Open Source Java Bio-Informatics Software - Page 22

Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.

The Molwind project aims at developing Open Source software to visualize relationships among molecular entities such as chemical structures on the basis of NASA WorldWind. Different levels of complexity get visible by zooming in areas of interest.

MooN is a free software tool that provides a fast heuristic and problem implementation framework in form of plugins.

Tool for knowledge acquisition / ontology building from narrative texts.

Java GUI to analyze one (or more, in batch mode) datasets with several feature selection methods at the same time and also performing an "ensemble" analysis. It can be easily extended to include any feature selection algorithm.

This plugin allow to visualize several e.g. gene expression values simultanously using pie charts. * Please cite http://www.biomedcentral.com/1752-0509/4/164 *

Musite provides a bioinformatics tool for predicting both general and kinase-specific protein phosphorylation sites.

PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/MutationMapper) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/MutationMapper/releases/latest). Predict functional consequences of mutations identified from sanger sequencing.

MutationFinder is a biomedical natural language processing (NLP) system for extracting mentions of point mutations from free text. MutationFinder achieves high performance (99% precision, 81% recall on blind test data) as an information extraction system

Extension of the DAS server MyDAS to support writeback capabilities.

"Neurons to Algorithms" (N2A) is a language for modeling neural systems, along with a software tool for editing models and simulating them. N2A is currently "alpha" software. The download provided on SF is for convenience to those who wish to preview the software. Please see our site on github for development status.

This software is to help the those connected with Biology,Biotechnology,Bio Informatics.The user can select from the choices of proteins, nucleotides,etc(All those found on NCBI's website)and search for the specific results

This is a pipeline that is used to store an EST or Genome assembly information including reads and their alignment in a mysql database. Further more, it provides a set of scripts to mine SNPs and other statistics from the assembly.

*NOTICE* The official software(NGSpop) will be updated soon, so please visit us in 2/29. Thank you.

To get access to the code, please check it out with svn as described in the code section.

OpenCV powered image stack analyser for data extraction and preparation. Can be used in conjunction with nanocalcFX. You can get sample data at the NISA homepage. Currently in pre-alpha state.

Bioinformatics tools and applications for the analysis of genomic sequence data.

NOVA is a program designed to analysis complexome profiling data (Heide et al., 2012). A graphical user interface (GUI) provides various visualization tools, such as heat maps and 2D plots. Several hierarchical clustering algorithms (e.g., single linkage, average linkage, Wards linkage), different distance measures (e.g., Euclidean distance, Manhattan distance, Pearson distance), and various normalization techniques are implemented. Many additional functions like zooming, searching for proteins, image export, and automatic file format recognition support intuitive handling for biologists. Giese, et al. NOVA: a software to analyze complexome profiling data. Bioinformatics, 2015, 31(3): 440-441

This is a java open source package for analyzing bio-data. We build this project as an inititive for people interested in bio-informatic to share new ideas and publish their innovative methods.

Narrator is a graphical modelling tool for the description of dynamical systems and processes. Narrator is SBML compatible.

NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.

NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues.

Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.

Simulator of virtual animals made up of biological neural networks for research in the Computational Neuroscience field.

Nexplorer is a web-based phylogenetic browser, used to view and edit comparative data, and ideal for creating publication-quality views in which the tips of a tree are aligned with the rows of a character matrix (e.g., a sequence alignment).