Open Source Java Scientific/Engineering Software - Page 9

GLPK for Java provides a Java language binding for the library GLPK. GLPK is a proven solver for linear and mixed integer mathematical programming problems. For Windows binaries see project GLPK for Windows (http://sourceforge.net/projects/winglpk/).

A framework and runtime environment for exploring agent-based models designed to support the definition of models using an expressive, high-level and extensible Java API and to support the exploration of these models in both interactive and batch mod

DataMelt (or "DMelt") is an environment for numeric computation, data analysis, computational statistics, and data visualization. This Java multiplatform program is integrated with several scripting languages such as Jython (Python), Groovy, JRuby, BeanShell. DMelt can be used to plot functions and data in 2D and 3D, perform statistical tests, data mining, numeric computations, function minimization, linear algebra, solving systems of linear and differential equations. Linear, non-linear and symbolic regression are also available. Neural networks and various data-manipulation methods are integrated using powerful Java API. Elements of symbolic computations using Octave/Matlab scripting are supported.

Wordcorr automates the tedious and risky process of tabulating and managing the sound correspondences used in working out the historical development of natural languages. Initial support was from NSF.

Kandid generates images using genetic algorithms. In a simulated evolution surprising images can be found calculated with Lisp expressions, Textures, Iterated Function Systems, Linear Cellular Automata, Voroni diagrams, Lindenmayer Systems and POVray

The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io

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.

Context-awareness is a key concept in ubiquitous computing. The Java Context-Awareness Framework (JCAF) is a Java-based context-awareness infrastructure and programming API for creating context-aware applications.

RPNCalc is the command-line based Reverse Polish Notation (RPN) calculator. RPN calculators make it very simple to do complex calculations, especially if there are parentheses involved. I've created a User Guide (https://frossm.github.io/RPNCalc-UserGuide) to do a better job of explaining how to use RPNCalc than the old readme.md file, which was getting really long. If you have questions, issues, feedback, or ideas, please let me know. You can contact me via the links in the **Introduction** page of the User Guide. ## RPNCalc User Guide: https://frossm.github.io/RPNCalc-UserGuide ##

TXM is a free and open-source cross-platform Unicode & XML based text analysis environment and graphical client, supporting Windows, Linux and Mac OS X. It can also be used online as a J2EE standard compliant web portal (GWT based) with access control built in. DOWNLOAD LATEST VERSION OF TXM : http://textometrie.ens-lyon.fr/spip.php?rubrique61&lang=en TXM offers a comprehensive range of analysis tools (concordances, collocate search, frequency lists, etc.) based on the powerfull CQP full text search engine (http://cwb.sourceforge.net) and a range of statistical functions (factorial analysis, classification, cooccurrency analysis, etc.) based on R packages (http://www.r-project.org). Read the scientific background at the Textométrie project web site http://textometrie.ens-lyon.fr/?lang=en. Read a full description at the TEI Tools wiki http://wiki.tei-c.org/index.php/TXM.

TomoJ is an ImageJ plug-in for tomographic reconstruction. It was designed for electron tomography, however any acquisition with parallel beam should work. TomoJ proposes the preprocessing and the registration of tilt-series prior to 3D reconstructions (WBP, ART, SIRT, OS-SART, compressed sensing). TomoJ is written in Java, the computations are multithreaded and reconstruction can be performed on CPU or GPU (OpenCL). registration is described in: Journal of Structural Biology: X. 2020, Volume 4. "Improvements on marker-free images alignment for electron tomography" C.O.S. Sorzano et al. https://doi.org/10.1016/j.yjsbx.2020.100037. BMC Bioinformatics. 2009 Apr 27;10:124."Marker-free image registration of electron tomography tilt-series." C.O.S. Sorzano et al. reconstruction part was described in: BMC Bioinformatics. 2007 Aug 6;8:288. "TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy."Messaoudi C et al

Projects and applications developed from the lab of Yuval Kluger at the Pathology department at Yale

openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.

protoFramework is a Dassault Aviation software based on a Java library and other modules as described below, and on specific software developed and maintained by Dassault Aviation. This protoFramework aims to simplify the development of prototypes of any types in several languages or technologies (such as Java, C++/C, Groovy, Python, etc..). protoFramework is based on a concept of service-oriented architecture design (“SOA”), which permits the interconnexion of application components through services, using an application protocol managed by the protoFramework.

OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets.

The development and curation of a range of XML-based tools for using Chemical Markup Language (CML), including XSD XML Schemas for validation, datatyping and constraining CML documents and XSLT Stylesheets for transforming, filtering and rendering.

Matrex is a lightweight vectorial spreadsheet: calculates blocks of values, not single cells; it is strongly multithreaded; users can work together on sheets using a server. Adapters to matlab, scilab, octave, R.

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

JSci is a set of open source Java packages. The aim is to encapsulate scientific methods/principles in the most natural way possible. As such they should greatly aid the development of scientific based software.

Statcato is a Java software application for elementary statistics. Its features include data and graph generation, probability distributions, descriptive statistics, confidence intervals, hypothesis tests, correlation, regression, and analysis of var

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.

A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.

OmniGene is a set of reausable components that have been packaged into frameworks. These frameworks are used to produce domain specific services for common bioinformatics tasks including: visualization, database access, and pipeline building.

An extensive and multi-platform visualisation, process control and HMI application that supports many different devices via an open plug-in interface. Beside a visual GUI editor a debugger is part of the package.

This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.