Database connection pool with support for lots of languages and databases.
A multimedia authoring and processing framework and a video playout server for television broadcasting.
Autopsy® is a digital forensics platform and graphical interface to The Sleuth Kit® and other digital forensics tools. It can be used by law enforcement, military, and corporate examiners to investigate what happened on a computer. You can even use it to recover photos from your camera's memory card.
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj
Crystal Space is an Open Source 3D SDK for Unix, Windows, and MacOS/X. It renders with OpenGL and features GLSL shaders, CG shaders, deferred rendering, dynamic shadows, bullet based physics library, terrain engine, skeleton based animation meshes, exporter for Blender, portals, etc...
WideStudio is an Integrated Development Environment (IDE) for building window applications in C++, Ruby, Python an Perl for Windows, MacOSX, Linux, FreeBSD, SOLARIS and other unix and BTRON and T-Engine. This is open and free (under MIT/X Consortiun Lice
A national virtual bridge engineering contest for kids of all ages.
**Unfortunately, the Bridge Contest is no longer operational. We hope the code base will be of use to others with similar projects in mind.** A national virtual bridge engineering contest with prizes for middle and high school kids, grades 6 to 12, but anyone can enter for fun. Based on the award-wining Bridge Designer client software, now open source through this project. Web site infrastructure supports worldwide participation in qualifying and semifinal rounds with a tiny administrative staff. The new Rails back end is a RubyMine project. Thanks to JetBrains for this mega development environment!
Digital Library Software
Greenstone is a complete digital library creation, management and distribution package created and distributed by the New Zealand Digital Library Project. There are two major versions of the software. Greenstone 3 is under active development, and is recommended for download. We also provide maintenance releases for its forerunner, Greenstone 2. Featured download not what you're looking for? Click "Browse all files" to access binaries and source releases of both versions.
A reference implementation of the Polish geobotanical grid
This project is a reference, open source implementation of the coordinate conversion algorithms for the Polish geobotanical grid called ATPOL.
Simple Scientific Workflow System for CAGE Analysis
Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project. MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. MOIRAI package comes with three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples.
This package collects and displays Oregon Scientific weather data.
WxTools (Weather Data Tool Suite) is a collection of software for collecting and displaying weather data from Oregon Scientific weather stations (though the code could be generalised for other weather data sources). The software works with the Oregon Scientific WMR180 weather station (and probably also similar models such as the WMR88 and WMR100) as well as the older WMR928. Sample weather data is provided.
The Software Testing Automation Framework (STAF) is a framework designed to improve the level of reuse and automation in test cases and test environments. The goal of STAF is to provide a complete end-to-end automation solution for testers.
A system for synchronizing Powerpoint slides (or other content) and Quicktime video for both live and archived display.
EPIC is an opensource Perl IDE for the Eclipse platform. Features supported are syntax highlighting, on the fly syntax check, content assist, perldoc support, source formatter, templating support, regular expression plugin and a Perl debugger.
Dictionnaire is an open-source French-English dictionary intended to cover modern phraseology as well as entries that are difficult to translate using traditional dictionaries.
Variations is a digital music library software system that provides online access to streaming audio and scanned score images with a flexible access control framework to ensure respect for intellectual property.
Human protein similarity network used to predict drug safety.
This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do not hesitate to contact us in the forum or by email. Please see the original manuscript: Lopes, TJS, et al. (2015) - "Identifying problematic drugs based on the characteristics of their targets" - Frontiers in Pharmacology doi: 10.3389/fphar.2015.00186
A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions
Our goal is to create a publicly available supporting architecture and design manifesto for an MMORPG. Eventually the design will be used as the basis for an Open Source MMORPG.
A neuroscientific knowledge management system for the published literature
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes.
Digital Library Software
This project has been merged with the main Greenstone project. Please visit https://sourceforge.net/projects/greenstone/ to download the latest version of Greenstone 3. Greenstone 3 is a complete redesign and reimplementation of the Greenstone digital library software, which facilitates digital library creation, management, and distribution. Created and distributed by the New Zealand Digital Library Project.
Pretty Damn Quick (PDQ) analytically solves queueing network models of computer and manufacturing systems, data networks, etc., written in conventional programming languages. Generic or customized reports of predicted performance measures are output.
A combination of useful tools for High School classes, including math classes ranging from prealgebra to calculus, and science classes ranging from IPS to AP Physics.
Opentick is a financial market data service which provides a suite of API's for connecting market data to custom software applications.