Open Source Solaris Bio-Informatics Software - Page 2

The Multi-purpose Automated Genome Project Investigation Environment (MAGPIE, http://magpie.ucalgary.ca/), is a software package for the automated curation and presentation of DNA and protein sequences. Freely available under terms of Apache license v2.0

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.

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

The OBO-Annotator is a semantic NLP tool that is designed to give its end-users a great deal of flexibility to combine any number of OBO ontologies from the OBO foundry regardless of their format and use them to annotate text-bases.

ORFer reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. ORFprimer is an extended software package for high throughput PCR primer design for biological sequences

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.

Palibino is a class library for Object Pascal supporting bioinformatics, large-scale genomic analysis in life sciences and computational biology.

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.

SIBsim4: an extensive rewrite of the sim4 program to improve execution speed and provide more informative output. Written in C, mainly targeted at Linux and Unix. Keywords: bioinformatics, genome, transcriptome, EST, splicing, exon, intron.

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.

SureFit generates 3D mesh surfaces (in VTK and Caret formats) from 3D structural MRI volumes (in formats such as Analyze, AFNI, raw).

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.

TaxonFinder is an application that annotates taxon found in literature. The application harnesses a hybrid algorithm that is necessarily a combination of morphological analysis, dictionary lookup and Levenstein Distance algorithm.

A neuroscientific knowledge management system for the published literature

Two Dimensional NOesy simulation (TDN) implementents an algorithm that creates a time-domain 2D NOesy spectrum. TDN does not calculated the nOe peak intensities, Therefore, you will need the CORMA (Complete nuclear Overhauser Relaxation Matrices).

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.

ea-fold is a platform to perform protein folding simulations by means of evolutionary algorithms. The program implements a parallelized distributed evolutionary algorithms and a flexible force field.

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).

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

As of July 07, 2007, the mpiBLAST Project has moved to http://www.mpiblast.org. The mailing lists and CVS repository has been moved here as well.

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.

Sampsize computes sample size and power for surveys, comparative studies including non-inferiority trials and case-control studies.

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

Sybil is a web-based software package for comparative genomics