Semantic Scholar Open Access 2019 1424 sitasi

Cytoscape Automation: empowering workflow-based network analysis

D. Otasek J. Morris Jorge Bouças Alexander R. Pico Barry Demchak

Lihat Sumber DOI

Abstrak

Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio. We expose over 270 Cytoscape core functions and 34 Cytoscape apps as REST-callable functions with standardized JSON interfaces backed by Swagger documentation. Independent projects to create and publish Python/R native CA interface libraries have reached an advanced stage, and a number of automation workflows are already published.

Topik & Kata Kunci

Biology Medicine

Penulis (5)

D. Otasek

J. Morris

Jorge Bouças

Alexander R. Pico

Barry Demchak

Format Sitasi

APA MLA BibTeX

Otasek, D., Morris, J., Bouças, J., Pico, A.R., Demchak, B. (2019). Cytoscape Automation: empowering workflow-based network analysis. https://doi.org/10.1186/s13059-019-1758-4

Akses Cepat

Lihat di Sumber doi.org/10.1186/s13059-019-1758-4

Informasi Jurnal

Tahun Terbit: 2019
Bahasa: en
Total Sitasi: 1424×
Sumber Database: Semantic Scholar
DOI: 10.1186/s13059-019-1758-4
Akses: Open Access ✓