Open Source Java Scientific/Engineering Software for Linux

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 Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.

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.

Converts Google Earth KML file to a CSV file, and vice versa. This enables you to plot all custom POIs with Google Earth first before transferring them into your Garmin GPS using the POI Loader.

Software for sustainability assessment, highly modular; initially focused on Life Cycle Assessments.

ProM is the comprehensive, extensible framework for process mining. Process Mining deals with the a-posteriori analysis of (business) processes using enactment logs.

GeoWebCache is a WMS tile cache that lets you serve cached map data to WMS clients, Goole Earth, Google Maps and MS Virtual Earth. The system is pluggable on both ends and does automatic matching to the best available tile. It is very fast and scalable.

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

The National Library of New Zealand's Metadata Extraction Tool automatically extracts preservation-related metadata from digital files, then output that metadata in XML formats. It can be used through a graphical user interface or command-line interface. Please take the latest code from 'https://github.com/DIA-NZ/Metadata-Extraction-Tool.git'. The code on source forge will not be updated henceforth as it is moved to github.

A real-time graph plotter. While your application is computing and logging results to a CSV file using the LiveGraph Writer API, the plotter lets you visualise and monitor the results live - by instantly plotting charts and graphs of the data.

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

Jitterbit is an open source integration tool that delivers a quick and simple way to design, configure, test, and deploy integration solutions. It supports many document types and protocols: XML, web services, database, LDAP, text, FTP, HTTP(S), file

Java based astronomical logging software which stores it's data in a free and open XML based format (OpenAstronomyLog). Discontinued project: Please check out the fork: https://github.com/capape/observation-manager for an updated version

DragMath is a drag and drop equation editor in the form of a Java applet. Once an expression is created the user can convert it into a variety of different linear syntax for mathematics, including MathML, LaTeX, Maple, Maxima or any user defined style. PLEASE NOTE: active code development has moved to GitHub. https://github.com/maths/dragmath

The ProM Import Framework allows to extract process enactment event logs from a set of information systems. These can be exported in the MXML format, which is the standard event log data format for Process Mining analysis techniques.

GPSdings (project name GPStools) is a set of free applications that let you manipulate and analyse GPS data from the command line.

This project provides and open source implementation of HELD and related specifications. A HELD client and Location Information Server are included.

Talend Spatial Module (aka Spatial Data Integrator or SDI) is an ETL tool for geospatial. Based on Talend Open Studio, input, output and transform geocomponents are available. IO components read/write GIS formats(eg.PostGIS, GeoRSS). Transformers all

XMLPipeDB is a suite of tools for building relational databases from XML sources with minimal manual processing of the data. While the applicability is general, our motivation was to facilitate the management of biological data from different sources.

IDL specified API for manipulating and processing CellML 1.0 and 1.1. Includes C++ implementation. Accessible from a C++ program, or from any language for which a CORBA language mapping is available Also, a Java wrapper of the API is available.

Goal of this projects is to design unified general binary data format and to provide open-source libraries and tools for it.

Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files

JFASTA is a lightweight framework for handling FASTA files. It supports reading, writing and parsing of single- or multi-FASTA files. Files may be read/ written at once, or stream-based (memory efficient). It's stable, very intuitive and good integrated with Java 1.5 SDK and later.

MetaMaster is a Java-based desktop application for defining, managing and manipulating metadata associated with a collection of data files or datasets (both locally and on the network) which are bundled together into "data packages". ANDS-funded

The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters is highly facilitated. SBFC can be executed in two modes: 1. standalone executable downloading the package provided in this website; 2. web-service at http://www.ebi.ac.uk/biomodels/tools/converters . For general discussion about SBFC, please use the forum sbfc-forum@googlegroups.com . A mailing-list is also available for developers: sbfc-devel@googlegroups.com Thanks for using SBFC! The SBFC Team