BioconductorBuntu: A Linux distribution that implements a web-based DNA microarray analysis server

Paul Geeleher; Dermot Morris; John P. Hinde; Aaron Golden

doi:10.1093/bioinformatics/btp165

BioconductorBuntu: A Linux distribution that implements a web-based DNA microarray analysis server

Paul Geeleher, Dermot Morris, John P. Hinde, Aaron Golden

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

Summary: BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets.

Original language	English (US)
Pages (from-to)	1438-1439
Number of pages	2
Journal	Bioinformatics
Volume	25
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btp165
State	Published - Jun 2009
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

Access to Document

10.1093/bioinformatics/btp165

Cite this

@article{87adc457153443908fdfffc1e715f3d1,

title = "BioconductorBuntu: A Linux distribution that implements a web-based DNA microarray analysis server",

abstract = "Summary: BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets.",

author = "Paul Geeleher and Dermot Morris and Hinde, {John P.} and Aaron Golden",

note = "Funding Information: Funding: Teagasc (Walsh Fellowship scheme, grant number 2007043 to P.G.); Science Foundation Ireland (grant RFP/05/CMS0001 to A.G.).",

year = "2009",

month = jun,

doi = "10.1093/bioinformatics/btp165",

language = "English (US)",

volume = "25",

pages = "1438--1439",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "11",

}

TY - JOUR

T1 - BioconductorBuntu

T2 - A Linux distribution that implements a web-based DNA microarray analysis server

AU - Geeleher, Paul

AU - Morris, Dermot

AU - Hinde, John P.

AU - Golden, Aaron

N1 - Funding Information: Funding: Teagasc (Walsh Fellowship scheme, grant number 2007043 to P.G.); Science Foundation Ireland (grant RFP/05/CMS0001 to A.G.).

PY - 2009/6

Y1 - 2009/6

N2 - Summary: BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets.

AB - Summary: BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets.

UR - http://www.scopus.com/inward/record.url?scp=65649147515&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=65649147515&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btp165

DO - 10.1093/bioinformatics/btp165

M3 - Article

C2 - 19307241

AN - SCOPUS:65649147515

SN - 1367-4803

VL - 25

SP - 1438

EP - 1439

JO - Bioinformatics

JF - Bioinformatics

IS - 11

ER -

BioconductorBuntu: A Linux distribution that implements a web-based DNA microarray analysis server

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this