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Avalon Excalibur's DataSource package allows you to manage pooled connections in one of two ways. You can have the package handle it for you, or you can use a J2EE server's DataSource management. It provides the same kind of access regardless of which method you choose--since they are obtained through Avalon's Component Manager infrastructure. The DataSource package requires that you load the necessary driver classes at init time, but it will take care of all necessary issues from there.

Pdf2Dom is a PDF parser that converts the documents to a HTML DOM representation. The obtained DOM tree may be then serialized to a HTML file or further processed. The inline CSS definitions contained in the resulting document are used for making the HTML page as similar as possible to the PDF input. A command-line utility for converting the PDF documents to HTML is included in the distribution package. Pdf2Dom may be also used as an independent Java library with a standard DOM interface for your DOM-based applications or as an alternative parser for the CSSBox rendering engine in order to add the PDF processing capability to CSSBox.

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 package contains a classifier that can be used to train a two-class kernel logistic regression model with the kernel functions that are available in WEKA. It optimises the negative log-likelihood with a quadratic penalty. Both, BFGS and conjugate gradient descent, are available as optimisation methods, but the former is normally faster. It is possible to use multiple threads, but the speed-up is generally very marginal when used with BFGS optimisation. With conjugate gradient descent optimisation, greater speed-ups can be achieved when using multiple threads. With the default kernel, the dot product kernel, this method produces results that are close to identical to those obtained using standard logistic regression in WEKA, provided a sufficiently large value for the parameter determining the size of the quadratic penalty is used in both cases.

MassBank of America (MoNA), is an auto curating repository for storing, comparing and querying mass spectra of chemical compounds. It is metadata centric and it was designed to allow easy integration into other tools by utilize its REST based application programming interface. At the current time it contains over 200k predicted and 40k unique experimental mass spectra and their associated metadata. The predicted spectra were obtained by utilizing the lipid blast library and the experimental spectra were acquired from 30 different facilities all over the world, including several major research facilities in the United States and Japan. MoNA is utilizing the InChI Key as unique identifier for chemicals and is designed for easy scalability and expendability. This is realized by utilizing common applications like nginx, grails, AngularJS, postgresSQL and tomcat. MoNA is currently integrated in applications like MSDial, BinBase, MZMine and the statistics package R. This was accomplished by utilizing its REST based API, which is also utilized by its main AngularJS based web interface. We consider MoNA to be highly useful for crosslinking mass spectra in publications, identification of unknowns and integration in data acquisition software. This package provides you with access to the REST api of the main MoNA installation.

MassBank of America (MoNA), is an auto curating repository for storing, comparing and querying mass spectra of chemical compounds. It is metadata centric and it was designed to allow easy integration into other tools by utilize its REST based application programming interface. At the current time it contains over 200k predicted and 40k unique experimental mass spectra and their associated metadata. The predicted spectra were obtained by utilizing the lipid blast library and the experimental spectra were acquired from 30 different facilities all over the world, including several major research facilities in the United States and Japan. MoNA is utilizing the InChI Key as unique identifier for chemicals and is designed for easy scalability and expendability. This is realized by utilizing common applications like nginx, grails, AngularJS, postgresSQL and tomcat. MoNA is currently integrated in applications like MSDial, BinBase, MZMine and the statistics package R. This was accomplished by utilizing its REST based API, which is also utilized by its main AngularJS based web interface. We consider MoNA to be highly useful for crosslinking mass spectra in publications, identification of unknowns and integration in data acquisition software. This package provides you with access to the REST api of the main MoNA installation.

This project aims to offer an easy-to-extend Java DAS server framework. It offers several advantages: * Implementing data sources is very easy but also flexible and powerful. * Data caching is built into the system, with access to the caching mechanism made available to the data sources. * All aspects of the server are highly configurable, including selecting options where the DAS 1.53 specification offers choices to the implementor. * The latest Java technologies have been used throughout the system to optimise performance and simplify data source development. * Wherever possible the same terminology is used in the API as in the DAS specification and XML - again, making data source development more easy. * The server allows XSLT transforms of the DAS XML to be configured to provide a simple DAS client view (limited to the single DAS source). More details of the DAS protocol, DAS servers and DAS clients can be found at http://www.biodas.org/wiki/Main_Page. The first version of this server is a complete implementation of Distributed Sequence Annotation System (DAS) Version 1.53. If you are interested in learning more about DAS 1.53, the specification is highly recommended as a concise and complete description of the DAS protocol that can be obtained from: http://biodas.org/documents/spec.html