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Maltcms, short for "Modular Application Toolkit for Chromatography Mass-Spectrometry" is an application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics. Its aim is to provide reusable, efficient datastructures, abstracting from the various low-level data-formats like netcdf (ANDIMS), mzXML, mzData and mzML and providing consistent access to data features like mass spectra, chromatograms and metadata. Furthermore, Maltcms provides a platform for the implementation and execution of processing pipelines. New and existing algorithms can be easily implemented or included and executed together with existing processing elements.

Java implementation of the Ziggurat algorithm for generating Gaussian distributed pseudorandom numbers. The Ziggurat algorithm is significantly faster than the more commonly encountered Polar method, and has some other desirable statistical properties. The ZigguratGaussian class is a Java port of the GNU Scientific Library's C implementation (Voss, 2005) of the Ziggurat method. In porting to Java, we have made several optimizations, the details of which can be found in the source code comments, which highlights any differences between this Java implementation and the C implementation on which it is based. This package also includes an implementation of the Polar Method, included to enable comparing speed advantage of the Ziggurat algorithm.

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 AppOptics Java instrumentation agent jar file. This artifact provides a convenient way to download the agent jar from public Maven repository. Please take note that this should NOT be included as a part of the project dependencies. Rather, this artifact should be integrated into the build process by using extra step such as the "copy" goal of "maven-dependency-plugin". For more information, please refer to https://docs.appoptics.com/kb/apm_tracing/java/install/#getting-the-agent-jar

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.

Ganymed SSH-2 for Java is a library which implements the SSH-2 protocol in pure Java (tested on J2SE 1.4.2 and 5.0). It allows one to connect to SSH servers from within Java programs. It supports SSH sessions (remote command execution and shell access), local and remote port forwarding, local stream forwarding, X11 forwarding, SCP and SFTP. There are no dependencies on any JCE provider, as all crypto functionality is included. Originally, Ganymed SSH-2 for Java was developed for the Ganymed replication project at ETH Zurich (Switzerland). Downloads and more information about JSch may be found at http://www.cleondris.ch/opensource/ssh2/. This library is the provider bridge for SSHAPI.