Search Results for "sandbox:/mnt/data/project_plan.pod"

...It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. ...

The PUMA Repository is a collection of Pascal units for medical informatics. It contains reusable source code for a wide field of health-care application development. The code includes a support engine for the European Data Format (EDF and EDF+), converting functions for units of measurement and an HL7 engine. PUMA is compatible with Lazarus and Free Pascal. Some of the units also support other Pascal implementations including Delphi, winsoft Pocket Studio and other compilers.

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.

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

For comparative plus/minus spreadsheet data, Coulson Plot Generator application creates a multiple pie diagram, for a rapid visual comparison of subunit occupancy across a range of entities. Numbers of pies, segments, labels and colours are customisable. Creates an editable PDF from a comma separated text file. Now with zoom capability and more memory, for larger datasets.

XNBC is a full featured application for computer naive neuroscientists. It simulates biological neural networks using graphic tools to edit neurons and networks, to run the simulation and to analyze results. Written in C, it runs on Unix and Windows. Web site : http://ticemed-sa.upmc.fr/xnbc/ All recent versions are on this site.

Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).

AgED performs automatic feature extraction from your image data and allows for their visualization and management. AgED relies on Elliptic Fourier Transcriptors to extract features from large quantities of image data. These features can then be visualized and you can evaluate them in a statistical manner. This type of analysis is particularly worthwile in the assessment of biological experiments.

The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.

Lucy is a program for DNA sequence quality trimming and vector removal. Its purpose is to process DNA sequence data acquired from DNA sequencers to prepare the data for downstream processing applications such as genome assembly.

EuroPhenome - a database for Mouse phenotype data

mccore is a bioinformatics data structures and tools library for efficient analysis and manipulation of RNA, DNA and protein 3D structures.

sibsim is designed to simulate either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scaleable way. sibsim is based on XML, completely written in C++ and published under the GNU General Public License

Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical represetations from Gene Ontology (GO) annotated interactions maintained by the BioGRID.

Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program. It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data.

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

CSBI is a component based framework that allows for inter-component data sharing and access. GINY is an Open Source Graph Library.

TM4 is a suite of applications for managing and analyzing microarray data. TM4 provides data storage and tracking, image analysis, normalization, data filtering, clustering and statistical analysis capabilities. Includes MADAM, Spotfinder, MIDAS, and MeV.

STARS is an alternative interface to staden for studying polymorphisms in short sequences with batch processing, manual editing, trace viewing and data management. STARS was initially designed for Multi Locus Sequence Typing of bacteria.

froi (FS-FAST ROI) is a suite of Perl scripts and modules to provide easy slice-, volume-, and surface-based ROI analysis of functional MRI (fMRI) data analyzed by FS-FAST and Freesurfer (http://surfer.nmr.mgh.harvard.edu).

GeneX is an gene expression database system with an integrated toolset that enables researchers to store, analyze, and communicate their data.