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. 2014 Oct 6;2:42. doi: 10.3389/fbioe.2014.00042

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Copyright © 2014 Marchisio.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Modular, rule-based modeling with Parts & Pools. A text file is converted into an MDL file containing a eukaryotic module description via the interaction of Parts & Pools and BioNetGen. MDL files are loaded into ProMoT where gene circuits are designed and exported, for instance, into SBML format for simulations and analysis.