Universität zu Köln

Deng, Mario, Braegelmann, Johannes, Kryukov, Ivan, Saraiva-Agostinho, Nuno ORCID: 0000-0002-5549-105X and Perner, Sven (2017). FirebrowseR: an R client to the Broad Institute's Firehose Pipeline. Database. OXFORD: OXFORD UNIV PRESS. ISSN 1758-0463

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Abstract

With its Firebrowse service (http://firebrowse.org/) the Broad Institute is making large-scale multi-platform omics data analysis results publicly available through a Representational State Transfer (REST) Application Programmable Interface (API). Querying this database through an API client from an arbitrary programming environment is an essential task, allowing other developers and researchers to focus on their analysis and avoid data wrangling. Hence, as a first result, we developed a workflow to automatically generate, test and deploy such clients for rapid response to API changes. Its underlying infrastructure, a combination of free and publicly available web services, facilitates the development of API clients. It decouples changes in server software from the client software by reacting to changes in the RESTful service and removing direct dependencies on a specific implementation of an API. As a second result, FirebrowseR, an R client to the Broad Institute's RESTful Firehose Pipeline, is provided as a working example, which is built by the means of the presented workflow. The package's features are demonstrated by an example analysis of cancer gene expression data.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Deng, Mario UNSPECIFIED UNSPECIFIED UNSPECIFIED Braegelmann, Johannes UNSPECIFIED UNSPECIFIED UNSPECIFIED Kryukov, Ivan UNSPECIFIED UNSPECIFIED UNSPECIFIED Saraiva-Agostinho, Nuno UNSPECIFIED orcid.org/0000-0002-5549-105X UNSPECIFIED Perner, Sven UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-242713
DOI:	10.1093/database/baw160
Journal or Publication Title:	Database
Date:	2017
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1758-0463
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language FORMAT Multiple languages Mathematical & Computational Biology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/24271