Open Source Java Medical Software

dcm4che is an implementation of DICOM and IHE actors in Java. Homepage: http://www.dcm4che.org, Google Group: http://groups.google.com/group/dcm4che?hl=en, Wiki: http://www.dcm4che.org/confluence, Issue Tracking: http://www.dcm4che.org/jira

OpenMRS is a community-developed, open source, enterprise electronic medical record system. Our mission is to improve health care delivery in resource-constrained environments by coordinating a global community to creates and support this software.

This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s. BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file. ...and more!

Grassroots DiCoM is a C++ library for DICOM medical files. It is accessible from Python, C#, Java and PHP. It supports RAW, JPEG, JPEG 2000, JPEG-LS, RLE and deflated transfer syntax. It comes with a super fast scanner implementation to quickly scan hundreds of DICOM files. It supports SCU network operations (C-ECHO, C-FIND, C-STORE, C-MOVE). PS 3.3 & 3.6 are distributed as XML files. It also provides PS 3.15 certificates and password based mecanism to anonymize and de-identify DICOM datasets.

The HAPI HL7v2 project has moved to the following home: https://hapifhir.github.io/hapi-hl7v2/

The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io

Taverna is *no longer* hosted on SourceForge, but has moved to the Apache Software Foundation: https://taverna.apache.org These pages and mailing list archives are provided for *archival purposes* for older Taverna 1.x releases. See https://taverna.apache.org/download/ for the latest releases from Apache Taverna.

Integrated Hospital Information System. PHP,mySQL,PostgreSQL. Surgery, Nursing,Outpatient,Wards,Labs, Pharmacy, Security,Admission,Schedulers, Repair, Communication & more. Multilanguage, WYSIWYG forms, userconfig, embedded workbots. Modular & scalab

Image Restoration and Inpainting: MinGW/OpenGL/Visual c++/Java image processing enhancing/restoring/detecting/recovering image parts(Old painting cracks...) FastRestorarion, 2D (Un)Splitted Linear Solver, nonlinear solver: conjugate gradient,QuasiNewton

Radiation detection and measurement education is necessary for a wide variety of people working with radiation. The equipment and laboratory setup needed for delivering this education are expensive and difficult to assemble due to the large variety of the type of experiments that are desirable to cover. For a basic education one needs to have gamma, beta, alpha and neutron sources, at least one detector to detect each type of radiation and other supplemental instrumentation to perform experiments. Although the radiation exposure due to these radioactive sources in an education laboratory is low, shielding and a private secured place is needed. Nearly two hundred thousand dollars is needed to construct such a basic laboratory described as above. In order to overcome these difficulties, a model of a basic Radiation Detection Laboratory has been created to provide a virtual environment for designing and simulating such experiments. Team: Dagistan Sahin, Muzaffer Sena Sahin, Korcan Kayrin

Life Science Identifier (LSID) resolution protocol, to locate biologically significant data over a network, within middle-ware providing a client A.P.I. for Life Science applications, and server software, for Industry data providers.

The HL7 Inspector project has moved to Bitbucket. https://bitbucket.org/crambow/hl7inspector All new releases can be found there. The web-based version can still be found at www.hl7inspector.com

CleverPsych is FREE software for psychologists and other allied health professionals who run their own practices. We have been using CleverPsych in our own practice in Australia since 2007. The system enables you to record your clients, appointments, services, organisations and referring doctors. The aim is to make operations like generating standard letters, claiming from the government and insurance companies, and reporting income, much easier. LOOK in the Files tab for DOWNLOAD and INSTALLATIONinformation. Download and execute CleverPsych.exe on Windows, otherwise you must download,unzip CleverPsych.zip to ~/Downloads/CleverPsych and run a script. Look at the CleverPsych demonstration videos on Youtube and read the manual. The web site can also be accessed below. Mail me at cleverco@users.sourceforge.net . Alternatively use the Discussion tab or post a ticket for problems. Runtime error messages appear in the terminal window; you can mail a copy to me

niftilib is a collection of i/o routines for the nifti1 neuroimage data format. C (nifticlib), Java (niftijlib), Matlab (niftimatlib), and Python (pynifti) code is available. For nifti format info see: http://nifti.nimh.nih.gov/

An Eclipse RCP program for all aspects of a medical practice: electronic medical record (EMR), laboratory findings etc., as well as accounting, billing (swiss TARMED-System, other systems to be developped) and other daily work. A fully functional version may be downloaded via http://download.elexis.info/3.1.0. Users may optionally include a demo database to have a playground for experiments. See also http://wiki.elexis.info/Installation_Elexis_3.0_OpenSource Elexis 3.1.0 was released on May, 4 2017. At http://elexis-forum.ch/ users have a place to share their experiences with other peoples. Developers and anybody trying to compile Elexis from scratch should look at https://github.com/elexis/elexis-3-core/tree/master/ch.elexis.sdk The documentation is found under http://wiki.elexis.info/

GNU Gluco Control (GGC) is diabetes management application. It helps managing user's daily data, food data. Has graphs, statistics, printing, diabetes devices support (meter, pump, CGMS). It works on any platform supporting at least Java 5 (1.5). Our repo moved to GIT (click on tab Git Code), Lowest supported Java now is 1.8 and project code base is in process of redesign (updating libraries and ways how application is built and run). IMPORTANT: Project was moved to GitHub: https://github.com/andyrozman/ggc on 4th April 2024

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

Parallel Spectral Deconvolution is a multithreaded ImageJ plugin for spectral image deblurring.

A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data

Application implements models described by classical mathematical equation for in vitro deposition prediction based on characteristics of formulation and assay conditions. This work was funded by Poland-Singapore bilateral cooperation project no 2/3/POL-SIN/2012. Published article: https://www.dovepress.com/empirical-modeling-of-the-fine-particle-fraction-fornbspcarrier-based--peer-reviewed-fulltext-article-IJN

Yawi 3D (Yet Another Wand for ImageJ) implements a 3D selection tool plugin for ImageJ suitable for CT scanned images; it helps in the selection of 3D Region Of Interest (ROI) containing a tumor mass; it also provides a measure of ROI volume

OpenVista(R) is the open-source version of VistA, an enterprise grade health care information system developed by the U.S. Veterans Affairs and deployed at 1,500 global facilities. OpenVista is a registered trademark of Medsphere Systems Corporation

Parallel Iterative Deconvolution is a multithreaded ImageJ plugin for iterative image deblurring.

The Development System for Auditory Modelling (DSAM) is a computational library designed specifically for producing simulations of the auditory system. It brings together many established auditory models within a flexible programming platform.

Protege is a free, open-source platform that provides a suite of tools to construct domain models and knowledge-based applications with frame-based and Semantic Web ontologies.