Class C1 records a network-influence score. The score does not by itself establish that a feasible intervention can reach the target. Class C3 records a modeled outcome or a certified control property. The claim reaches only as far as the model, its reachable set, and the outcome it predicts. Boundary conditions.
OCSANA+
Marazzi L, Gainer-Dewar A, Vera-Licona P
2020 · Bioinformatics (Oxford, England)
SUMMARY: OCSANA+ is a Cytoscape app for identifying nodes to drive the system toward a desired long-term behavior, prioritizing combinations of interventions in large-scale complex networks, and estimating the effects…
Abstract
From the original paper, Bioinformatics (Oxford, England) · PubMed
SUMMARY: OCSANA+ is a Cytoscape app for identifying nodes to drive the system toward a desired long-term behavior, 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 optimal combinations of interventions from network analysis 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 signal flow. All these algorithms are based on the network's topology. OCSANA+ is implemented as a Cytoscape app to enable a user interface for running analyses and visualizing results. AVAILABILITY AND IMPLEMENTATION: OCSANA+ app and its tutorial can be downloaded from the Cytoscape App Store or https://veraliconaresearchgroup.github.io/OCSANA-Plus/. The source code and computations are available in https://github.com/VeraLiconaResearchGroup/OCSANA-Plus_SourceCode. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Summary
Editorial summary pending review by the maintainer. The paper's own abstract appears above; the Atlas summary in the maintainer's voice will explain how OCSANA+ relates to the inverse-design framework of the review.
Why this class
OCSANA+ is one publication with two selection objects, so it is not placed in a single explicitness class and is outside the single-class census. Combinations of interventions are a network-influence score with no post-intervention state (Class C1). Feedback-vertex-set control with Boolean signal-flow analysis reads a modeled steady state (Class C3A).