Scanning probe microscopy data visualisation and analysis
A data visualization and processing tool for scanning probe microscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry data, useful also for general image and 2D data analysis.
HaploPainter - a pedigree and haplotypes drawing tool written in Perl/Tk. The software processes pedigree information in standard linkage formats combining haplotype information outputs from Simwalk, Genehunter, Allegro and Merlin.
Neuroshare is created to support the collaborative development of open library and data file format specifications for neurophysiology and distribute open-source data handling software tools for neuroscientists.
openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.
LutefiskXP is ANSI C compliant software used to perform de novo peptide sequencing from tandem mass spectra.
Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.
MSQuant is a tool for quantitative proteomics/mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.
A software for generating DNA patterns
The DNA pattern represents a new method of analysis for DNA sequences. In general it can easily detect relationships among species over the evolutionary landscape. Largely, in bioinformatics the DNA pattern method is unexplored and many discoveries can be made through it. One of the questions to which an answer was given is: How many types of promoters are out there regulating the genes ? It seems that there are 10 types of promoters. The project also contains 20,000 images (DNA patterns) that can be analyzed in relation to various genetic disorders (if Homo Sapiens) or for understanding the evolutionary mechanisms between species. References:  Gagniuc and Ionescu-Tirgoviste: Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. BMC Genomics 2012, 13:512.  Gagniuc and Ionescu-Tîrgoviste. Gene promoters show chromosome specificity and reveal chromosome territories in humans, BMC Genomics 2013, 14:278. Source code VB6 (Visual Basic 6.0)
Weighted Implementation of Suboptimal Paths (WISP)
Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. We present a program called Weighted Implementation of Suboptimal Paths (WISP) capable of rapidly identifying additional suboptimal pathways that may also play important roles in the transmission of allosteric signals. Aside from providing signal redundancy, suboptimal paths traverse residues that, if disrupted through pharmacological or mutational means, could modulate the allosteric regulation of important drug targets.
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A JAGS extension module provides additional distributions including the Pareto family of distributions, the DuMouchel prior and the half-Cauchy prior.
ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.
ARGonWin - Automatic retrosynthesis generator on (X)Windows: COMPUTERASSISTED ORGANIC SYNTHESIS / Chemoinformatics package to propose a chemical synthesis for an organic compound given its structural formula. (C++ XWindows/MSWindows). Based on OpenBabel.
Affymetrix GeneChip Operating Software (GCOS) is used to control Affymetrix Microarray scanners and fluidic stations. Using the DCOM API, this project provides programmatic scripting of GCOS using Python.
Athena is a visual tool for building and simulating biological circuits. It provides visual interface for construction of modules/devices. Features: RegulonDB, Sequence editing, automatic rate equations, interface with SBW, interface with R.
If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).
BioCSharp is an open-source project designed to provide a bioinformatics .NET framework for processing biological data. It will include objects for manipulating sequences, file parsers, DAS, database access and analysis and statistical routines.
The Biomolecule Naming Service (BNS) is loosely inspired by DNS servers used to resolve host names and IP addresses. BNS uses the Lightweight Directory Access Protocol (LDAP) to resolve gene/protein names and identifiers.
This set of C++ classes allows the user to load data from custom Affymetrix microarrays. This is a good platform for new method development and it contains several common normalization algorithms.
Laboratory Information Management System
Laboratory Information Management System for in Vitro Genebank.
CyberMedica Foundation - Improving Responsible Human Research Throughout the World by Providing an Open Systems Standard for Peer Reviewed Ethics Review and Decisioning in the Medical Research Clinical Trials Governance Process.
This project is a Genetic Algorithm engine able to be reused for other projects with minimal additional programming. To use GA to search for a problems solution, program a fitness function, the project settings, and a few virtual functions.
IGBM (Identification of gene blocks in microorganisms) implements a BLAST-like method to infer conserved gene clusters among closely related prokaryotes, and provides a graphical user interface to navigate the identified clusters and their annotated info
This program will provide a new way to visualize molecular marker data.
The Molecular Object Library, MOL is a c#-based object-oriented component for chemoinformatics and molecular modeling.
A medical information system for Windows-based systems (95-XP/CE/PocketPC) based on Open Source platforms