Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

Gonçalvès, Emanuel; Sáez-Rodríguez, Julio

doi:10.12688/f1000research.2-192.v1

Cited by 3 publications

(2 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…CellNOpt is a software which can work with logic descriptions (Boolean, fuzzy) and differential equations, and automatically suggests the best network topologies to match a given data set. Thanks to the CytoCopteR plug-in for Cytoscape [ 36 ], which provides an accessible user interface, CellNOpt can be used in tandem with ANIMO: after computing the most likely network topologies with CytoCopteR, the biologist can carry on the analysis process with ANIMO, working on new hypotheses to explain the experimental data. Please note that this workflow is currently not implemented in a user-friendly way, and in order to perform it both CytoCopteR and ANIMO need to be installed.…”

Section: Discussionmentioning

confidence: 99%

Modelling with ANIMO: between fuzzy logic and differential equations

et al. 2016

View full text Add to dashboard Cite

BackgroundComputational support is essential in order to reason on the dynamics of biological systems. We have developed the software tool ANIMO (Analysis of Networks with Interactive MOdeling) to provide such computational support and allow insight into the complex networks of signaling events occurring in living cells. ANIMO makes use of timed automata as an underlying model, thereby enabling analysis techniques from computer science like model checking. Biology experts are able to use ANIMO via a user interface specifically tailored for biological applications. In this paper we compare the use of ANIMO with some established formalisms on two case studies.ResultsANIMO is a powerful and user-friendly tool that can compete with existing continuous and discrete paradigms. We show this by presenting ANIMO models for two case studies: Drosophila melanogaster circadian clock, and signal transduction events downstream of TNF α and EGF in HT-29 human colon carcinoma cells. The models were originally developed with ODEs and fuzzy logic, respectively.ConclusionsTwo biological case studies that have been modeled with respectively ODE and fuzzy logic models can be conveniently modeled using ANIMO. The ANIMO models require less parameters than ODEs and are more precise than fuzzy logic. For this reason we position the modelling paradigm of ANIMO between ODEs and fuzzy logic.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-016-0286-z) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionmentioning

confidence: 99%

Modelling with ANIMO: between fuzzy logic and differential equations

et al. 2016

View full text Add to dashboard Cite

show abstract

“…A notable alternative to cyREST is the Cyrface app 6 , which allows R and Bioconductor 7 functions to be executed from Cytoscape 3, with the results returned to Cytoscape 3 – the opposite of a cyREST call. While this approach enables Cytoscape to act as the workflow orchestrator, it requires that a target application act as a server, which often requires idiosyncratic and complex support for each target application.…”

Section: Introductionmentioning

confidence: 99%

CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API

Ono

Muetze

Kolishovski³

et al. 2015

F1000Res

View full text Add to dashboard Cite

As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks.In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C#) and tools (e.g., IPython/Jupyter Notebook and RStudio) to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST’s API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines.cyREST is available in the Cytoscape app store (http://apps.cytoscape.org) where it has been downloaded over 1900 times since its release in late 2014.

show abstract

Network Analysis in the Investigation of Chronic Respiratory Diseases. From Basics to Application

Díez

Agustí

Wheelock

2014

Am J Respir Crit Care Med

View full text Add to dashboard Cite

Chronic respiratory diseases are complex multifactorial disorders whose pathogenesis depends on the interplay between host and environmental factors. To fully understand them and to identify novel treatments, a holistic approach that integrates multiple types and levels of clinical and biological data is necessary. Toward this end, the application of systems biology-based strategies, in particular, network analysis, offers great potential. These systems-based approaches rely heavily on computational methods that can be challenging for the nonspecialist. Accordingly, this Pulmonary Perspective: (1) outlines the basic concepts of networks in biology and the fundamentals of network analysis, and (2) discusses recent applications of network analysis to understand respiratory diseases. The intent of this Perspective is to provide readers with increased understanding of the strengths and weaknesses of network analysis methods as well as their usefulness in addressing research questions involving chronic respiratory diseases.

show abstract

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages

Cited by 3 publications

References 15 publications

Modelling with ANIMO: between fuzzy logic and differential equations

Modelling with ANIMO: between fuzzy logic and differential equations

CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API

Network Analysis in the Investigation of Chronic Respiratory Diseases. From Basics to Application

Contact Info

Product

Resources

About