ObjectWeb JOnAS – Java Open Application Server, a J2EE application server. JBoss Application Server – Application server. Jakarta Tomcat – Servlet container and standalone webserver. Bonita Open Solution – a J2EE web application and java BPMN2 compliant engine. Apache Axis2 – Web service framework (implementations are available in both Java & C). 
VTK – Toolkit for 3D computer graphics, image processing, and visualisation.ParaView – Plotting and visualization functions developed by Sandia National Laboratory capable of massively parallel flow visualization utilizing multiple computer processors.JasperSoft – Data mining with programmable abstraction layer.Weka – Data mining software written in Java featuring machine learning operators for classification, regression, and clustering.Provides connectors to CSV, LDAP, XML, JDBC/ODBC, and other data sources Supports integration with J2EE and Spring. Scriptella ETL – ETL (Extract-Transform-Load) and script execution tool.– the previous version is available as open-source
RapidMiner – Data mining software written in Java, fully integrating Weka, featuring 350+ operators for preprocessing, machine learning, visualization, etc. Extensions for bioinformatics and text mining Orange (software) – Data visualization and data mining for novice and experts, through visual programming or Python scripting. OpenNN – Open-source neural networks software library written in the C++ programming language. FrontlineSMS – Information distribution and collecting via text messaging ( SMS). Environment for DeveLoping KDD-Applications Supported by Index-Structures (ELKI) – Data mining software framework written in Java with a focus on clustering and outlier detection methods. Ninithi – Visualise and analyse carbon allotropes, such as Carbon nanotube, Fullerene, Graphene nanoribbons. RasMol – Visualisation of biological macromolecules. QuteMol – Interactive molecule representations offering an array of innovative OpenGL visual effects. PyMOL – High-quality representations of small molecules as well as biological macromolecules. MeshLab – Able to import PDB dataset and build up surfaces from them. Jmol – 3D representation of molecules in a variety of formats, for use as a teaching tool. BALLView – Molecular modeling and visualisation. Avogadro – Plugin-extensible molecule visualisation. NWChem – Quantum chemical and molecular dynamics software. NAMD – Parallel efficient simulation of large systems involving millions of atoms. MDynaMix – General-purpose molecular dynamics, simulating mixtures of molecules. GROMACS – Protein, lipid, and nucleic acid simulation. 3DSlicer – Medical image analysis and visualisation. VTK – C++ toolkit for 3D computer graphics, image processing, and visualisation. KNIME – Data analytics, reporting, and integration platform. ITK – Development framework used for creation of image segmentation and registration programs. IMOD – 2D and 3D analysis of electron microscopy data. ImageJ – Image processing application developed at the National Institutes of Health. Ilastik – Image-classification and segmentation software. FIJI (software) – ImageJ-based image processing. 
Endrov – Java-based plugin architecture designed to analyse complex spatio-temporal image data.CellProfiler – Automatic microscopic analysis, aimed at individuals lacking training in computer vision.
P-GRADE Portal – Grid portal software enabling the creation, execution and monitoring of workflows through high-level Web interfaces.RawTherapee – Digital image workflow management aimed at RAW photo processing.LightZone - Free, open-source digital photo editor software application.Krita – Digital painting and sketching application, with a variety of brush engines.Karbon – Scalable vector drawing application in KDE.GIMP – Raster graphics editor aimed at image retouching/editing.digiKam – Integrated photography toolkit including editing capabilities.Darktable – Digital image workflow management, including RAW photo processing.refbase – Web-based institutional repository and reference management software.Evergreen – Integrated Library System initially developed for the Georgia Public Library Service's PINES catalog.It can also create animated and interactive PDF presentations and forms. Scribus - Designed for layout, typesetting, and preparation of files for professional-quality image-setting equipment.SimPy – Queue-theoretic event-based simulator written in Python.flightgear – Flight simulator written for Windows, Mac OS X, and GNU/Linux.Blender – 3D modeling software written in C, C++, and Python containing cloth, hair, fluid, particle, and rigid body simulation techniques.Link: List of free and open-source computer simulation software
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