Search Results for "git:/git.code.sf.net/p/docfetcher/code" - Page 7

An implementation of the Markovian Jensen Shannon divergence (MJSD). The code recursively segments a sequence of symbols and then assesses the divergence of each segment with respect to the entire sequence.

Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions of TraceTuner, which support mixed base calling, have been used by the research community, the private biotech sector, and the U.S. government as components of different variant detection, genotyping and forensic software applications (e.g. ...

sd_clust is Expressed Sequence Tag (EST) clustering software. It produces clusters very similar to those produced by d2_cluster. The project is now being hosted on google and can be found here - http://code.google.com/p/sdclust/

Testing tools source code of the Integrating the Healthcare Enterprise (IHE) PIX and PDQ v3 Integration Profiles

The Shrimp suite provides interactive visualizations of graph-based data. Creole (Eclipse plug-in) visualizes Java source code. Jambalaya (Protege plug-in) visualizes ontologies (including OWL), & Stand-Alone Shrimp visualizes RSF/GXL/PRJ/PPRJ files.

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.

pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use. Please see our new project page and wiki at http://code.google.com/p/pygr.

The ExactFDR software package is an improvement of permutation-based False Discovery Rate (FDR) estimation methods that takes advantage from exact p-value computations for analyzing Genome-wide association studies data

Parallel IBDWS is an upgrade from IBDWS that utilizes parallel processing. Also, the incorporation of DNA sequence data has been added since the last code release

WGAViewer is a suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the full set of P values emerging from a whole genome association (WGA) study.

NOTE: The IntAct package is now hosted at google code: http://intact.googlecode.com IntAct is an open source package to store and manipulate molecular interaction data.

PRIDE: PRoteomics IDEntifications database. Please note that the PRIDE project has relocated to http://code.google.com/p/ebi-pride

Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Source code is contained in jar files. Download contains GSH reactivity plugin.

RepeatFinder is a command line tool for generating non-overlapping matches of microsatellite DNA from FASTA format code.

Manuelito is a Java tool for decrypting posttranslational modification (PTM) patterns of proteins based on MALDI mass spectrometry spectra. It was built for analysing the 'histone code' but it can be applied to any other highly modified protein.

Cellular Automata simulator. Native code (fast) and modular design: update rule, topology, time, measurement, initialization are independant. No GUI (for now...): configuration file (commented default automatically generated) overridable by command line.

The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io

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.

A toolbox for quantitative morphometric analysis of early development in spherical embryos, such as Xenopus laevis (African Clawed Frog). The toolbox is developed for Matlab 6.5 and higher and combines C-Mex code with Matlab functions.

Sight provides a friendly interface to create and connect agents for bioinformatics. The workflow supports multiple responses to a single request, structure transforms, filters and request history access.Can talk with ordinary http servers (get and post)

Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.

Mister Model is a code generation system. It takes a UML model expressed as XMI and generates source code specifically designed to work in a cross-platform web service environment. It fixes the legendary 'Serialization Failed' messages in web services

openevo is a project started to find out about behaviour of evolutionary generated machine code. It implements a certain set of CPU instruction codes and a few interrupts for interaction with the runtime environment.

Sequence studio main package provides classes and interfaces for various kinds of sequence alignment. Differently from regular expressions it computes similarity with two initially unknown strings. Project page provides code generating applet.

The purpose of this project is to make available a variety of tools written in Python.