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Plexus is a Java library with specifications and implementations for generic graph data structures. Like the Java Collections Framework, vertices and edges are containers for arbitrary user-defined objects.
JCrocus is a GUI (Graphical User Interface) that allows representing the network topology definition of microwave cavity filters based on the coupling matrix approach as well as simulating and plotting its frequency response
A java interface to the open source LabRAD framework for distributed instrument control and data acquisition. JLabRAD facilitates rapid development of client/server LabRAD applications.
MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
A Java library that works with Java3D to simulate and visualize, in real-time, dynamics of multiple rigid bodies that are restricted by implicit and explicit constraints (e.g., robotics); designed for efficiency, ease-of-use, and extensibility.
netcdf-tools is a set of tools for creating netCDF files. It supports command line use on both Windows and Unix as well as use directly as a Java library. Written by CSIRO Australia and funded by the ANDS Australian Research Data Commons Project
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Gemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
Real time micro benchmark multi-lingual suite (RTMB) provides a good way to measure the deterministic quality of hardware, an operating system, or a Java Virtual Machine. RTMB consists of benchmarks in C, C++ and Java
Anna is lightweight Java framework to build pipeline systems of any kind.
It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.
Wikipedia Concept Association Map (WCAM) is new approach for textual knowledge representation and understanding. All concepts and associations are stored in a graph database for better performance and easy distribution.
Trial Criteria Online Data Entry (trialCODE): a Java-based user interface that codifies eligibility requirements used to automate the screening of potential subjects to clinical trials. Used for caMATCH screening engine on BreastCancerTrials.org site.
vMAGIC is a Java-API which helps creating VHDL generators and analyzers. vMAGIC comprises three parts: 1st a VHDL'93 compliant parser, 2nd a programming model to easily create and modify VHDL constructs, and 3rd a VHDL Writer to generate code.
DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG).
Elly is a reasoner for entailment and satisfiability checking of ELP knowledge-bases. It is written in java and relies on the IRIS Datalog reasoner (https://sourceforge.net/projects/iris-reasoner) for its implementation.
The Evolutionary Environment Simulator (EvESimulator) is an agent-based economy simulation framework which provides a broader view on evolutionary aspects within a Digital Business Ecosystem.