225 projects tagged "Bioinformatics"
Updated 01 May 2013
MetaPath
| Pop | 67.81 |
|---|---|
| Vit | 2.10 |
MetaPath is a tool for the analysis of metabolic pathways and associated visualization of experimental data. Built on the MetaCyc database, it provides an interactive map in which multiple pathways can be simultaneously visualized. Multiple annotations from the MetaCyc database are available, including synonyms, associated reactions and pathways, and database unification links. Metabolomics change data can be imported via simple CSV formats for visualization on targeted pathways. Pathways can be mined and removed algorithmically to identify key regulated pathways within a given dataset, providing a simper route to metabolic functions.
Updated 18 Nov 2012
codonPhyML
| Pop | 18.41 |
|---|---|
| Vit | 13.58 |
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 25 Sep 2012
Bio::SeqReader
| Pop | 30.56 |
|---|---|
| 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 29 Sep 2012
Fqutils
| Pop | 41.61 |
|---|---|
| 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 27 Jan 2013
SimThyr
| Pop | 46.86 |
|---|---|
| Vit | 3.14 |
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.
Updated 07 May 2013
Orthanc
| Pop | 114.19 |
|---|---|
| Vit | 13.39 |
Orthanc is a lightweight, RESTful DICOM server for health care and medical research.
Updated 26 Oct 2012
VPLG
| Pop | 25.38 |
|---|---|
| Vit | 2.38 |
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 28 Jul 2012
MSAProbs
| Pop | 25.46 |
|---|---|
| Vit | 2.31 |
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.
Updated 30 Jul 2012
ScalaBLAST
| Pop | 42.39 |
|---|---|
| Vit | 2.32 |
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.
Updated 03 Sep 2012
Emergent
| Pop | 59.09 |
|---|---|
| Vit | 3.28 |
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.
