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2018-01-31Zeitschriftenartikel DOI: 10.3390/proteomes6010007
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework
dc.contributor.authorBlank, Clemens
dc.contributor.authorEasterly, Caleb
dc.contributor.authorGruening, Bjoern
dc.contributor.authorJohnson, James
dc.contributor.authorKolmeder, Carolin A.
dc.contributor.authorKumar, Praveen
dc.contributor.authorMay, Damon
dc.contributor.authorMehta, Subina
dc.contributor.authorMesuere, Bart
dc.contributor.authorBrown, Zachary
dc.contributor.authorElias, Joshua E.
dc.contributor.authorHervey, W. Judson
dc.contributor.authorMcGowan, Thomas
dc.contributor.authorMuth, Thilo
dc.contributor.authorNunn, Brook L.
dc.contributor.authorRudney, Joel
dc.contributor.authorTanca, Alessandro
dc.contributor.authorGriffin, Timothy J.
dc.contributor.authorJagtap, Pratik D.
dc.date.accessioned2018-05-07T21:05:03Z
dc.date.available2018-05-07T21:05:03Z
dc.date.created2018-02-12
dc.date.issued2018-01-31none
dc.identifier.otherhttp://edoc.rki.de/oa/articles/re1PPEqkwSRJA/PDF/23ioLm4tnwBGw.pdf
dc.identifier.urihttp://edoc.rki.de/176904/2982
dc.description.abstractThe impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics “Contribution Fest“ undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.eng
dc.language.isoeng
dc.publisherRobert Koch-Institut
dc.subjectmetaproteomicseng
dc.subjectfunctional microbiomeeng
dc.subjectbioinformaticseng
dc.subjectsoftware workflow developmenteng
dc.subjectGalaxy platformeng
dc.subjectmass spectrometryeng
dc.subjectcommunity developmenteng
dc.subject.ddc610 Medizin
dc.titleDisseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework
dc.typeperiodicalPart
dc.identifier.urnurn:nbn:de:0257-10057498
dc.identifier.doi10.3390/proteomes6010007
dc.identifier.doihttp://dx.doi.org/10.25646/2907
local.edoc.container-titleProteomes
local.edoc.fp-subtypeArtikel
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttp://www.mdpi.com/2227-7382/6/1/7
local.edoc.container-publisher-nameMDPI
local.edoc.container-volume6
local.edoc.container-issue7
local.edoc.container-year2018

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