Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation
Fig 3
Example of the Drosophila cell cycle initial SBGN drawing (left) and beautified SBGN network (right).
We generated the SBGN map of the following study “Dynamical modeling of syncytial mitotic cycles in Drosophila embryos” by Calzone et al. [16, 17]. First, we created an initial map with the different reactions found in the Drosophila cell cycle. Then we beautified the map by duplicating FZY with clone markers in order to reduce edge crossings, adding colors, and optimising arc positions. The colors categorise the different reactions: green processes represent creation or degradation of entities (“source and sink”) and grey processes show import and export of entities between compartments. The red processes and arcs visualise the positive feedback exerted by the MPF. The purple processes highlight the switch between the activation and the inactivation of MPF. FZY, fizzy; MPF, maturation promoting factor; SBGN, Systems Biology Graphical Notation.