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. 2023 Jun 22;3:1197310. doi: 10.3389/fbinf.2023.1197310

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Copyright © 2023 Mazein, Acencio, Balaur, Rougny, Welter, Niarakis, Ramirez Ardila, Dogrusoz, Gawron, Satagopam, Gu, Kremer, Schneider and Ostaszewski.

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) and the copyright owner(s) 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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An example that compares two representations in CellDesigner that correspond to Activity Flow (Reduced Notation palette in CellDesigner) and Process Description (default palette in CellDesigner). The two diagrams represent the same biological events but in two conceptually different languages. (A). The Process Description representation of the RAF-MEK-ERK signalling: the process of MEK1/2 phosphorylation is catalysed by RAF1 and the process of ERK1/2 phosphorylation is catalysed by the phosphorylated MEK1/2. (B). The Activity Flow representation of the RAF-MEK-ERK signalling: the activity of RAF1 stimulates the activity of MEK1/2 (MAP2K1 and MAP2K2 in official HGNC names), and the activity of MEK1/2 stimulates the activity of ERK1/2 (MAPK3 and MAPK1 in official HGNC names).