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.
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.
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.
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.
jsoup is a Java library for working with real-world HTML. It can parse HTML from a URL, file, or string. It can find and extract data, using DOM traversal or CSS selectors. The HTML elements, attributes, and text can be manipulated. It can clean user-submitted content against a safe white-list. jsoup is designed to deal with all varieties of HTML found in the wild, from pristine and validating to invalid tag-soup; jsoup will create a sensible parse tree.
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.