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The Systems Biology Simulation Core Library provides an efficient and exhaustive Java™ implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution. This library is based on the JSBML project. It can be used on every operating system for which a Java Virtual Machine is available. Version 2.0 and beyond support simulation in three frameworks: constraint-based analysis, stochastic simulation, and ordinary differential equation systems. SBSCL supports SED-ML and COMBINE archives in OMEX format.

The main module contains the GeoTools public interfaces that are used by other GeoTools modules (and GeoTools applications). Where possible we make use industry standard terms as provided by OGC and ISO standards. The formal GeoTools public api consists of gt-metadata, jts and the gt-main module. The main module contains the default implementations that are available provided to other GeoTools modules using our factory system. Factories are obtained from an appropriate FactoryFinder, giving applications a chance configure the factory used using the Factory Hints facilities. FilterFactory ff = CommonFactoryFinder.getFilterFactory(); Expression expr = ff.add( expression1, expression2 ); If you find yourself using implementation specific classes chances are you doing it wrong: Expression expr = new AddImpl( expression1, expressiom2 );

This project contains a JNA (Java Native Access) implementation built on top of the native Hnswlib (Hierarchical Navigable Small World Graph) which offers a fast approximate nearest neighbor search. It includes some modifications and simplifications in order to provide Hnswlib features with native like performance to applications written in Java. Differently from the original Python implementation, the multi-thread support is not included in the bindings itself but it can be easily implemented on the Java side.

A very simple, no-dependencies drawing API providing some primitive operations including lines, rectangles, circles, ellipses, arcs. It doesn't actually draw TO anything, you must provide your own implementation of Backing to actually paint the pixels. This project is intended for use with Snake, my project for Razer devices on Linux, but is made available in case others may find it useful. It doesn't have anything fancy like anti-alias, transformations or even line widths, contributions welcome though!

Samply.Common.MDRFaces is a Java Server Faces library which eases the user interface design of web applications where the respective data model relies on well defined data elements. Especially in case of systems for electronic data capturing, where the necessary data model is not known beforehand and can even vary over time, the user interface has to be easily adjustable. This often means the user instead of the developer designs the various forms for data entry and therefore an easy to use mechanism has to be provided. By using Samply.MDRFaces the developer can focus on the implementation of that mechanism, e.g. some editor component, but does not have to cope with the visualization of every single data element as for that is taken care of automatically.

JSON is a light-weight, language independent, data interchange format. See http://www.JSON.org/ The files in this package implement JSON encoders/decoders in Java. It also includes the capability to convert between JSON and XML, HTTP headers, Cookies, and CDL. This is a reference implementation. There is a large number of JSON packages in Java. Perhaps someday the Java community will standardize on one. Until then, choose carefully. The license includes this restriction: "The software shall be used for good, not evil." If your conscience cannot live with that, then choose a different package.