Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+ is an app for identifying driver nodes that control non-linear systems’ long-term dynamics, prioritizing combinations of interventions in large scale complex networks, and estimating the effects of node perturbations in signaling networks, all based on the analysis of the network’s structure. OCSANA+ includes an update to the previously introduced OCSANA (optimal combinations of interventions from network analysis) Cytoscape 2 software tool with cutting-edge and rigorously tested algorithms, together with recently-developed structure-based control algorithms for non-linear systems and an algorithm for estimating the signal flow. All these algorithms are based on the network’s topology. <br/> <br/> #Features ## Optimal Combinations of Interventions OCSANA (Optimal Combinations of Interventions from Network Analysis), originally introduced in [https://www.ncbi.nlm.nih.gov/pubmed/23626000 Vera-Licona et al., 2013], identifies and prioritizes optimal minimal combinations of interventions (CIs) that disrupt the elementary paths from selected source nodes to the specified target nodes. When indicated by the user, OCSANA seeks to additionally minimize the side-effects that CIs can cause on specified off-target nodes. <br/> <br/> ## Feedback Vertex Set Control Feedback Vertex Set Control (FC) is an attractor based control method specifically developed for networks with non-linear dynamics that uses a component of the network's topology, the Feedback Vertex Set (FVS) ([https://www.ncbi.nlm.nih.gov/pubmed/23774067 Mochizuki et al., 2013 ]). The FVS of a network is defined as the minimal set of nodes whose removal would leave a graph without cycles. Later, an extended FC control version adding the the network’s source nodes was proposed by [https://www.ncbi.nlm.nih.gov/pubmed/28655847 Zanudo et al., 2017]. <br/> <br/> ## Signal Flow Analysis The SFA algorithm ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869720 Lee and Cho, 2018]) estimates the steady state activity of a node by a linear difference equation that considers (i) The activity of a node at the previous time step, (ii) The effect (activating or inhibiting) and influence of incoming edges to a node, and (iii) the initial activities of the node


Works with Cytoscape 3.8


Works with Cytoscape 3.6


Version 0.1.0.SNAPSHOT

Released 12 Jul 2021

Works with Cytoscape 3.8

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