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Atlas of Computational Cell Reprogramming

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L2 · Proxy inverse design D P

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 cross-modality inverse-design framework of the review.

Why this level

Level 2 because the method instantiates the inverse-design objective through an empirical or learned proxy response map F^proxy(PS,u)\hat F_{\mathrm{proxy}}(P_S, u) rather than a mechanistic intervention-dependent model. Representation family is regulatory-network influence. Cited in §3.3 of the review. Editorial rationale pending review by the maintainer.

Classification

Level
L2
Representation
Regulatory-network influence
Modalities
D, P
Intervention
Transcription factors
Framework
Machine learning

Software

Code
github.com/VeraLiconaResearchGroup/OCSANA-Plus_SourceCode
Web tool
apps.cytoscape.org/apps/ocsana
Reproducibility
4 of 4
FAIR4RS
2 of 5

Last audited 2026-05-24

Citation

Marazzi L et al. (2020). OCSANA+: optimal control and simulation of signaling networks from network analysis., Bioinformatics (Oxford, England).

DOI: 10.1093/bioinformatics/btaa625

PMID: 32879935

BibTeX 
@article{ocsana-plus2020,
  title  = {OCSANA+: optimal control and simulation of signaling networks from network analysis.},
  author = {Marazzi L et al.},
  year   = {2020},
  journal = {Bioinformatics (Oxford, England)},
  pmid = {32879935},
  doi  = {10.1093/bioinformatics/btaa625}
}