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!

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

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.

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

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

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 installation information. Download and execute CleverPsych.exe on Windows, otherwise you must download,unzip CleverPsych.zip to ~/Downloads/CleverPsych and run 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 (I am often away). Alternatively use the Discussion tab or post a ticket for problems. 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/

Full featured free PACS based on dcm4chee and mysql, with remote web accession available for Linux in Debian packaging format for x86 32 and 64 bit processors. (KEYWORDS: PACS,DICOM,HL7,WORK LIST)

The Tolven platform and ePHR and eCHR applications enable interoperability across electronic health records for consumers and clinicians. Using Java, EJB3, Faces, Facelets, AJAX, relational database, and LDAP for security.

ECMOjo is a simulator and trainer for extracorporeal membrane oxygenation (ECMO). ECMOjo consists of a graphical user interface to allow interaction and train ECMO practitioners.

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

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

OpenVigil provides a webinterface to analyse pharmacovigilance data, i.e., spontanous or systematic collections of treatments (drugs) and observed adverse events ("drug side effects"). FDA Adverse Event Reporting System (AERS) and other pharmacovigilance data (e.g., Canadian or German) are supported. The OpenVigil web-based analysis tools offer several analysis modes like extraction, filtering, mining of data and analyses via measurements of disproportionality like proportional reporting ratio or reporting odds ratios) and export to spreadsheets programs like Microsoft Excel or statistics programs like R. OpenVigil 1 operates on raw data, OpenVigil 2 on cleaned data (using drugbank.ca and drugs@FDA), OpenVigilFDA uses the official FDA online API. OpenVigil 2 supports query for ATC codes or certain chemical moieties. Other tools of the OpenVigil project include a calculator for measurements of disproportionality for a 2x2 contingency table and a drugname mapper using RxNorm.

this java project creates a simple user interface with some basic statistical tools to access the Eye Express(tm) Eye tracker hardware. Including serial port access, etc.

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

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.

NOTE: THIS PROJECT HAS MOVED TO GITHUB Link: https://github.com/hacklaen/virtualmri A realistic simulation of a MR scanner shall be developed. For the user it shall be possible to change all relevant setting of the virtual scanner and to adapt them to the expected pathology. Students and doctors in education are the target group.

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

Natural Family Planning(NFP)/Fertility Awareness(FA) mobile (j2me,midp 1.0/2.0) application. Supports basal-body temperature, mucus/ovulation and calendar methods. Optimized for daily storing of records with the ability to display complex graph analysis.

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.

The purpose of the project is to develop a quantitative medical imaging & visualization program for use on brain MR, DTI and MRS data. It is a joint project of the Kennedy Krieger Institute & the Johns Hopkins University, Psychiatric Neuroimaging Lab

A small Java program for reading, analysing, viewing and animating the data from an EEG machine during a psychology experiment.

FM100 is a computer simulation of the Farnsworth-Munsel 100 hue colour (color) vision test. The results of the test can be used to assess the user's colour vision.