Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework

Show simple item record

dc.contributor University of Helsinki, Immunobiology Research Program en
dc.contributor.author Blank, Clemens
dc.contributor.author Easterly, Caleb
dc.contributor.author Gruening, Bjoern
dc.contributor.author Johnson, James
dc.contributor.author Kolmeder, Carolin A.
dc.contributor.author Kumar, Praveen
dc.contributor.author May, Damon
dc.contributor.author Mehta, Subina
dc.contributor.author Mesuere, Bart
dc.contributor.author Brown, Zachary
dc.contributor.author Elias, Joshua E.
dc.contributor.author Hervey, W. Judson
dc.contributor.author McGowan, Thomas
dc.contributor.author Muth, Thilo
dc.contributor.author Nunn, Brook L.
dc.contributor.author Rudney, Joel
dc.contributor.author Tanca, Alessandro
dc.contributor.author Griffin, Timothy J.
dc.contributor.author Jagtap, Pratik D.
dc.date.accessioned 2019-02-26T09:35:01Z
dc.date.available 2019-02-26T09:35:01Z
dc.date.issued 2018-03
dc.identifier.citation Blank , C , Easterly , C , Gruening , B , Johnson , J , Kolmeder , C A , Kumar , P , May , D , Mehta , S , Mesuere , B , Brown , Z , Elias , J E , Hervey , W J , McGowan , T , Muth , T , Nunn , B L , Rudney , J , Tanca , A , Griffin , T J & Jagtap , P D 2018 , ' Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework ' , Proteomes , vol. 6 , no. 1 , 7 . https://doi.org/10.3390/proteomes6010007 en
dc.identifier.issn 2227-7382
dc.identifier.other PURE: 122468136
dc.identifier.other PURE UUID: 0f49c9f7-15cb-4529-90cc-d79387fc50b2
dc.identifier.other Bibtex: urn:bf130268dd2f487205c73aed6bf13b56
dc.identifier.other Scopus: 85042664585
dc.identifier.other WOS: 000428563100006
dc.identifier.uri http://hdl.handle.net/10138/299496
dc.description.abstract The 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. fi
dc.format.extent 15
dc.language.iso eng
dc.relation.ispartof Proteomes
dc.rights en
dc.subject 1182 Biochemistry, cell and molecular biology en
dc.title Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework en
dc.type Article
dc.description.version Peer reviewed
dc.identifier.doi https://doi.org/10.3390/proteomes6010007
dc.type.uri info:eu-repo/semantics/other
dc.type.uri info:eu-repo/semantics/publishedVersion
dc.contributor.pbl
dc.contributor.pbl

Files in this item

Total number of downloads: Loading...

Files Size Format View
proteomes_06_00007_v2.pdf 3.680Mb PDF View/Open

This item appears in the following Collection(s)

Show simple item record