Open Source Java Scientific/Engineering Software

Software for pixelization, hierarchical indexation, synthesis, analysis, and visualization of data on the sphere. Please acknowledge HEALPix by quoting the web page http://healpix.sourceforge.net (or https://healpix.sourceforge.io) and publication: K.M. Gorski et al., 2005, Ap.J., 622, p.759 Full software documentation available at https://healpix.sourceforge.io/documentation.php Wiki Pages: https://sourceforge.net/p/healpix/wiki/Home Exchanging Data with HEALPix (in FITS files): https://sourceforge.net/p/healpix/wiki/Exchanging%20Data%20with%20HEALPix/ GDL and FL users should read https://sourceforge.net/p/healpix/wiki/HEALPix%20and%20GDL/

Eclim is a set of eclipse and vim plugins to integrate the two projects.

Do you work with chemical reactors? Are you curious about them? ASALI is the open-source code that you are looking for. Chemical reactor models, transport/thermodynamic properties of gases, equilibrium calculations. ASALI couples all these features with an user friendly graphical interface. Modeling chemical reactors has never been so easy.

Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).

F2what is an open source project to translate algorithmic fortran to a variety of languages (java, dotnet and VBA so far). It offers a Fortran77 parser with code transformations, variable disambiguation, and modular output to other programming languages. It also offers already translated versions of Lapack and quadprog to Java, .Net and VBA, to give access to SVD, LU, QR, Cholesky, eigenvalue decomposition, linear system solving and QP optimization in those three languages.

This is a simulation package developed for numerical simulation of ultrashort pulse propagation in optical media and pulse generation from mode-locked lasers. Although the code is primarily intended for investigations of fiber links, fiber amplifiers and fiber lasers, it can be applied to any other setting for which the governing equiations are valid. The physics included in the code is based on a generalized nonlinear Schrödinger equation, including higher order dispersion, stimulated Raman effect, gain with bandwidth limitation and saturation, loss, and saturable absorption. Disclaimer: The simulation code is provided free of charge for the use of the academic community only. We kindly ask the users to acknowledge use of the code in academic settings. We do not accept responsibility for any errors or omissions that may be present. Çağrı Şenel, Punya Prasanna Paltani, Fatih Ömer Ilday

Generic data-assimilation toolbox written in java, with native (c and fortran) libraries for high performance computing. Provides tools to couple to your own model and a wide range of algorithms, ranging from parameter calibration to Kalman filters.

BMDExpress is a bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.

Computational modelling is a interdisciplinary field spanning many techniques and programming languages. AgenTools is a project dedicated to establishing increased modularity in scientific computing packages and a portal linking to other existing project

Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)

The Canopy project is an initiative to merge and expand the functionality of Perl-speaks-NONMEM (PsN), Census, Xpose and PopED. The goal is to produce a coherent, inclusive and convenient platform for pharmacometric data analysis.

This is a project to prove the existence of space travel by observing the international space station. This will include some history about non-believers, maths and a program to calculate the heigth and velocity of the ISS.

The Inverse Ocean Model (IOM) is a software system for developing customized data-assimilation systems for numerical ocean models. It has also been used with general purpose hydrodynamic and geodynamic models.

Numerikus is an attempt to build a set of numerical libraries written in C/C++, Fortran, Java and C# for single processor and multi-core processors. It wil have from basic functions to Linear Algebra solvers and ODE's and PDE's methods.

The Open Source Risk Engine (OSRE) is a natural hazards loss estimation software.

The Open Source Space Flight Dynamics (OSSFD) project is intended to provide the community with an open source solution to space flight dynamics.

OpenChem Workbench is an enterprise software suite designed for creating, saving, searching, and exchanging chemical data. It uses existing tools (NIST, Gaussian, CHEMKIN) and its own (easy molecule building, mechanism management, group additivity, etc.)

News: since 2015 we continue all related developments within Collective Knowledge Framework: http://github.com/ctuning/ck/wiki Simple and universal event-based plugin framework and interface to open up hardwared black-box software (tools, application), make them interactive through external plugins, and connect them with other higher-level tools such as Collective Mind. For example, it is used to open up compilers (GCC, LLVM, Open64) for external tuning of optimization of internal heuristics, or to open up applications for online tuning and adaptation particularly on heterogeneous systems. It is based on successful Interactive Compilation Interface (ICI) which was added to mainline GCC >= 4.5. It supports C,C++,Fortran and Java. OpenME requires just one include file "openme.h" and 2 functions to register events or to have a call-back. The usage of this interface is briefly described in an open access publication available at http://arxiv.org/abs/1308.2410

PEBLS Evolutionary Biology Libraries (PEBLs) provides a framework to develop programs quickly and effectively in Java, C++, and C.

PUPIL (Program for User Package Interface and Linking), is a software environment that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most of the functionalities that may have those external programs interfaced without the necessity to be reimplemented again on independent interfaces. In fact, this simulation interface concentrates all the common code involved in the coupling terms of the QM/MM approach.

SMP 4 LiNuX Balls 2 To Wall high performance dual CPU applications.

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

VectTens is an object-oriented numerical library designed to manipulate vectors, tensors, and other mathematical quantities in a simple and efficient manner.

This project and all source code has moved to GitHub, see https://github.com/virtualcell

WEST (Wind Energy Simulation Toolkit) is a wind simulation application. It can be use to obtain high resolution results at various altitudes.