222 projects tagged "Bioinformatics"
Updated 07 May 2013
Orthanc
| Pop | 114.73 |
|---|---|
| Vit | 8.01 |
Orthanc is a lightweight, RESTful DICOM server for health care and medical research.
Updated 01 May 2013
MetaPath
| Pop | 71.17 |
|---|---|
| Vit | 1.73 |
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 30 Apr 2013
Wandora
| Pop | 260.82 |
|---|---|
| Vit | 31.80 |
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 17 Mar 2013
SHOGUN
| Pop | 248.17 |
|---|---|
| Vit | 26.99 |
SHOGUN is a machine learning toolbox whose focus is on large scale kernel methods and especially on Support Vector Machines (SVM). It provides a generic SVM object interfacing to several different SVM implementations, all making use of the same underlying, efficient kernel implementations. Apart from SVMs and regression, SHOGUN also features a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons, and algorithms to train hidden Markov models. SHOGUN can be used from within C++, Matlab, R, Octave, and Python.
Updated 27 Jan 2013
SimThyr
| Pop | 47.29 |
|---|---|
| Vit | 2.95 |
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 26 Dec 2012
massXpert mass spectrometry package
| Pop | 142.76 |
|---|---|
| Vit | 25.77 |
The massXpert software package is a mass spectrometry environment for linear (bio-)polymers. It inherits all the innovations of GNU polyxmass. It allows the detailed definition of new polymer chemistries in the XpertDef module. These chemistry definitions are then used in the desktop calculator-like mass calculator (XpertCalc) and in the sophisticated polymer sequence editor and (bio-)chemical/mass spectrometric simulations module (XpertEdit). Available simulations include polymer and monomer chemical modifications, polymer sequence cleavage, gas-phase fragmentation, m/z ratio calculations, and more.
Updated 18 Nov 2012
codonPhyML
| Pop | 19.16 |
|---|---|
| Vit | 14.58 |
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 28 Oct 2012
Renal Growth
| Pop | 36.21 |
|---|---|
| Vit | 12.20 |
Renal Growth is a tool for radiologists and paediatricians to plot renal length and volume measurements against nomograms for age and weight. It allows for multiple observations from birth to 13 years. Individual patient data files can be stored and reused. Length and volume charts can be exported as JPEG files for importing into a PACS system or other clinical record.
Updated 26 Oct 2012
VPLG
| Pop | 25.92 |
|---|---|
| Vit | 2.31 |
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 | 41.82 |
|---|---|
| Vit | 2.03 |
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.
