174 projects tagged "Bioinformatics"
Updated 07 May 2013
Orthanc
| Pop | 114.42 |
|---|---|
| Vit | 12.18 |
Orthanc is a lightweight, RESTful DICOM server for health care and medical research.
Updated 30 Apr 2013
Wandora
| Pop | 254.12 |
|---|---|
| Vit | 45.31 |
Wandora is a general purpose data extraction, management, and publishing application based on Topic Maps and Java. Wandora has a graphical user interface, layered presentation of knowledge, several data storage options, rich data extraction, import and export capabilities, and an embedded HTTP server that enables dynamic publication of Topic Maps. Wandora is well suited for rapid ontology construction and knowledge mashups.
Updated 18 Nov 2012
codonPhyML
| Pop | 18.55 |
|---|---|
| Vit | 13.69 |
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.
Updated 26 Oct 2012
VPLG
| Pop | 25.42 |
|---|---|
| Vit | 2.37 |
Visualization of Protein Ligand Graphs (VPLG) uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, usually alpha helices and beta strands) or ligand molecules, while the edges model contacts and relative orientations between them. The graphs can be visualized, written to a database, and saved in a text-based file format.
Updated 29 Sep 2012
Fqutils
| Pop | 41.24 |
|---|---|
| Vit | 2.04 |
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.
Updated 25 Sep 2012
Bio::SeqReader
| Pop | 30.50 |
|---|---|
| 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.
Updated 06 Sep 2012
VTD-XML
| Pop | 113.00 |
|---|---|
| Vit | 14.48 |
Virtual Token Descriptor for eXtensible Markup Language (VTD-XML) refers to a collection of efficient XML processing technologies centered around a non-extractive XML parsing technique called Virtual Token Descriptor (VTD). Depending on the perspective, VTD-XML can be viewed as either an XML parser, a native XML indexer or a file format that uses binary data to enhance the text XML, an incremental XML content modifier, an XML slicer/splitter/assembler, or an XML editor/eraser.
Updated 03 Sep 2012
Emergent
| Pop | 53.85 |
|---|---|
| Vit | 3.27 |
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.
Updated 30 Jul 2012
VULCAN
| Pop | 66.08 |
|---|---|
| Vit | 11.67 |
VULCAN (Viscous Upwind aLgorithm for Complex flow ANalysis) offers computational fluid dynamics for subsonic speed through hypersonic turbulent reacting and non-reacting flows on a variety of serial and parallel computational platforms. The computational cost of propulsion flow analysis is reduced through the use of special turbulent wall treatments, multi-grid methods for elliptic and space marching schemes, and conditioning of the governing equations to reduce numerical stiffness. Physical modeling capabilities are improved through the inclusion of models for compressibility, Reynolds stress anisotropies, turbulent diffusivity, finite rate chemistry, and turbulence/chemistry interaction effects. VULCAN can simulate two-dimensional, three-dimensional, or axi-symmetric multi-block problems.
Updated 30 Jul 2012
ScalaBLAST
| Pop | 42.71 |
|---|---|
| Vit | 2.31 |
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.
