Search Results for "c-sharp" - Page 2

Open Source project for the development of the IEEE 11073-20601 reference implementation.

FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.

A collection of tools to transform common biosequence formats (e.g. EMBL, SWISS-PROT, UniProtKB, GenBank and RefSeq) into the fasta sequence format.

The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes.

Phosphorylation motifs represent position-specific amino acid patterns around the phosphorylation sites in the set of phosphopeptides. The discovery of phosphorylation motifs is a very valuable work in bioinformatics. Although several algorithms have been proposed to uncover phosphorylation motifs, the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. In this paper, we propose an algorithm called C-Motif...

To get access to the code, please check it out with svn as described in the code section.

The DEPRECATED legacy of the Gene Ontology project on SourceForge. Please see http://geneontology.org for current software and downloads.

OpenCV powered image stack analyser for data extraction and preparation. Can be used in conjunction with nanocalcFX. You can get sample data at the NISA homepage. Currently in pre-alpha state.

..., ...) 3. Evaluate statistical distributions of internal variables: a. single variable distributions (including the most relevant in the atomistic representation, e.g. PHI and PSI and a number of those for the Cα based representation) b. two variables correlations (including the PHI-PSI Ramachandran map and its equivalent in the Cα based representation) c. three variables correlations

The characterization of genomic sites is a major challenge in the understanding and exploitation of next generation sequencing data. Most genomic sites are represented by short, degenerated motifs with a scattered distribution and sometimes with biological function (ex: regulation of gene expression, splicing patterns or epigenetics signals). These motifs are associated with a huge amount of noise and thus, the development of a computational platform for accurate detection of genomic sites...

IDL specified API for manipulating and processing CellML 1.0 and 1.1. Includes C++ implementation. Accessible from a C++ program, or from any language for which a CORBA language mapping is available Also, a Java wrapper of the API is available.

This project is an implementation of an algorithm by J. Keijsper and R. Pendavingh. The goal of the algorithm is to construct a phylogenetic level-1-network that is consistent with a given set of quartets.

BMDExpress is a bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.

An assessmemt tool of sequence repeats for short read sequencing.

Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files

rNA is an aligner for short reads produced by Next Generation Sequencers

Web application to make user-friendly requests on large XML database. Tools to XML-ize large bodies of semi-formal texts (like floras). Computer-assisted specimen identification. Uses natural language processing, 2D/3D images analysis and generation.

OpenVista(R) is the open-source version of VistA, an enterprise grade health care information system developed by the U.S. Veterans Affairs and deployed at 1,500 global facilities. OpenVista is a registered trademark of Medsphere Systems Corporation

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.

Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.

Corra [BMC Bioinformatics 2008] is a computational framework & tools for discovery proteomics using label free LC-MS and ATAQS [BMC Bioinformatics 2011] is a computational framework & tools for validation proteomics using SRM LC-MS method.

gfit creates an interface between computational models and experimental data and provides tools for their analysis

This is bionically project.

FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.