228 projects tagged "Bioinformatics"

Download No website Updated 14 Feb 2008 SMA

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Pop 13.78
Vit 1.82

SMA consists of a small collection of programs that perform different tests for association between genotypes at a single marker and a binary disease status.

Download Website Updated 14 Feb 2008 SNPfile

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Pop 18.25
Vit 1.82

SNPfile is a library and API for manipulating large SNP data sets with associated meta-data, such as marker names, marker locations, individuals' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPfile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols.

Download Website Updated 21 Mar 2012 CGAL

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Pop 106.77
Vit 3.56

CGAL, the Computational Geometry Algorithms Library, is a large C++ library of geometric data structures and algorithms such as Delaunay triangulations, mesh generation, Boolean operations on polygons, and various geometry processing algorithms. CGAL is used in various areas: computer graphics, scientific visualization, computer aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning, and numerical methods.

Download Website Updated 26 Dec 2012 massXpert mass spectrometry package

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Pop 207.70
Vit 16.07

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 17 Feb 2014 SHOGUN

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Pop 277.13
Vit 29.79

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.

No download Website Updated 27 Mar 2007 gfit

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Pop 9.59
Vit 51.17

gfit analyzes data using models. gfit lets the user create a model for virtually any type of system using a minimal amount of computer code. It is particularly useful for studying various systems in biophysics, biochemistry, and cell biology. The interface for gfit models specifies relationships between input and output variables in a rule-based fashion. It provides flexibility and allows the user to reuse same models for many related problems.

No download Website Updated 07 Mar 2007 xpress-analyzer

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Pop 17.66
Vit 51.37

xpress-analyzer is a suite of programs for analyzing functional genomics data. Programs are included for analysis of variance, multiple test correction for significance tests, a non- linear least square fitting algorithm (four parameters), general linear models, Kolmogorov-Smirnov distance, nearest neighbor algorithm, principal component analysis, and Student's t-test. It is intended to be used as a faster alternative to R on large data sets.

No download Website Updated 24 Feb 2007 PDB2PQR

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Pop 13.42
Vit 51.48

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.

No download Website Updated 24 Feb 2007 APBS

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Pop 23.62
Vit 51.48

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.

Download Website Updated 28 Mar 2007 ESTScan

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Pop 14.90
Vit 1.42

ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. It is not a gene prediction program, nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity.

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Open Camera

A camera app for Android.

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mcl-edge

A command-line network analysis workbench.