An object relational-mapping (ORM) library for Java
Hibernate is an Object/Relational Mapper tool. It's very popular among Java applications and implements the Java Persistence API. Hibernate ORM enables developers to more easily write applications whose data outlives the application process. As an Object/Relational Mapping (ORM) framework, Hibernate is concerned with data persistence as it applies to relational databases (via JDBC).
Armadeus is an OpenSource Hardware and Software project based on an ARM core (Freescale i.MX) and Linux. You can consult our wiki at http://www.armadeus.org to join our non profit association or our commercial website at http://www.armadeus.com .
A collection of machine-checkend mathematical proofs
The Archive of Formal Proofs is a collection of proof libraries, examples, and larger scientifc developments, mechanically checked in the theorem prover Isabelle. It is organized in the way of a scientific journal. Submissions are refereed.
MESA: Modules for Experiments in Stellar Astrophysics -- a set of thread-safe fortran 95 libraries for stellar astrophysics, including physics (e.g., eos, opacities, nuclear nets) and algorithms (e.g., ODE solvers). Available by svn checkout or as zip file. See project webpage (http://mesa.sourceforge.net/).
Regulus is a Prolog-based toolkit for building spoken dialogue systems.
The Free / Libre / Open Source Web App with the most built-in features
"Software made the wiki way" A full-featured, web-based, multilingual (40+ languages), tightly integrated, all-in-one Wiki+CMS+Groupware, Free Source Software (GNU/LGPL), using PHP, MySQL, Zend Framework, jQuery and Smarty. Tiki can be used to create all kinds of Web applications, sites, portals, knowledge base, intranets, and extranets. Tiki is the Open Source Web Application with the most built-in features. Highly configurable and modular, all features are optional and administered via a web-based interface. Major features include a wiki engine, news articles, discussion forums, newsletters, blogs, file galleries, bug and issue trackers (form generator), polls/surveys and quizzes, banner management system, calendar, maps, mobile , RSS feeds, category system, tags, an advanced themeing engine, spreadsheet, drawings, inter-user messaging, menus, advanced permission system for users and groups, search engine, external authentication, etc. Security reports: email@example.com
Lazarus is a free and open source development tool for the Free Pascal Compiler. The purpose of this project is to serve as a Code Repository, Wiki Knowledgebase and support site for converting existing components and libraries to work with Lazarus and the Free Pascal Compiler.
A file format for exchanging computational models in systems biology
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.
ShelXle is a Qt GUI for SHELXL
ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps. See J. Appl. Cryst. (2011). 44, 1281–1284. for details.
wxArt2D gives wxWindows applications sophisticated vector drawing functionality. It is based on a framework supporting multiple views within a hierarchical document. Supports drawing & (Graph) editing. In-output in SVG, GDSII, XML, easy to extend.
a R package. 'Qair' gives access to data bases used by air quality monitoring associations in France. It also contains functions to manipualte air quality datas.
java library for XML, HTML, or SVG generation + bioinformatics classes
The com.hfg (hairyfatguy.com) library is a collection of utility classes that make it easy to construct XML, HTML, XHTML, or SVG in an object-oriented way from within your Java application or webapp. It also contains other IO utilities and bioinformatics classes for phylogenetic trees, taxonomy, and multi-chain proteins. Requires JDK1.8.
C++ Statistical ToolKit
STK++ (http://www.stkpp.org) is a versatile, fast, reliable and elegant collection of C++ classes for statistics, clustering, linear algebra, arrays (with an Eigen-like API), regression, dimension reduction, etc. Some functionalities provided by the library are available in the R environment as R functions (http://cran.at.r-project.org/web/packages/rtkore/index.html). At a convenience, we propose the source packages on sourceforge. The library offers a dense set of (mostly) template classes in C++ and is suitable for projects ranging from small one-off projects to complete data mining application suites.
The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
Open Source Solid Modeling CAD
BRL-CAD is a powerful cross-platform constructive solid geometry solid modeling system that includes an interactive geometry editor, ray-tracing for rendering & geometric analyses, network distributed framebuffer support, image & signal-processing tools.
Educational Linux Distribution
Main goals: * Prepare operating system based on Linux kernel and free software for use at home from scratch by building sources. Binary packages/images are also available. * Each package is installed in separate directory, so you can use different versions of applications and libraries by design. * There is only one user 'kanapi' with root permissions, so you don't have to login, remember passwords, etc. * Simple configuration * Automatic compilation.
A symbolic framework for C++, Python and Octave implementing automatic differentiation by source code transformation in forward and reverse modes on sparse matrix-valued computational graphs.
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
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.
The portable software collection
winPenPack is a project that aims at collecting the most frequently used and most popular open source applications made portable, so that they can be executed without installation from any USB Flash Drive or Hard Disk. The winPenPack suites offer a wide range of portable applications like office tools, internet tools, multimedia tools, development tools, security applications and other frequently used utilities. Everything you need, completely free, open source and portable!
NETGEN is an automatic 3d tetrahedral mesh generator
NETGEN is an automatic 3d tetrahedral mesh generator. It accepts input from constructive solid geometry (CSG) or boundary representation (BRep) from STL file format. The connection to a geometry kernel allows the handling of IGES and STEP files. NETGEN contains modules for mesh optimization and hierarchical mesh refinement. Netgen is open source based on the LGPL license. It is available for Unix/Linux and Windows.
Toolkit for working with and mapping geospatial data
GeoTools is an open source (LGPL) Java code library which provides standards compliant methods for the manipulation of geospatial data. GeoTools is an Open Source Geospatial Foundation project. The GeoTools library data structures are based on Open Geospatial Consortium (OGC) specifications.
FreeWRL is an Open Source, cross platform VRML2 and X3D compliant browser, with script, SAI and EAI support. Platforms supported: Linux and other Unix-style platforms; Mac OS/X; Windows. Support for mobile platforms (iOS, Android, QNX) is under development.
SAGA - System for Automated Geoscientific Analyses - is a Geographic Information System (GIS) software with immense capabilities for geodata processing and analysis. SAGA is programmed in the object oriented C++ language and supports the implementation of new functions with a very effective Application Programming Interface (API). Functions are organised as modules in framework independent Module Libraries and can be accessed via SAGA’s Graphical User Interface (GUI) or various scripting environments (shell scripts, Python, R, ...). Please provide the following reference in your work if you are using SAGA: Conrad, O., Bechtel, B., Bock, M., Dietrich, H., Fischer, E., Gerlitz, L., Wehberg, J., Wichmann, V., and Boehner, J. (2015): System for Automated Geoscientific Analyses (SAGA) v. 2.1.4. Geosci. Model Dev., 8, 1991-2007, doi:10.5194/gmd-8-1991-2015. http://www.geosci-model-dev.net/8/1991/2015/gmd-8-1991-2015.html.
Chemical structures database & machine learning with web services API
AMBIT offers a cheminformatics data management for chemical substances, structures and nanomaterials. Flexible structure, similarity and study queries storage, descriptor calculation and predictive models building via REST web services.User interface for creating read across assessment and generating reports, aligned with regulatory and industrial requirements. Command line applications also available. Integration with third party tools and databases.