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.
yEd is a powerful diagram editor which can be used to quickly create diagrams manually or import external data for analysis and auto-magically arrange even large data sets by just pressing a button. You can use yEd to quickly create flow charts, BPMN and UML diagrams, organization charts, mind maps, Entity Relationship diagrams, and many other kinds of diagrams, graphs, and networks. Choose from a wide range of highly sophisticated layout algorithms to automatically arrange diagrams in no time. An intuitive and visually appealing user interface makes creating diagrams fun. Once a diagram has been created, it's easy to save, print, or export it to popular formats like PDF, SWF, EMF, SVG, JPEG, GIF, PNG, or HTML image maps.
OrgApp is a Java library to handle and draw organizational charts (organigrams). The library also has an applet and a Swing Java client able to view an organizational chart read from a file, in different formats (one of them based upon XML). The applet supports charts with different layouts and boxes with hyperlinks, customizable colors, sizes, positions, etc., and it is easy to embed it in an HTML page.