BioUML is a free, open source, extensible software framework for systems biology.
"Systems biology" can be narrowly defined as the "mathematical modeling of biological systems," Luke V. Schneider
>> or more broadly as "the synergistic application of experiment, theory and modeling towards understanding biological processes as whole systems instead of isolated parts," Herbert M. Sauro
>> "Using the analogy of an automobile, systems biology is like understanding the different parts of a car and how the different parts work together to achieve motion"
BioUML spans the entire range of capabilities including access to databases with experimental data, tools for formalized description of biological system's structures and functions, as well as tools for their visualization and simulations.
The language is similar to UML to define biological systems. Users can create diagrams from the set of predefined elements and specify a relationship between them.Similar to UML, the language defines a set of diagrams to describe any biological system as a whole. There are the following types of diagrams:
Structural diagrams on organism, organ/tissue and cell level.
Classification diagram for organs, tissues, cells etc. as a hierarchical tree.
Maps of genes, genomes, viruses and prokaryotes.
Biological systems state and transition graphs.
Stepwise description of the assembly and functioning of multi-component biological systems, e.g. ribosome, RNA-polymerase, DNA reparation.
Development and life cycles for organisms, organs and cells.
BioUML is an open source extensible workbench based on Eclipse runtime from IBM. BioUML is integrated with many biological databases and new databases can be easily added. BioUML supports many formats: SBML (level 1 and 2 completely), CellML, GXL, BioPAX (under development).