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.
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.
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.
Markdown Doclet is a replacement for the standard Sun Java Doclet that allows developers to use Markdown syntax in their Javadoc comments rather than embedding unreadable HTML. The advantage of Markdown is that the syntax allows for HTML to be passed through, allowing the Markdown doclet to be applied to any existing codebase which may contain HTML Javadoc comments. It also includes a patched version of UMLGraph which calls the Markdown Doclet instead of the Sun standard doclet. The doclet also writes a more modern stylesheet for more attractive Javadocs.
ClassPublic.java is a Java .class file converter which makes a Java class public and non-final, its fields public, and its methods public and non-final. ClassPublic.java has a compact implementation, depending only on J2SE 1.5.0 or newer. ClassPublic.java can be used to increase interoperability and code reusability of a .class file whose .java source is not available or is not feasible to recompile.
Groowiki is a Wiki program and a document management system together. It is a wiki program that utilizes Subversion, Groovy, Velocity, and many more existing products. It lets you edit Wiki pages in a tree structure just like any other wiki, but it also gives you SVN access that makes it very easy to add files to the content. It stores everything in SVN. This way all information is versioned and (optionally) accessible offline, and you can upload your modifications in batches. This is especially useful if you work with large files and the Wiki pages mainly summarize the contents of the documents.