Search Results for "java open source" - Page 55

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

PhyloCpp is (will be...) a C++ toolkit designed for the reading, writing and manipulation of phylogenetic trees with an emphasis on comparative methods, ancestral state reconstruction and characterization of the evolutionary process.

Machine learning approaches to finding features that correlate with the function of small interfering RNAs

ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the automatic annotation of genome-wide tiling-array data in Arabidopsis. ARTADE is a program originally written by Dr. Tetsuro Toyoda, RIKEN, Japan.

BEDTools is a suite of utilities for comparing genomic features in BED format. These utilities allow one to quickly address tasks such as: 1. Intersecting two BED files. 2. Merge overlapping features. 3. Paired-end overlaps.

Controversial ideas of Williamson, Margulis & others suggest speciation by hybridizing might be more common than originally thought. Taking this concept to the nth degree & assuming that indeed, speciation mostly occurs by hybridizing events, not the accumulation of mutations or genetic drift, here is a catalogueoflife2gedcom converter. It allows the tree of life to be displayed as a human genealogy tree with hybridizing events depicted as "marriages." The idea then is that mutation...

A GUI-based search tool that allows the exploration of the relationships between Metabolites.

SDFCherry is a command-line program that searches for textual matches in molecular structure files of SDF format and outputs the structures that match. Optionally adds a data field to the matched structures, e.g., biological activity. Useful for QSAR.

Palex is a two-stage biological sequence searching system. Library will contain functions for searching patterns, palindromes and structures in DNA sequence.

Harmonize + gene = Harmogene Efficiently create sets of genome annotations ("consensus annotations") from one or more source genomes using simple rules and and apply those annotations to one or more target genomes. See the Trac page for more info.

Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output.

Maq is a set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.

ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models of signaling systems, according to the layer-based approach.

The MML Framework is a temporal-spatial biological model representation language. The MML Project provides the application tool set which facilitates the goals of representing biological models using the MML specifications.

FMR Eyetrack is a SPM plugin that allows to directly estimate the point of gaze from the functional MRI data without the help of a dedicated eye tracker. I am no longer working in this field. If anyone wants to pick up this project, please contact me.

Decima is a database that was designed to support time-series data mining. It consists of PostgreSQL custom type definition, implementation of GiST index for that type and snowflake database schema.

Spotfinder is an image processing software tool for microarray image analisys. It is written on C++ with QT GUI toolkit and runs on Windows, X11, and Mac OSX.

The HuRef Genome Browser is a Web resource for the navigation of an individual human genome, termed HuRef, published in PLoS Biology. The browser is a unified framework of annotation, assembly and synteny tools. It is online at http://huref.jcvi.org.

LeafAnalyser has been developed as a fast throughput leaf shape analysis application. It contains features such as automated image processing, data analysis and interactive 2D/3D graphs.

UPDATE(2017-07-24) This repository has moved to BitBucket: https://bitbucket.org/parkinsonlab/cell-2017 Cell++ is a novel stochastic simulation environment which is capable of modeling diverse biochemical phenomena including signal transduction pathways, metabolic pathways and intracellular calcium signaling.

jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.

MIVF - Medical Imaging and Visualization Factory, is a framework for medical applications. It supplies a platform, in which image processing and 3D visualization algorithms can be employed as reusable components (functional modules or plugins).

Shape is a molecular conformation prediction program. It uses a genetic algorithm to efficiently search the conformational space of a biomolecule and then clusters the results. It is very simple to use.

EDGE3 is an open-source, web-based application allowing for the management, storage, analysis, and controlled sharing of transcription-based microarray data generated on the Agilent DNA platform.

E-BioFlow enables the scientists to design workflow using three different perspectives: control flow, data flow and resource perspective. The workflow tool is based on the Yawl engine and has support for BioMOBY and WSDL services and Perl and R scripts.