Category/Biology

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.

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

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/

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.

Sispread

Sispread allows users to simulate the dynamics of an hypothetical infectious disease within a contact network of connected people. It is intended to help people concerned by public health to easily perform epidemic simulations and to analyze their results.

Yanuca

YaNuCa is a JavaScript web tool to calculate plans for artificial nutrition (enteral+parenteral) in intensive care patients, with special regard to the different phases of critical illness, stress metabolism and stages of rehabilitation. Proper nutrition can be crucial for the outcome of critically ill patients at every stage of treatment and rehabilitation. This tool has been successfully used for years by two intensive care units at the University Clinic for Internal Medicine in Heidelberg/Germany. It is based on the ESPEN Guidelines for parenteral nutrition in intensive care (ESPEN = European Society for Clinical Nutrition and Metabolism).