Assimilate is a Maven2 plugin that allows developers to import dependencies from other pre-built Maven projects without a formal parent-child hierarchy existing between the projects. There is no limit to the number of project dependencies. Maven 2.0.9's "import" scope acts not on managed dependencies, but on those declared in the dependency management section of the imported pom file. Assimilate, in contrast, is designed to act on managed dependencies of any prebuilt Maven project (stored in the local repository), as though they were declared in the local project's managed dependency section.
BRAP is a Java remoting protocol that uses native Java object serialization encapsulated in HTTP. It aims to be an alternative to Spring HttpInvoker and Spring Security, especially when you don't need or want the dependencies of Spring in your client, such as when building a rich client application where size might be an issue. The authentication mechanism lets you use your own domain objects as credentials. BRAP gives you "pass by reference" even though the object arguments are serialized and passed to the remote service: changes that happen on the remote side can be applied to the client side automatically. BRAP focuses on being easy to use, small in size, yet powerful and extensible.
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.
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.
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.