Search Results for "molecular"
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Showing 15 open source projects for "molecular"
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CGAL
The Computational Geometry Algorithms Library
CGAL or the Computational Geometry Algorithms Library is a C++ library that gives you easy access to a myriad of efficient and reliable geometric algorithms. These algorithms are useful in a wide range of applications, including computer aided design, robotics, molecular biology, medical imaging, geographic information systems and more. CGAL features a great range of data structures and algorithms, including Voronoi diagrams, cell complexes and polyhedra, triangulations, arrangements of curves, surface and volume mesh generation, spatial searching, alpha shapes, geometry processing, and many more. ... -
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Optimizer_sovkov
Constructing and optimizing general mathematical and physical models
...Many of these programs are already available along with the main package. Currently, the main focus of these is computational quantum mechanics, analysis and simulation of molecular spectra, and general-purpose approximants. The package provides the most reliable modern strategies for linear and non-linear model optimization, regularization, and hypothesis tests. Parallel computing is supported. -
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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MORPHE
MORphological PHenotype Extraction
MORphological PHenotype Extraction (MORPHE) is a suite of automated image processing, visualization, and classification algorithms to facilitate the analysis of heritable and clonal red-to-green transitions that occurred during the growth of a colony. -
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allink
Software for data analysis, image processing, simulations, solver.
...VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all the operation of Matematica on different sets of data visualized on a Qt graphical interface. DrImage) image manipulation on the Matematica filters. The program is intended to use as less as possible external libs (optional: openGL, gsl, fftw, cgal, png, tiff, boost, MPI, Qt...). -
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StochDecomp
User Manual describing theory behind the package, installation instruc
Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise enters and propagates in biochemical systems provided us with nontrivial insights into the origins of stochasticity, in total however they constitute a patchwork of different theoretical analyses. Here we present a flexible and generally applicable noise decomposition tool, that allows us to calculate contributions of individual reactions to the total variability of a system’s... -
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QTASEP
Visualization application for various TASEP, ASEP and SSEP models.
Visualization of TASEP, ASEP, SSEP models with various update rules based on Zarja simulation library using QT GUI library. -
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gfit creates an interface between computational models and experimental data and provides tools for their analysis
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SpecMark (spectral Markov) is a method for calculating the joint probability distribution over species in a regulatory network.
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Develop a basic understanding of the behavior of polar spherical coordinates through selected examples. Provide sample files for diverse mathematics engines
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Little b is a Lisp-based language which allows scientists to build shareable, reusable mathematical models of complex systems based on shared parts. The initial focus is molecular and multicellular networks. Project web page: http://www.littleb.org
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GLARE is a library and a software for product based optimization of reagent lists in the context of a chemical combinatorial library design. Large virtual combinatorial libraries containing 10^12 products have been optimized within a second.
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ĄHola!, for "Hordes of Little Atoms," is a project to develop a lean, modular, scalable toolkit for massive simulations of particle (molecular) dynamics. It is written in C and Python to get the best balance between programmer and run time.
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