JAGS is Just Another Gibbs Sampler. It is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.
JabRef is a graphical application for managing bibliographical data
JabRef is a graphical application for managing bibliographical databases. JabRef is designed specifically for BibTeX bases, but can import and export many other bibliographic formats. JabRef runs on all platforms and requires Java 1.8 or newer.
ScadaBR is a SCADA (Supervisory Control and Data Acquisition) system with applications in Process Control and Automation, being developed and distributed using the open source model.
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team
open Transportation Control System
openTCS is a platform-independent transportation control system (TCS) intended to manage fleets of automatic guided vehicles (AGVs), but can be used to manage virtually any automatic vehicle. It consists of an abstract kernel that implements replaceable algorithms and strategies (computation of routes, dispatching of orders to vehicles, scheduling of resources etc.), pluggable vehicle drivers that implement communication protocols and a graphical frontend for creating and visualizing logical models of areas the vehicles are moving in.
jMetal is an object-oriented Java-based framework for solving multi-objective optimization problems with metaheuristics.
Portable Ubuntu Linux for Scientific Computing
Released August 22, 2013 Lubuntu Blends: Biochemistry 13.04 (Raring) v5.44 Linux Kernel Image 3.8.0-29 Lubuntu Blends are pre-installed Wubi disk image remixes of Ubuntu and Debian Science meta packages, A custom boot loader allows installations to be copied and automatically booted from most external or USB flash drives. Once up and running, use earlier Lubuntu Remix README instructions here until documentation is updated. https://sourceforge.net/projects/portable-linux/files/ Installation 1. Download the Wubi installer http://releases.ubuntu.com/saucy/wubi.exe 2. Install any flavor of Ubuntu. 3. Swap out the root.disk with the ones provided here. Overview LAMP stack running on localhost (127.0.0.1). Scientific, productivity & media packages include R (Rattle Data Miner), GridEngine, Condor, cooperative computing tools, WINE, LibreOffice, Evolution, Clinica, Neuro Debian Desktop, PsycoPy, OpenVibe, 3DSlicer, Paraview, Openshot. Cheers, Gregory Remington
Zocalo is a toolkit for building Prediction Markets, markets in securities that pay out depending on outcomes of future events. A prediction market can provide estimates of the likelihood of specific outcomes that are more reliable than other sources of
HaploView is a Java based tool for use by biologists in the study of genetic haplotype data. It provides a quick, easy interface to many common tasks involved in such analyses. Please go to the homepage below for the latest version!
FusionCharts Free is a flash charting component for web applications, desktop applications and presentations. It livens up your boring data by converting it to animated and interactive charts.
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.
The Open Modeling Interface and Environment (OpenMI) defines a standardized way to exchange data between computational models that run simultaneously. OpenMI aims to enhance process interaction representation in integrated environmental modelling.
Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
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
TagCentric is RFID middleware that controls heterogeneous RFID devices and gathers RFID-related data into a user-specified database. It's cost (free!) and simplicity make it ideal for use by small businesses, RFID testing facilities, and universities.
Mathematics, linear algebra and optimisation
oj! Algorithms - ojAlgo - is Open Source Java code that has to do with mathematics, linear algebra and optimisation; particularly (but certainly not exclusively) suitable for the financial domain.
TNV visualizes pcap data to graphically depict network packets, links, and ports for network traffic analysis to facilitate learning what constitutes 'normal' behavior, investigating security events, or network troubleshooting.
Stop to rack your brain, start using process-oriented decision tables!
This tool is about a method called "process-oriented decision tables". It fixes all flaws of traditional decision tables making it a joy to work with. But they keep all benefits of traditional decision tables. First of all they present the logic in a very dense form. 1. Explore all possible combinations of conditions and actions by question-and-answer. 2. Have a compact one-sheet-view on complex logic. 3. Have abandoned combinations documented. 4. Make sure that your decision table is (formally) neither incomplete nor inconsistent with one click. And the mathematics behind it is very easy and well documented ;-) 5. Get the test cases necessary to test your piece of logic with one click. 6. Other than in traditional decision tables, you can mix conditions and actions. => Stop to to rack your brain - start using process-oriented decision tables! <=
Java SDK useful to develop handwritten signature verification app
Handwritten Signature SDK supports: dynamic time wrapping (DTW), extended regression (ER), signature sampling, direction hash and features extraction: see wiki for more info.
A simulator for biological and physiological models
Flint is a simulator for biological and physiological models written in PHML and SBML.
The Network Camera Tool is a collection of various Java tools that work with cameras and encoders from Axis Communications. Please see the project website http://imagelogistix.sourceforge.net for more details.
Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. The command line tools of Hadoop-BAM should be understandable to all users, but they are limited in scope. See the SeqPig project for a higher-level interface to the file formats supported by Hadoop-BAM: http://seqpig.sourceforge.net See Seal for Hadoop-based read alignment tools, Seal: http://biodoop-seal.sourceforge.net
The Video Annotation and Reference System (VARS) is a software interface and database system that provides tools for describing, cataloging, retrieving, and viewing the visual, descriptive, and quantitative data associated with video.
The Rossum Project is an attempt to collect and distribute robotics software. We are seeking help with our first project, a mobile-robot simulator featuring a 2-D virtual world, and new work including artificial intelligence and robot-control logic.
A treemap visualization java library, to implement Shneiderman's treemap easily (http://www.cs.umd.edu/hcil/treemaps/). Shows efficiently tree data as a rectangle colored map. Usefull to monitor thousand of files in a little window.