RSS 225 projects tagged "Bioinformatics"

No download Website Updated 12 Apr 2014 wunderbar

Screenshot
Pop 17.52
Vit 2.96

Wunderbar is a program which is able to identify mislabeled samples in genotype data when a few extra independent genotypes are available ("genetic barcoding"). Wunderbar calculates the likelihood that genotype mismatches have occurred by chance. It is capable of reliable and sensitive detection of sample mismatches and swaps even in the presence of numerous genotyping errors and in the presence of linkage disequibrilium between the individual genotypes. It only requires a few SNPs to work well.

Download No website Updated 14 Apr 2014 Pathomx

Screenshot
Pop 171.01
Vit 23.67

Pathomx is a workflow-based tool for the analysis of metabolomic and other omics datasets. It is interactive, visual, extensible, intelligent, and free for any use. It lets you dynamically build analysis workflows using the interactive editor. Drag and drop connections between plugin tools to create a complete workflow through which to run your analysis. Data can be loaded and processed automatically, and new approaches tested simply by connecting tools.

Download No website Updated 18 Nov 2012 codonPhyML

Screenshot
Pop 15.36
Vit 22.77

codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, it will return the phylogenetic tree which best describes their evolutionary relationship.

No download No website Updated 25 Sep 2012 Bio::SeqReader

Screenshot
Pop 21.31
Vit 1.00

Bio::SeqReader provides a lightweight alternative to Bioperl when all you really need is a helper for reading sequence data. The Bio::SeqReader::Fastq class correctly handles FASTQ input with multiline sequence or quality data.

Download Website Updated 29 Sep 2012 Fqutils

Screenshot
Pop 33.54
Vit 2.02

Fqutils provides a basic set of bioinformatics command line tools for working with sequence data in FASTQ format. It complements Greg Hannon's fine Fastx Toolkit suite. One characteristic of Fqutils is that it correctly handles the full FASTQ format as described by the published standard, which specifically allows multi-line sequence and quality score information per record. Fqutils is intended to be useful as part of the early portions of post-sequencing pipelines and quality assessment processes.

Download Website Updated 14 Oct 2013 SimThyr

Screenshot
Pop 45.39
Vit 4.44

SimThyr is a continuous simulation program for pituitary-thyroid feedback control. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses, and patients.

Download Website Updated 16 Apr 2014 Orthanc

Screenshot
Pop 210.98
Vit 52.10

Orthanc is a lightweight, RESTful DICOM server for health care and medical research.

Download Website Updated 28 Jul 2012 MSAProbs

Screenshot
Pop 17.32
Vit 2.03

MSAProbs is a protein multiple sequence alignment algorithm. It achieves the statistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, and OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons, and Probalign.

Download Website Updated 30 Jul 2012 ScalaBLAST

Screenshot
Pop 38.26
Vit 2.03

ScalaBLAST is a high-performance multiprocessor implementation of the NCBI BLAST library. It supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, and XML). It will run on most multiprocessor systems which have MPI installed, and can run over a wide variety of interconnects, including infiniband, quadrics, and ethernet. It is designed to run a large number of queries against either large or small databases. It parallelizes the BLAST calculations by dynamically scheduling them across processors using a fault-resilient scheme.

No download Website Updated 03 Sep 2012 Emergent

Screenshot
Pop 40.00
Vit 2.74

Emergent is a neural network simulator with a built-in scripting language which allows for the creation and analysis of complex, sophisticated models of the brain in the world. Networks and all of their state variables are visually inspected in 3D, allowing quick "visual regression" of network dynamics and robot behavior. Emergent is a direct descendant of the PDP and PDP++ neural network packages.

Screenshot

Project Spotlight

Tiny Tiny RSS

A Web-based AJAX news feed aggregator.

Screenshot

Project Spotlight

Novius OS

A CMS that takes up the challenge of managing Web content in today’s multi-channel environment.