Computational

PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that 'simple things should be simple'. It should be possible to write one-liners that use this toolkit to do meaningful 'molecular munging'.

A computational tool to discover location of promoter consensus sequences in bacterial genomes.

The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.


Platforms: Mac, Solaris, Linux

R Tools for Biologists (RT4Bio) is a multi-functional package writen in R language developed in the Laboratory of Behavioral and Computational Ecology at State University of Montes Claros - MG - Brazil. Formerly known as RRJ.


Platforms: Windows, Mac, Linux

This is a multi-threaded Java program that tries to maximise CPU utilization by separating and distributing the computational part of the work from the file reading and writing part by using separate threads.


Platforms: Windows, Mac, Linux

The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.


Platforms: Windows, Mac, Linux

The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes.


Platforms: Windows, Mac, Linux

The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.


Platforms: Windows, Mac, Linux

Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.


Platforms: Mac, BSD, Linux

MacMolPlt is a Chemistry visualization tool that can be used to build molecules with an integrated graphical model builder, create input files for the GAMESS computational chemistry program, and then visualize the results of computational chemistry runs. Features include a high-quality 3D...


Platforms: Mac

This application is a computational holography program.It generates diffraction patterns for 2-D images.


Platforms: Windows, Mac, *nix, C/C++, BSD Solaris

GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.The code is written entirely in C with an object-oriented approach based mostly on the design...


Platforms: Windows, Mac, *nix, C/C++, BSD Solaris

This is the 2-D Fast DOST Decomposition. The computational complexity is O(NlnN)


Platforms: Matlab

MGWT: Identification of protein coding regions using the ModifiedGabor-wavelet transform.Sequence of test:F56F11.4.fasta (included into the zip file)http://www.ncbi.nlm.nih.gov/entrez/viewer....de&val=AF099922http://www.vision.ime.usp.br/~jmena/projec...ome_results/F5/References:[1] J. P....


Platforms: Matlab

the current version includes: hwt.m: harmonic wavelet transform whwt:windowed harmonic wavelet transform Gabor_wt: Gabor wavlet transform test_simple.m: phase estimation on needed frequency band by windowed harmonic, Gabor methods, with comparison to Hilbert transform followed by the...


Platforms: Matlab

Simulate a time dependent solution of Schrodinger's equation and calculate energy spectrum of a 1D finite square well using split-operator method.Reference: M. D. Feit, J. A. Fleck, Jr., and A. Steiger, "Solution of the Schrodinger Equation by a Spectral Method", Journal of Computational Physics...


Platforms: Matlab

A computational method for quantitative analysis by multiwavelength absorption spectroscopy, called the Tfit method, based on fitting a model of the instrumentally-broadened transmission spectrum to the observed transmission data. It has the advantages of wider dynamic range and greatly improved...


Platforms: Matlab

GloptiPoly is a MATLAB/SeDuMi add-on to build and solve convex linear matrix inequality (LMI) relaxations of the (generally non-convex) global optimization problem of minimizing a multivariablepolynomial function subject to polynomial inequality, equality or integer constraints.The software...


Platforms: Matlab

Based on the concept of the Taylor Table given in Fundamentals of Computational Fluid Dynamics by Lomax, Pulliam, and Zingg.Given the terms of the point operator, "TaylorTable" will determine the coefficients of the terms which minimizes the Taylor series error. It will also determine the Taylor...


Platforms: Matlab

This package is created with the highly appreciated theoretical help and under the supervision of Prof. DSc. Ketty Peeva.Theoretical results and methods can be found in:1. B. De Baets, Analytical solution methods for fuzzy relational equations, in the series: Fundamentals of Fuzzy Sets, The...


Platforms: Matlab