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Disseminating metaproteomic informatics capabilities and knowledge using the Galaxy-P framework

(2018) PROTEOMES. 6(1).
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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.
Keywords
metaproteomics, functional microbiome, bioinformatics, software workflow development, Galaxy platform, mass spectrometry, community development, MICROBIAL COMMUNITIES, GUT MICROBIOTA, IDENTIFICATION, FRACTIONATION, LOCALIZATION, ANNOTATIONS, PROTEOMICS, PROTEINS, PIPELINE, SAMPLES

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Citation

Please use this url to cite or link to this publication:

Chicago
Blank, Clemens, Caleb Easterly, Bjoern Gruening, James Johnson, Carolin A Kolmeder, Praveen Kumar, Damon May, et al. 2018. “Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.” Proteomes 6 (1).
APA
Blank, C., Easterly, C., Gruening, B., Johnson, J., Kolmeder, C. A., Kumar, P., May, D., et al. (2018). Disseminating metaproteomic informatics capabilities and knowledge using the Galaxy-P framework. PROTEOMES, 6(1).
Vancouver
1.
Blank C, Easterly C, Gruening B, Johnson J, Kolmeder CA, Kumar P, et al. Disseminating metaproteomic informatics capabilities and knowledge using the Galaxy-P framework. PROTEOMES. 2018;6(1).
MLA
Blank, Clemens, Caleb Easterly, Bjoern Gruening, et al. “Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.” PROTEOMES 6.1 (2018): n. pag. Print.
@article{8548277,
  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.},
  articleno    = {7},
  author       = {Blank, Clemens and Easterly, Caleb and Gruening, Bjoern and Johnson, James and Kolmeder, Carolin A and Kumar, Praveen and May, Damon and Mehta, Subina and Mesuere, Bart and Brown, Zachary and Elias, Joshua E and Hervey, W Judson and McGowan, Thomas and Muth, Thilo and Nunn, Brook L and Rudney, Joel and Tanca, Alessandro and Griffin, Timothy J and Jagtap, Pratik D},
  issn         = {2227-7382},
  journal      = {PROTEOMES},
  keyword      = {metaproteomics,functional microbiome,bioinformatics,software workflow development,Galaxy platform,mass spectrometry,community development,MICROBIAL COMMUNITIES,GUT MICROBIOTA,IDENTIFICATION,FRACTIONATION,LOCALIZATION,ANNOTATIONS,PROTEOMICS,PROTEINS,PIPELINE,SAMPLES},
  language     = {eng},
  number       = {1},
  pages        = {15},
  title        = {Disseminating metaproteomic informatics capabilities and knowledge using the Galaxy-P framework},
  url          = {http://dx.doi.org/10.3390/proteomes6010007},
  volume       = {6},
  year         = {2018},
}

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