Open Source Bio-Informatics Software

CaspLab - Comet Assay Software Project Lab is a cross-platform image analysis software to measure level of DNA damage in SCGE (Single Cell Gel Electrophoresis) method called also comet assay method.

CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal.

The PUMA Repository is a collection of Pascal units for medical informatics. It contains reusable source code for a wide field of health-care application development. The code includes a support engine for the European Data Format (EDF and EDF+), converting functions for units of measurement and an HL7 engine. PUMA is compatible with Lazarus and Free Pascal. Some of the units also support other Pascal implementations including Delphi, winsoft Pocket Studio and other compilers.

ProtoMol is an object-oriented component based framework for molecular dynamics simulations.

Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)

DigiOz .NET Portal is a FREE web based portal CMS system written in ASP.NET MVC 5 in C# which uses a Microsoft SQL Database to allows webmasters to setup and customize an instant website for either business or personal use. List of Technologies used: - ASP.NET MVC 5 - Microsoft SQL Server - Bootstrap - HTML 5 - jQuery Demo Site: http://digioznetportal.digioz.net/ Source Code: https://sourceforge.net/p/digioznetportal/codenew/ci/master/tree/ Installation Instructions: https://sourceforge.net/p/digioznetportal/wiki/Home/ Help Wanted: If you are a developer, and wish to join the project, please email us at support@digioz.com.

For comparative plus/minus spreadsheet data, Coulson Plot Generator application creates a multiple pie diagram, for a rapid visual comparison of subunit occupancy across a range of entities. Numbers of pies, segments, labels and colours are customisable. Creates an editable PDF from a comma separated text file. Now with zoom capability and more memory, for larger datasets. Save images in several formats including SVG.

EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)

This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

Hy3S uses advanced MPI parallelized hybrid stochastic simulation methods to quickly compute the dynamics of biochemical networks with thousands of species/reactions. Many features included (see Home Page). An easy-to-use GUI (Matlab req) is included.

IU parallel fastDNAml is a program that infers evolutionary histories from genetic sequences, modified and extended from the serial version of fastDNAml to run in parallel on heterogeneous and widely distributed systems.

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

PHP-PBS, is a Graphical Interface to PBS written in PHP. It should work on all Linux platforms with apache and a MySQL database.

Palibino is a class library for Object Pascal supporting bioinformatics, large-scale genomic analysis in life sciences and computational biology.

ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.

ea-fold is a platform to perform protein folding simulations by means of evolutionary algorithms. The program implements a parallelized distributed evolutionary algorithms and a flexible force field.

a cross-platform framework and environment for haplotype analysis with a special focus on human and medical genetics in python/wxpython

Distributed Genetic Programming SRVM (Simple Risc Virtual Machine) Distributed function approximator of nonlinear functions with automatic induction of machine code.

sibsim is designed to simulate either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scaleable way. sibsim is based on XML, completely written in C++ and published under the GNU General Public License

ĄHola!, for "Hordes of Little Atoms," is a project to develop a lean, modular, scalable toolkit for massive simulations of particle (molecular) dynamics. It is written in C and Python to get the best balance between programmer and run time.