Draw vector graphics to scale using a descriptive language
JaxoDraw: Feynman Diagrams made easy!
an Open Source BPMN 2.0 / DMN 1.1 Modeler
Webbased modeling tool
Particle Image Velocimetry
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
java API for tabular reports and pivot tables
cy2fluxviz : Cytoscape 2 plugin for flux distribution visualization