Lattice Miner is a data mining prototype for creating, visualizing and exploring concept (Galois) lattices. It allows the generation of formal concepts and association rules.
The MML Framework is a temporal-spatial biological model representation language. The MML Project provides the application tool set which facilitates the goals of representing biological models using the MML specifications.
One of the fastest parallel short read assemblers for large genomes.
PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. Moreover, PASHA achieves the fastest speed for all three datasets on a single CPU. For the human genome, PASHA achieves competitive assembly quality with ABySS and is able to complete the assembly in about 21 hours, which is about 2.38× faster than ABySS on the same hardware configurations.
Simple CAD program
SAMoCAD - its program to create simple drawings, partially supports DXF. Main features: - create simple objects (line, arc, circle) - create complex objects (text, dimensions) - edit drawn objects - save drawing to SVG format - output drawing in PostScript format - export/import content DXF files (primitives LINE, CIRCLE, ARC, TEXT, DIMENSION) Program written in Python 2 and use the library Tkinter. Program requires no installation, but you need install Python 2.7 or later on your PC. Run file SAMoCAD.pyw to run the program. Its very old version of program!!! For more information see
Framework for Agent-oriented MOdelling and Simulation
Famos is a Java-based framework for developing agent-based models. It uses the discrete-event simulation framework Desmo-J (http://desmoj.sourceforge.net) as its simulation engine. Famos implements event-driven time advance and focusses on supporting an explicit model of space for the environment, including the movement of agents. Famos was developed in the context of a PhD project. Many aspects of its implementation are therefore still in the prototype stage. It does come with two example models (a re-implementation of Schelling's segregation model and of Epstein and Axtell's Sugarscape model). Famos
The goal of the OSM2PostGIS project is to develop an OpenStreetMap data processor that can import any amount of .osm XML data into a PostGIS database, and produce evaluated navigation network topologies to support routing.
This is a collection of (hopefully) useful productivity enhancements of Mentor Graphics IC-Station tools
Singularity is a suite of RFID Middleware to support RFID enabled Supply Chain Management, integration to the enterprise, and EPCglobal. It includes edge services for device management, event filtering, workflow, as well as integration components.
Pure Java Fuzzy API
Nebular is a fuzzy logic API written in Java. It is written in pure Java and comprehends fuzzy logic, fuzzy sets and operations, fuzzy control, decision support, type 2 fuzzy logic and type 2 fuzzy intervals.
xFunc allows you to build mathematical and logical expressions.
xFunc is a simple and easy to use application that allows you to build mathematical and logical expressions. It's written on C#. This project consists two libraries and an execution file. The libraries include the code that converts strings to expressions.
Library of Java code to interact with the data-recording formats (RPFITS and PSRFITS) used at the Australia Telescope National Facility (ATNF). It also provides tools for extracting metadata from the files for supply to Virtual Observatory instances.
Data Visualization application written in JavaFX, Groovy, and HTML5.
Data Explorer, or Dex is a tool for exploring data. Dex is a JavaFX application which aims to provide a general purpose framework for data visualization. The basics are easy to learn, however Dex offers advanced capabilities in the form of SQL and groovy transformations. Dex integrates many excellent visualization frameworks into one consistent GUI package. This is an early release, so you are likely to find functional gaps for your particular problem space. In such cases, you are free to extend Dex to suit your needs.
Expression4J (Math Expression Parser) is a java framework used to manage mathematic expression stored in String object like "f(x,b)=2*x-cos(b)" or "g(x,y)=f(y,x)*-2". Expression gramar can be define by user (add new operator or type ...)
Accurately predicts disease association of single nucleotide mutations
GESPA (GEnomic Single nucleotide Polymorphism Analyzer) is a bioinformatics tool for classifying Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs). GESPA predicts if a nsSNP is pathogenic using reports from literature and various algorithms to assess conservation in orthologous and paralogous protein alignments. Using reports from literature, GESPA is also able to predict the phenotype of a nsSNP with high accuracy. The software can be used clinically to determine if observed nsSNPs are associated with disease. A host of annotations are provided: orthologous and paralogous multiple sequence alignments, UCSC annotations, reports detailing conservation of a nsSNP in alignments, and links to external nsSNP and gene information such as relevant publications. GESPA is connected to a constantly updating SQL server allowing for fast data retrieval. NOTE: REQUIRES Java 1.7.0+. Port 1433 cannot be blocked by firewall, network, or antivirus program. Please cite: http://tinyurl.com/oj7p84a
Linking Language to Knowledge with Distributional Semantics
JobimText is a software solution for automatic text expansion using contextualized distributional similarity. It provides text analysis tools for large corpora and has capabilities to create distributional semantic models (JoBimText models) and multi-word expressions.
Tile Cache Server
Tila (TIles on LAn) is a java tile map cache server. Tila will solve performance problems in applications using a map tile server by storing the tiles on your LAN. Tila is still on development but downloable versions are usable. For version 0.1.2 Tila support the folowing caches: - Google Maps - Open Street Map - TMS (OSGeo Tile Map Service) - WMS (OGC Web Map Service) - WMTS (OGC Web Map Tile Service) - Virtual Earth The management web application lets you to easily configure the tile caches.
The fastest Smith-Waterman protein database search algorithm on GPUs
CUDASW++ software is a public open source software for Smith-Waterman protein database searches on Graphics Processing Units with CUDA. This software have been added to the NVIDIA Tesla Bio Workbench (http://www.nvidia.com/object/swplusplus_on_tesla.html
Cybervision is a 3D reconstruction software for SEM images
Project has moved Github at https://github.com/zlogic/cybervision Cybervision is a 3D reconstruction software for SEM images. It's an abandoned project, but can be useful as a working example for many, many technologies, such as: * Qt (including threads, vectors, graphics and OpenGL) * Eigen library (http://eigen.tuxfamily.org/) * libsift library (https://sourceforge.net/projects/libsift/) * OpenCL and of course, 3D reconstruction in general.
TCAD Device Simulator
TCAD Device Simulator. DEVSIM is a semiconductor device simulation software, using the finite volume method. This software solves partial differential equations on a mesh. The Python interface allows the user to specify their own equations.
A simple Web Scraper using Regular Expression or Html Agility
JAWS or Just Another Web Scraper, is part of the Data Scraping Softwares developed by SVbook, alongside JATI (Image to Text) and JAVT (Video to Text). JAWS offer easy interface to scrape data from the website using regular expression, text preprocessing, or HTML Agility Pack.
A bridge from Java to Octave, useful if you want to do some Octave calculations from inside a Java application.
Pulga is a program for numerical simulation of dynamical systems designed to provide students and researchers an easy way to model and qualitatively analyse their systems on a computer without the difficulty of traditional computer programming languages.
Visual Environment for Remote Virtual Exploration
Visual Environment for Remote Virtual Exploration
X-RIME is a open source project devoted to provide Hadoop based solution for large scale social network analysis.
Common accessible environment for system dynamics simulation.
The Sphinx project is dedicated to create common accessible environment for system dynamics simulation. This software is developed on Java 6 platform and use Java Swing GUI.