A file format for exchanging computational models in systems biology
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.
IRBEM-LIB provides routines to compute magnetic coordinates for any location in the Earth's magnetic field, to perform coordinate conversions, to evaluate geophysics/space-physics models, and to propagate orbits in time.
A symbolic framework for C++, Python and Octave implementing automatic differentiation by source code transformation in forward and reverse modes on sparse matrix-valued computational graphs.
CoRoPa stands for Computational Rough Paths. The aim of CoRoPa is to provide a software framework for various ideas related to Rough Path Theory, including rough differential equations and the digital description of serial data streams.
A framework for the Automatic Control systems investigations for Matlab/Octave. Includes Gurvitz, Raus, Nikvist, Mihailov stability kriteries.
MEX/JNI is a set of bindings between MATLAB and Java using Mathworks' External Interface API and Java Native Interface (JNI).
A cross-platform library that computes fast and accurate SIFT image features. libsiftfast provides Octave/Matlab scripts, a command line interface, and a python interface (siftfastpy). Optimized with SIMD instructions and OpenMP .
SegyMAT is a set of Matlab/Octave m-files to read and write SEG Y data following SEG Y Revision 0 and 1
lasYmat provides a set of Matlab routines for reading and writing LAS files. LAS is a world wide Oil & Gas industry standard for distribution of Well Log data.
QLib is a Matlab package providing the Quantum Information Theory community with the tools needed to efficiently frame questions, explore them, form intuitions via visualizations and rule-out or validate hypothesis through the use of optimization
TIM is a cross-platform C++ library for efficient estimation of information-theoretic measures from continuous-valued time-series' in arbitrary dimensions. It has a Matlab interface as well as a console interface.
Image Acquisition Dynamic Link Library for Matlab and C/C++. It is free acquisition tool for those who has no money for MATLAB(R) Image Acquisition Toolbox and want to capture images from FireWire cameras. It is based on CMU driver.
This is a universal interface for various functions and programs, mathematical or any others.
math lib for .NET. n-dim arrays, complex numbers, linear algebra, FFT, sorting, cells- and logical arrays as well as 3D plotting classes help developing algorithms on every platform supporting .NET. Sources from SVN, binaries: http://ilnumerics.net
Locally Weighted Projection Regression (LWPR)
Locally Weighted Projection Regression (LWPR) is a fully incremental, online algorithm for non-linear function approximation in high dimensional spaces, capable of handling redundant and irrelevant input dimensions. At its core, it uses locally linear models, spanned by a small number of univariate regressions in selected directions in input space. A locally weighted variant of Partial Least Squares (PLS) is employed for doing the dimensionality reduction. Please cite:  Sethu Vijayakumar, Aaron D'Souza and Stefan Schaal, Incremental Online Learning in High Dimensions, Neural Computation, vol. 17, no. 12, pp. 2602-2634 (2005).  Stefan Klanke, Sethu Vijayakumar and Stefan Schaal, A Library for Locally Weighted Projection Regression, Journal of Machine Learning Research (JMLR), vol. 9, pp. 623--626 (2008). More details and usage guidelines on the code website.
Inter University Multi-Modal Imaging
SB:M/O is a cross-platform toolbox for systems biology. It fully supports both Matlab and the open source alternative, Octave. The aim is to make it easy for the systems biology community to develop new, portable systems biology solutions.
wiccoder is an open source cross-platform lossy image compression codec. Its main idea is to cut brunches of wavlelet transformation tree.
Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.
The Matlab SRTM Library is designed to be an easy-to-use interface for importing and manipulating NASA's Shuttle Radar Topography Mission (SRTM) Digital Elevation Model (DEM) dataset.
A library for fast computation of Gauss transforms in multiple dimensions, using the Improved Fast Gauss Transform and Approximate Nearest Neighbor searching. This library is useful for efficient Kernel Density Estimation (KDE) using a Gaussian kernel.
PopED (Population Experimental Design) is a software tool for computing optimal experimental designs. The software has been developed with an emphasis on drug trials based on population models (non-linear mixed effects models).
TKK Voice Source Analysis and Parametrisation Toolkit (Aparat) is a flexible software package and a graphical user interface for glottal inverse filtering and parametrisation of the voice source.
An evaluation framework for assessing contours generated by segmentation algorithms acting on cardiac magnetic resonance (MR) images. These contours are important for clinical assessment of left ventricular volume and mass.
<Temporarily Unavailable Online> This project is aiming at completing a library of open codes (mainly based on MATLAB at present) to deal with Dipoles-Cavity Interaction problems. Common methods, including Green's function method and Master Equation method et al, will be applied to the coding. Samples of calculations and standard comparison with publications using the library will be given for demonstration of the usage. Interface to some commonly used software, such as Lumerical FDTD Solutions, will also be developed in the project. This project is titled under nanophotonics, quantum optics, nano-optics, computational physics and physics.