GKIN: a tool for drawing genetic networks

We present GKIN, a simulator and a comprehensive graphical interface where one can draw the model specification of reactions between hypothesized molecular participants in a gene regulatory and biochemical reaction network (or genetic network for short). The solver is written in C++ in a nearly platform independentmanner to simulate large ensembles of models, which can run on PCs, Macintoshes, and UNIX machines, and its graphical user interface is written in Java which can run as a standalone or WebStart application. The drawing capability for rendering a network significantly enhances the ease of use of other reaction network simulators, such as KINSOLVER (Aleman-Meza et al., 2009) and enforces a correct semantic specification of the network. In a usability study with novice users, drawing the network with GKIN was preferred and faster in comparison with entry with a dialog-box guided interface in COPASI (Hoops, et al., 2006) with no difference in error rates between GKIN and COPASI in specifying the network. GKIN is freely available at http://faculty.cs.wit.edu/~ldeligia/PROJECTS/GKIN/.