Erudite is an application for training and testing back propogation neural networks using the ANNeML (Artifical Neural Network Markup Language) XML format. It supports testing and training neural nets with CSV files and has support for randomized training sets, optional adapting learning rate, sigmoid or hyperbolic tangent transfer functions, optional bias and weight adjustment locking, and more.
Salad (short for Letter Salad) is an efficient and flexible implementation of the well-known anomaly detection method Anagram by Wang et al. (RAID 2006). Salad is based on n-gram models, that is, data is represented as all of its substrings of length n. During training these n-grams are stored in a Bloom filter. This enables the detector to represent a large number of n-grams in little memory and still being able to efficiently access the data. Salad extends Anagram by allowing various n-gram types, a 2-class version of the detector for classification, and various model analysis modes.
Mokka (MOtion Kinematics and Kinetics Analyzer) is a software solution for analyzing biomechanical data. It reads and writes C3D files and many other file formats, and allows you to visualize marker trajectories in 2D and 3D, and force platforms, segments, joint angles, forces, moments, and analog signals like EMGs.
Biomechanical ToolKit (BTK) is a cross-platform library for biomechanical analysis. It can read and write a large variety of file formats used in biomechanics, and can modify them. All these operations can be done with the C++ API or with the wrappers included (Python, Octave, and Matlab). The goal of this project is to help the community share data without the restriction of the file format or the biomecanical model provided by the manufacturer of the acquisition system.
FreeFuzzyTime is a time reasoner based on Fuzzy Temporal Constraint Networks (FTCN), which treats fuzzy temporal information efficiently. It can be integrated into applications for diagnosis. This is especially important in areas like Intensive Care Units, where patients' data are handled by a temporal database. FuzzyTime uses a structure which consists of three levels of abstraction. The upper layer is the user interface, where a translator transforms the expressions introduced by the user into temporal relations between temporal entities (points and intervals). The semantics of a user’s expressions are analyzed and stored in the intermediate layer, or temporal world. Finally, the bottom layer is based on the FTCN model.
Open Grid Scheduler/Grid Engine is a batch-queuing system for distributed resource management. It is used by many high-performance clusters and computation farms. Together with basic batch job scheduling, it supports advance reservation, array jobs, parallel make, parallel job management, and GPU management.
openEMS is an electromagnetic field solver using the FDTD method. It employs a fully 3D Cartesian and cylindrical coordinate graded mesh. Matlab (or Octave) is used as an easy and flexible scripting interface. Advanced Features include: multi-threading, SIMD (SSE), and MPI support for high speed FDTD.
openPLM is a Web-based Product Lifecycle Management (PLM) application. It provides a configuration management system that manages all kind of files and data as documents in a product structure. It supports documents, parts, BOMs, part-document links, electronic signatures for objects, revision management, check in and check out for all files, plain text search using the Xapian engine, navigation between objects using Graphviz, and user management that allows sponsorship, delegation, and rights. Plug-ins are available for Thunderbird, OpenOffice/LibreOffice, FreeCAD, and Gedit.
The Scalable Assembler at Notre Dame (SAND) replaces the early stages of the Celera Assembler with scalable versions that can run on collections of commodity computers. By harnessing clusters, clouds, grids, or just random machines in your office, many bioinformatics tasks can be reduced from weeks or months down to minutes or hours.