The Janelia Automated Animal Behavior Annotator
The Janelia Automatic Animal Behavior Annotator (JAABA) is a machine learning-based system that enables researchers to automatically compute interpretable, quantitative statistics describing video of behaving animals. Through our system, users encode their intuition about the structure of behavior by labeling the behavior of the animal, e.g. walking, grooming, or following, in a small set of video frames. JAABA uses machine learning techniques to convert these manual labels into behavior detectors that can then be used to automatically classify the behaviors of animals in large data sets with high throughput. JAABA combines an intuitive graphical user interface, a fast and powerful machine learning algorithm, and visualizations of the classifier into an interactive, usable system for creating automatic behavior detectors. Documentation is available at: http://jaaba.sourceforge.net/
Choco is not hosted on sourceforge anymore. Please now visit http://choco-solver.org/ !
Cocoa/Objective-C chemical analysis and computation program; includes gas laws, solutions/solubility, stoichiometry, periodic tables, et alii.
jCharts is a 100% Java based charting utility that outputs a variety of charts. This package is ideal for displaying charts via Servlets.
Repository for open source software re-packaged into MSI packages for enterprise deployment.
Tail probability calculator for continuous random variable
A suite of Matlab functions that calculate the tail probability / cdf / pdf / quantile of linear combination of random variables in one of the following classes: (1) symmetric random variables with support on the real axis (normal, Student's t, uniform and triangular); (2) random variables with support on the positive real axis (chi-squared and log-Lambert W x chi-squared distributions; inverse gamma distribution is temporarily disabled due to numerical issues).
zimg generates png / jpeg images from arbitrary formatted 2-D ascii or binary data. zimg is a command line tool and suitable for rendering large amounts of 2-D data. zimg is highly configurable via command line switches and dynamically loadable objects.
TinyOS is an operating system for embedded sensors and networks. Versions 2.0 and later of TinyOS should be downloaded from www.tinyos.net.
An easy to use mathematical function graph plotter written in Python and GTK.
TMVA is a ROOT-integrated toolkit for multivariate classification and regression analysis. TMVA performs the training, testing and performance evaluation of a large variety of multivariate methods.
Zinnia is a simple and portable, and open source handwriting recognition system with Support Vector Machines.
extJWNL is a Java library to handle dictionaries in WordNet format.
extJWNL (Extended Java WordNet Library) is a Java API for creating, reading and updating dictionaries in WordNet format. extJWNL is an upgraded version of JWNL. The library features support for creating, editing and writing dictionaries; dictionary encodings, including UTF-8; Java generics; huge dictionaries; instance dictionaries and static singletone dictionary; Maven and more.
Java Kohonen Neural Network Library Kohonen neural network library is a set of classes and functions for design, train and use Kohonen network (self organizing map).
Data Plotting and Analysis for Science and Engineering
- Save and open a Work/Project (spf) file - Single fitting/ Batch fitting (user defined custom func) - Matrix to XYZ in Tool menu - Symbol plot: makers, curve, landscape, bar, etc. - Implemented a 3d surface plot (GLSurface) based on OpenGL (ScienPlot v1.3.2 and above) - ColorMap surface, trisurface, Pie, Polar plots, and 3D height field, 3dBar, scatter plots (under developing), and more - Column by column plotting/calculation - LaTex commands enclosed by $ symbols can be used for the labels in Graph - Accept txt(Text) and csv(Comma separated values) formatted data - Save, copy, print Graph - Use spread sheets to display data - Textboard to organize the results - Graphs in a publishable quality - Source codes based on: Python Numpy Scipy Matplotlib WxPython Visvis etc. - Special functions - Drag and drop data files - Python console is back (since v1.3.3), capable of reusing column data - Debye and Guinier models for SANS / SAX data - More apps in our Web below
The GPSD project has moved to Savannah in advance of Berlios's planned shutdown.
An automatic tool for binning metagenomics sequences
MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users could use MEGAN or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished. The most current version is 2.2.4. MaxBin was published on Microbiome journal (2:26)! Please cite the Microbiome paper if you use MaxBin in your work. More information can be found at the official MaxBin website: http://downloads.jbei.org/data/MaxBin.html to
The Trinity RNA-Seq Assembly project provides software solutions targeted to the reconstruction of full-length transcripts and alternatively spliced isoforms from Illumina RNA-Seq data.
Torch5 provides a matlab-like environment for state-of-the-art machine learning algorithms. It is easy to use and provides a very efficient implementation, thanks to a easy and fast scripting language (Lua) and a underlying C++ implementation.
OpenAI is dedicated to creating a full suite of highly interoperable Artificial Intelligence components that make the best use of today's technologies. Current tools include Mobile Agents, Neural Networks, Genetic Algorithms and Finite State Machines.
MSR Tools is a source code evolution analysis tool. It consists of a framework for mining software repositories and tools for metric calculation, visualization, defect prediction.
Matlab Toolbox for reading and writing videos.
Matlab Toolbox to process video files, which consists on a set of classes for reading, writing, correcting light changes and generating gaussian pyramids in real time. This toolbox is designed for Windows x64, Max OS X x64 and Linux x64. Through to use of Ffmpeg, it can reproduce and create videos very fast and also do no require to load the entire video file in memory. In addition the C++ code is already compiled in order to simplify the toolbox installation. In order to stay tuned for updates, you can follow the Matlab VideoUtils on Twitter (@VideoUtils): https://twitter.com/#!/VideoUtils If anyone is interested in collaborate, please contact to me -> https://sourceforge.net/sendmessage.php?touser=3811831
Scientific Visualisation Made Easy
The Simple Medical Imaging Library Interface (SMILI), pronounced 'smilie', is an open-source, light-weight and easy-to-use medical imaging viewer and library for all major operating systems. The main sMILX application features for viewing n-D images, vector images, DICOMs, anonymizing, shape analysis and models/surfaces with easy drag and drop functions. It also features a number of standard processing algorithms for smoothing, thresholding, masking etc. images and models, both with graphical user interfaces and/or via the command-line. See our YouTube channel for tutorial videos via the homepage. The applications are all built out of a uniform user-interface framework that provides a very high level (Qt) interface to powerful image processing and scientific visualisation algorithms from the Insight Toolkit (ITK) and Visualisation Toolkit (VTK). The framework allows one to build stand-alone medical imaging applications quickly and easily.
Java Disk Benchmark Utility
Simple Java utility to help bench mark disk IO. Benchmark is done by creating and reading data files to a user directory that can be configured. Suggestions would be very appreciated. https://gitlab.com/jamesmarkchan/jDiskMark/ Note: When doing a combined read and write operation the disk cache is not cleared automatically so the app must be restarted to avoid the cache from affecting read IO performance.
Volumetric image processing software
Plastimatch is an open source software for image computation. Our main focus is high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET).
DIS(IEEE 1278.1) Fully Implemented in C++
A complete open source implementation of DIS (Distributed Interactive Simulation) in C++. 1278.1 and 1278.1a are fully implemented including enumerations. Includes several utility classes to help with developing your DIS app. DIS 7 work is ongoing.