Ujorm is an easy-to-use ORM framework based on key-value objects. The framework was designed for rapid Java development with great performance and a small footprint. The key features are type safe queries, relation mapping by Java code, no entity states, and a memory overloading protection cache.
Perfmon4j is a suite of performance monitoring tools that are intended to be used to diagnose performance bottlenecks and monitor throughput and response time in production Java applications. Its main features include servlet response time monitoring, detailed thread trace sampling, Java instrumentation that enables Package, Class, and Method monitoring without code modification, snapshot monitoring of system metrics including Garbage Collection, Memory Pools, etc., an API for applying additional monitoring points via method annotations or in-line timers, and support for dynamically enabling monitors in running applications.
JEFF is an explanation facility framework written in Java. Explanation facilities date from the era of expert systems (ES), where they were used in order to provide an explanation about the inference process. The explanation they provided was supposed to clarify how the ES reached its conclusions or why it asked some question during fact acquisition. Nowadays, traditional ES development environments ("shells") have been replaced by rule engines (RE) and business rule management systems (BRMS), which seem to lack explanation facility functionality. JEFF was created in order to remedy this.
Zynaptic Reaction is a flexible asynchronous programming framework for Java which may be used to implement complex event-driven applications. It is heavily influenced by the Twisted programming framework developed by TwistedMatrix Labs for the Python programming language. The focus of the Reaction library is on the concurrency and callback model and as such it is application neutral. It can be used to manage lots of concurrent I/O or to farm out compute intensive tasks to multicore processors. As well as being usable as a basic Java library, Reaction can also run as an independent OSGi service and integrate into any GUI framework you choose.
PathVisio is a bioinformatics tool that lets you do everything with biological pathway diagrams. PathVisio helps you organize biological information and lets you present or publish that information easily. You can create and draw pathways, export them to many image formats, annotate them with links to online biological databases such as Ensembl, Entrez or HMDB, and add comments and literature references from pubmed. PathVisio also lets you sort through high-throughput experimental data in pathway context. This is a much more pleasant way to present data than just a large table. You can import microarray, proteomics or metabolomics data. PathVisio has a plugin interface that lets users customize it to new analysis types, new visualization methods, and new pathway formats. PathVisio is compatible with WikiPathways.
The Whole Brain Catalog is a 3D virtual environment to facilitate solutions for currently intractable challenges in brain research. It is meant to enable the synthesis of data measured from brains at different scales into more coherent models of brain structure and function. The Whole Brain Catalog is a client-server platform that provides rich 3D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. A 3D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations.
BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph. The main advantage of the algorithm is that it does not need parametrization to compute results of high accuracy.