming. An evolution strategies framework is also planned for a future release.

PerlPrimer 'PerlPrimer' designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR), and sequencing by automating and simplifying the process of primer design. Current features include calculation of possible primer-dimers, retrieval of genomic or CDNA sequences from Ensembl, the ability to BLAST search primers using the NCBI server, ORF, and CpG island detection algorithms, the ability to add cloning sequences to primers, automatically adjusted to be in-frame, and QPCR primer design without manual intron-exon boundary entry.

Phylographer PhyloGrapher helps you visualize and study evolutionary relationships within families of homologous genes or proteins (elements). It is a drawing tool that generates custom graphs for the given set of elements. It can be used to visualize any type of interactions between elements you want. Each gene or protein on a graph is represented as a colored node (vertex) and connected to other nodes (vertices) by lines (edges) of variable thickness and color based on the similarity of genes or proteins (distance matrix). The user positions these nodes in such a way as to optimize visualization of the inter-relationships between the nodes. Unlike classical phylogenetic trees, the physical distances on the graph between nodes have no information content. The level of similarity between genes or proteins on PhyloGrapher's graphs is indicated by color and line thickness.

Py-ACQUA 2 PY ACQUA is the first Italian Free Source software dedicated to the to the world of the acquariophilia. Py-Acqua traks all events of an Aquarium Tanks (see the ScreenShots of the program), from the insertion date of the species of plants and fish, to the water values control. The program has special alarms that perceives the owner of a tank of the presence of anomalous values of water assuring him a more careful management of his aquarium.

QDist 'QDist' implements the O(n log^2 n) time method for computing the quartet distance between unrooted evolutionary trees. It takes as input two trees in newick format over the same set of species and computes the quartet distance between them.