The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Cytoscape Automation: empowering workflow-based network analysis
Open accessAbstract
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.
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Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Reimand, J., Isserlin, R., Voisin, V., Kucera, M., Tannus-Lopes, C., Rostamianfar, A., Wadi, L., Meyer, M., Wong, J., Xu, C., et al. (2019) · Nature Protocols · doi:10.1038/s41596-018-0103-9 · Cited by 1,970
Research works printed but not linked: 11
- Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016;44:W3–W10. · DOI · Paper page
- Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, et al. The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res. 2013;41:W557–61. · DOI · Paper page
- Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80. · DOI · Paper page
- Ono K, Muetze T, Kolishovski G, Shannon P, Demchak B. CyREST: turbocharging Cytoscape access for external tools via a RESTful API. F1000Res. 2015;4:478. · DOI
- Richardson L, Amundsen M, Ruby S. RESTful Web APIs: services for a changing world. “O’Reilly Media, Inc.”; 2013.
- Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. Network propagation in the cytoscape cyberinfrastructure. PLoS Comput Biol. 2017;13:e1005598. · DOI
- Workshops and Use Cases. Github; Available: https://github.com/cytoscape/cytoscape-automation/wiki#workshops-and-use-cases . [cited 16 May 2019]
- F1000Research. The Cytoscape Automation App article collection. Available: https://f1000research.com/gateways/cytoscapeapps/automation . [cited 7 May 2019]
- Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. GenePattern 2.0. Nat Genet. 2006;38:500–1. · DOI · Paper page
- Altintas I, Wang J, Crawl D, Li W. Challenges and approaches for distributed workflow-driven analysis of large-scale biological data: vision paper. Proceedings of the 2012 Joint EDBT/ICDT Workshops. New York: ACM; 2012. p. 73–8.
- Roure DD, Goble C, Stevens R. Designing the myExperiment virtual research environment for the social sharing of workflows. Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007); 2007. p. 603–10. · DOI
Cited by
Codo, A. C., Davanzo, G. G., Monteiro, L. D. B., de Souza, G. F., Muraro, S. P., Virgilio-da-Silva, J. V., Prodonoff, J. S., Carregari, V. C., de Biagi Junior, C. A. O., Crunfli, F., et al. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2020.07.007 · Cited by 733
The DisGeNET cytoscape app: Exploring and visualizing disease genomics data
Piñero, J., Saüch, J., Sanz, F., & Furlong, L. I. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.05.015 · Cited by 544
State of the field in multi-omics research: from computational needs to data mining and sharing
Krassowski, M., Das, V., Sahu, S. K., & Misra, B. B. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.610798 · Cited by 351
Li, X., Qin, X.-M., Tian, J.-S., Gao, X.-X., Du, G.-H., & Zhou, Y.-Z. (2021) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2020.113281 · Cited by 92
Neuronal cholesterol synthesis is essential for repair of chronically demyelinated lesions in mice
Berghoff, S. A., Spieth, L., Sun, T., Hosang, L., Depp, C., Sasmita, A. O., Vasileva, M. H., Scholz, P., Zhao, Y., Krueger-Burg, D., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109889 · Cited by 76
Metadata
- Authors
- Otasek, D., Morris, J. H., Bouças, J., Pico, A. R., & Demchak, B.
- Venue
- Genome Biology
- Published
- 2019-09-02
- Volume
- 20
- Issue
- 1
- Pages
- 185-185
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2970534831
- Cited by
- 1,791
- References
- 2
- FWCI
- 45.83
- Type
- journal article
- Language
- en
- Open access
- gold
- Licence
- creativecommons.org/licenses/by/4.0/ (tdm)
- creativecommons.org/licenses/by/4.0/ (vor)
- Funders
- National Institute of General Medical Sciences (P41 GM103504)
- National Human Genome Research Institute (R01 HG009979)
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- Otasek, D., Morris, J. H., Bouças, J., Pico, A. R., & Demchak, B. (2019). Cytoscape Automation: empowering workflow-based network analysis. Genome Biology. https://doi.org/10.1186/s13059-019-1758-4
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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