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Category/Biology

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Antidote
Antidote is an open source implementation of the IEEE 11073-20601 standard. It also contains the implementation of a D-Bus based 11073 manager service.

Bamtools
BamTools provides both a programmer's API and an end-user's toolkit for handling genome alignment files in the BAM and SAM format. A BAM file (.bam) is the binary version of a SAM file. A SAM file (.sam) is a tab-delimited text file that contains sequence alignment data.

DataStatix
DataStatix is a free software for GNU/Linux and Windows useful to manage data of every kind (although it has been written to manage biomedical data), to create descriptive statistics and graphs and to export items easily to R environment or to other statistic softwares. In order to handle properly big amount of data and many concurrent users, DataStatix works with MySql database and it has been developed and tested with MySql community edition 5.5. Some features of the software are: users management (create, delete, modify password) within the software; different users levels of data access (administrator, default, read only); user defined templates (models) of data, to create new databases easily; importation and esportation of data in CSV format (used also by Calc and Excel); updating of existing data from a CSV file created with DataStatix; descriptive statistics from every data (some more kind of statistics to come); graphs from every data.

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.

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.

Health Heckert gnu.small.png
GNU Health is a program designed for hospitals, offering the following functionalities:

  • 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/

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.

Orthanc
Orthanc aims at providing a simple, yet powerful standalone DICOM server. It is designed to improve the DICOM flows in hospitals and to support research about the automated analysis of medical images.

Orthanc can turn any computer running Windows or GNU/Linux into a DICOM store (in other words, a mini-PACS system). Its architecture is lightweight and standalone, meaning that no complex database administration is required, nor the installation of third-party dependencies.

What makes Orthanc unique is the fact that it provides a RESTful API. Thanks to this major feature, it is possible to drive Orthanc from any computer language. The DICOM tags of the stored medical images can be downloaded in the JSON file format. Furthermore, standard PNG images can be generated on-the-fly from the DICOM instances by Orthanc.

Orthanc lets its users focus on the content of the DICOM files, hiding the complexity of the DICOM format and of the DICOM protocol.

SimThyr
SimThyr is a continuous simulation program for pituitary-thyroid feedback control. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients.

SimThyr is based on a physiologically-grounded nonlinear mathematical theory of thyroid homeostasis. The application supports simulation in time domain and various methods of sensitivity analysis.

Source code is provided for Lazarus and Free Pascal. The program is compatible with most desktop Linux distributions, Mac OS X and Windows.

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