RSS 41 projects tagged "Bioinformatics"

Download Website Updated 26 Dec 2012 massXpert mass spectrometry package

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Pop 214.62
Vit 16.61

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.

Download Website Updated 30 Jul 2012 VULCAN

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Pop 59.24
Vit 8.40

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.

Download Website Updated 30 Jul 2012 ScalaBLAST

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Pop 38.46
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.

Download Website Updated 28 Jul 2012 NCBI C++ Toolkit

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Pop 49.23
Vit 5.08

The NCBI C++ Toolkit provides portable libraries and applications for assisting genetic science. These include libraries for networking, SQL and BerkeleyDB access, CGI and HTML handling, ASN.1 and XML handling, sequence alignment engines, sequence retrieval engines, BLAST database engines, FLTK and OpenGL graphics toolkits, and basic system utilities.

Download Website Updated 28 Jul 2012 MSAProbs

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Pop 17.72
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.

No download No website Updated 20 Jul 2012 REMITT

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Pop 52.48
Vit 4.16

REMITT Electronic Medical Information Translation and Transmission is a standalone electronic medical billing solution. It works independent of any specific electronic medical record (EMR) or practice management (PM) system, and can interface with any EMR or PM system that implements its API. The first system to do so is FreeMED.

Download Website Updated 15 Dec 2011 mcl-edge

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Pop 119.50
Vit 6.31

MCL-edge is an integrated command-line driven workbench for large scale network analysis. It includes programs for the computation of shortest paths, diameter, clustering coefficient, betweenness centrality, and network shuffles. A module for loading and analyzing gene expression data as a network is provided. The MCL algorithm is a fast and highly scalable cluster algorithm for networks based on stochastic flow. The flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure, which is revealed as the imprint left by the process. The threaded implementation has handled networks with millions of nodes within hours and is widely used in the fields of bioinformatics, graph clustering, and network analysis.

Download Website Updated 22 May 2011 Chemistry Development Kit

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Pop 113.98
Vit 11.45

The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.

Download Website Updated 06 Apr 2011 Raster3D

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Pop 53.83
Vit 3.72

Raster3D is a set of powerful tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm that is independent of any graphics hardware.

Download No website Updated 24 Feb 2011 Bioinformatics Benchmark System

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Pop 28.46
Vit 1.00

The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems. It is not trying to be the last word in informatics benchmarking, as there are simply too many codes, tests, data sets, and databases. The goal is to create a core of tests that all may download and use to probe specific elements of system performance. The end goal is to enable a pluggable set of tests, including the core tests, so that performance data may be gathered.

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kcov

A code coverage tester.

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Aspose.Words for .NET

A word processing component for .NET applications.