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User support in visual editing for signaling and regulatory networks in ProMoT

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Steinmetz,  K.
Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society;

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Samaga,  R.
Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society;

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Ginkel,  Martin
Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society;

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Gilles,  E. D.
Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society;

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Citation

Steinmetz, K., Samaga, R., Ginkel, M., & Gilles, E. D. (2008). User support in visual editing for signaling and regulatory networks in ProMoT. Poster presented at Conference on Systems Biology of Mammalian Cells (SBMC08), Dresden, Germany.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0013-955D-0
Abstract
In systems biology tools for model editing are indispensable for the creation, management and maintenance of complex networks and GUI-supported visual editors play a key role. Compared to textual editors they communicate a better understanding of the model because they are very close to network maps used by biologists so far. They mostly also provide a more efficient and comprehensible setup of models. Special functionality is developed to assist the modeler in building up structurally correct signaling and regulatory networks. On the one hand, there are automatisms which combine often used editing steps to get the modeler rid of complicated manual interactions to create often-used network structures. On the other hand, there is a checker-system which emphasizes obvious modeling errors e. g. falsely used library elements, wrong connections between them or incomplete network-parts. Different colored boxes are drawn around the elements to differentiate error types, together with a specific textual description for every error. These functionalities are implemented in ProMoT, a software for the creation and maintenance of complex biological systems.