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BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project.
Our software can test for HLA allele and amino-acid differences between two populations. It examines zygosity, tests for strongest association, interaction & linkage disequilibrium among amino acid epitopes.
User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files
Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.
FreeLIMS is a Laboratory Information Management System ( LIMS ). Manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. FreeLIMS is Open Source and Free.
Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.
SeEvolution is the first application that lets you see the effects of mutation events on 3D models of chromosomes. It takes you on a journey through time, showing you the changes that are necessary to go from the genome of an organism to another.
ProteinShader is a molecular visualization tool that can produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent program is written in Java and OpenGL Shading Language.
The goal of this project is to make a biologic pathway simulation / emulation application. The ultimate goal is to feed different file types to the application and configure a pathway and its behaviour.
Genome Data Visualization Toolkit (GDVTK) is a Java library for building bioinformatics visualization application. See Bioinformatics, 2004 Mar 22;20(5):727-34. Java-based application framework for visualization of gene regulatory region annotations.
BioSunMS, a flexible software platform for submission, management, retrieval of sample and MS data(MALDI or SELDI), and clinical proteomics-related statistical analysis. BioSunMS integrated all functions into a user-friendly desktop RCP application.
IGRAFU is an open source program to integrate solutions to rebuild phylogenetic trees. It supports various well-known algorithms, such as Maximum Parsimony and Distance-matrix methods.
A simple Javaapplication for the analysis and identification of gene networks. ProPesca takes as input shorts temporal series of realtime-PCR expression levels and it clusters genes that exhibit either similar or specular behaviors.
Cytoprophet is a Cytoscape plugin that helps researchers infer new potential protein (PPI) and domain (DDI) interactions. Users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score.
MZ-Analyzer is a tool for visualization and analysing of multiple mass spectrometry data in 2D and 3D mode, including the function of quantitating the LC-peak of the specified identified peptides.
Protege is a free, open-source platform that provides a suite of tools to construct domain models and knowledge-based applications with frame-based and Semantic Web ontologies.
Open Screening Environment is a open source system for management of High Throughput Screening related experiments. The platform consists of new research tools that will enhance significantly management and analysis of HTS data. More information can be f
The Disease Simulation Framework (DiSiF) represents a spatial simulation environment for infectious viral disease spread. The framework currently embodies a very simple framework for simulation in 2D space with focus on SARS and the Common Flu.
This program will read in data generated by ABI DNA Analyzers using GeneScan or GeneMapper, CEQ 2000 and SCF instruments and construct gel images which are straightened and sized. Please download and view the tutorial, no documentation is included in 2.1
LAMINA (Leaf shApe deterMINAtion) is a tool to provide classical measures of leaf shape (blade dimensions) and size (area) as well as measures that indicate asymmetry in leaf shape and measures of herbivory damage (missing leaf area).