The main goal of this project is to develop new algorithms of machine learning and collect examples of existing methods. This collection pursues scientific and educational purposes.
Portable OS X FOSS applications
OS X FOSS portable applications are packaged so you can carry around on any portable device, USB thumb drive, iPod, portable hard drive, memory card, other portable device (or also on your internal hard disk), taking your preferences with you.
Building blocks for the renewable energy industry.
RenewNet Foundry is a repository for an integrated set of simulation components for system simulation of wind, wave and tidal energy systems.
Dynamics of quantum systems, controlled by external fields
WavePacket is a program package for numerical simulation of quantum-mechanical wavepacket dynamics for distinguishable particles. It can be used to solve one or more (i.e. coupled channels) time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can simulate modern experiments using ultrashort light pulses in photo-induced physics or chemistry, including optimal control. The extended graphical capabilities allow visualization 'on the fly', including Wigner transforms to phase space. WavePacket is especially suitable for teaching of quantum mechanics as well as for research projects in physics and chemistry, see also the numerous demo examples in the Wiki here. While the Matlab version is already in a stable and mature state, the C++ version is still under construction aiming at an object-oriented rewrite.
BioSig is a software library for processing of biomedical signals (EEG, ECG, etc.) with Matlab, Octave, C/C++ and Python. A standalone signal viewer supporting more than 30 different data formats is also provided.
The Multivariate Regression Composer, a Matlab toolbox. It generates a regression model of the optimal structure. Uses the source data set, the initial models and the primitive functions.
A Matlab toolkit for analyzing EEG/ERP datasets, especially PCA. If you run into a problem, please send me a note and I'll fix it. The tutorial is in the documentation folder and the tutorial data is a separate download (tutorial data.zip).
ReViSP, a 3D volume rendering MATLAB tool for multicellular spheroids
Reconstruction and Visualization from a Single Projection (ReViSP) tool: a 3D volume rendering method we developed to reconstruct the 3D shape of multicellular spheroids, besides estimating the volume by counting the voxels (3D pixels) fully included in the 3D surface. ReViSP is written in MATLAB (©, The MathWorks, Inc., Massachusetts, USA) and the source code is freely provided. Requirements for running ReViSP from the source code: MATLAB 2015a and Image Processing Toolbox 9.2 or later versions.
High-performance package for SemiDefinite Programs The software SDPA (SemiDefinite Programming Algorithm) is one of the most efficient and stable software packages for solving SDPs based on the primal-dual interior-point method.
Titan allows service-oriented processing of context recognition applications on Wireless Sensor Networks. It includes an execution environment developed for TinyOS and a Java ME (Personal Profile) Network Manager intended to be run on a mobile phone.
Obsolete project - archived at https://github.com/darrenleeweber/bioelectromagnetism This is a public release of a Matlab toolbox for working with data from electroencephalography (EEG/ERP) and magnetic resonance imaging (MRI). It contains functions to process and visualize ERP/MRI data and associated electrode positions.
This project aims to develop and share fast frequent subgraph mining and graph learning algorithms. Currently we release the frequent subgraph mining package FFSM and later we will include new functions for graph regression and classification package
EigenMS is a normalization method implemented in R (and older version in Matlab) available as a set of two functions that should be used in a sequence. Please download EigenMS.zip file (latest version). Latest version uploaded in October 2017 has a bugfix for single treatment group normalization. Rescaling has been omitted from 2015. EigenMS utilizes SVD to detect bias trends in the data and eliminates them. EigenMS eliminates effects from known and unknown factors and can be utilized for any -omic platform. We have shown its utility in LC-MS/MS and metabolomics in the following two papers: 1) PMID: 19602524. "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition". Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR. Bioinformatics 2009 2) "Metabolomics data normalization with EigenMS" Karpievitch YV, Nikolic SB, Wilson R, Sharman JE, Edwards LM. PLoS One 2014
GTK+iostream, Data plots, ORB, Neural Networks, WSOLA
Create GTK+ interfaces using IOStream style code. Its simple and quick! Also providing simple data plotting (similar to Matlab/Octave), ORB (Object Request Broker), and Neural Network computations. You can create GTK+ GUIs in a few lines of code. Labels<<"Thanks for reading"; (HBox<<Labels).show(); or even one line : (HBox() << (Labels()<<"Thanks for reading")).show(); Inline code destructs the classes, but leaves the widgets/callbacks operating. This is great for embedded memory saving code. You can also plot like so : Plot figure; figure.plot(x, y, x.size()); Plotting utilises GtkDataBox.sf.net ORB utilises www.zeroc.com Feed forward neural networks with different activation functions. Audio playback/recording and digital signal processing (DSP) - utilising Jack www.jackaudio.org
Projeny (Probablistic Networks Generator in Java) is a graphical (Java SWT) front-end to BNT (Bayes Net Toolbox for Matlab). Projeny requires BNT, JMatLink and a Matlab back-end. There is no installable release package, but source code is available on SVN - please check out from SVN to use Projeny. Projeny was started with BNJ as the base.
Hytool is a matlab toolbox for the interpretation of hydraulic tests in wells. The version on SourceForge is not maintained anymore. Please go to https://github.com/UniNE-CHYN/hytool to get the latest version.
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.
Motion library for steppers control through PLC
To automatically obtain mosaics of partially overlapping images.
MicroMos is an open-source software tool written in MATLAB (The MathWorks, Inc., Massachusetts, USA), for automatically obtaining mosaics of partially overlapped images, also manually acquired. It was designed for stitching microscopy images, but thanks to the many parameters available it works also for other types of images. For more details, please, read: a) F. Piccinini, M. Pierini, E. Lucarelli, A. Bevilacqua, Semi-quantitative monitoring of confluence of adherent mesenchymal stromal cells on calcium-phosphate granules by using widefield microscopy images. Journal of Materials Science: Materials in Medicine, 25(10):2395-2410, October 2014. 2) F. Piccinini, A. Bevilacqua, E. Lucarelli, Automated image mosaics by non-automated light microscopes: the MicroMos software tool. Journal of Microscopy, 252(3):226-250, December 2013.
All future developments will be implemented in the new MATLAB toolbox SciXMiner, please visit https://sourceforge.net/projects/scixminer/ to download the newest version. The former Matlab toolbox Gait-CAD was designed for the visualization and analysis of time series and features with a special focus to data mining problems including classification, regression, and clustering.
SparesPOP is a MATLAB implementation of a sparse semidefinite programming (SDP) relaxation method proposed for polynomial optimization problems (POPs). Please send a message to email@example.com if you have any question and/or request. We also release SparsePOPC++ and SparsePOPC++-windows. Both implementations are SparsePOP which does not use MATLAB, but only C++. In particular, SparsePOPC++-windows contains a binary file which works on Windows, and does not require to compile.
The mfBox is a Matlab toolbox for performing model-free analysis of multivariate data sets. It also plugs into SPM used for the analysis of multivariate brain recordings such as fMRI, SPECT and PET data sets.
A simple yet powerful mesh generator based on matlab/octave language, making finite-element mesh from surfaces or arbitrary 3D volumetric images (such as MRI/CT scans) with fully automatic workflows.
SoundRuler is a tool for acoustic analysis, graphing and teaching. It interactively recognizes and measures 35 temporal and spectral properties of each sound in a file. It also features several measurement, graphing and didactic modules.
A framework to run MATLAB programs as batch jobs. Features a structured input description, integrity constraints and GUI.Independent parts of a job can execute in parallel on a cluster computer. Developed at Freiburg Brain Imaging (FBI) - http://fbi.uniklinik-freiburg.de/