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In general, a schema is a mental construct consisting of a cluster or collection of related concepts (Bartlett, 1932). There are many different types of schemata, and they all have one thing in common: schemata are a method of organizing information that allows the brain to work more efficiently. When a schema is activated, the brain makes immediate assumptions about the person or object being observed.
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A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
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Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework.

Clemens Blank1, Caleb Easterly2, Bjoern Gruening3

  • 1Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Germany. blankclemens@gmail.com.

Proteomes
|February 1, 2018
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Summary

Researchers can now access user-friendly metaproteomics tools on the Galaxy-P platform. This initiative enhances microbiome research by providing accessible bioinformatics workflows for analyzing microbial protein data.

Keywords:
Galaxy platformbioinformaticscommunity developmentfunctional microbiomemass spectrometrymetaproteomicssoftware workflow development

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Proteomics

Background:

  • The microbiome's impact on health and environment is increasingly recognized.
  • Metaproteomics is crucial for understanding microbiome functions and host interactions.
  • Sophisticated bioinformatics tools are needed for analyzing complex metaproteomic data.

Purpose of the Study:

  • To develop and disseminate accessible metaproteomics software and workflows.
  • To train researchers in using these bioinformatics resources for microbiome studies.
  • To foster community-based development of metaproteomics tools.

Main Methods:

  • Developed modular workflows for database generation, peptide spectral matching, taxonomic, and functional analysis.
  • Utilized the Galaxy for proteomics (Galaxy-P) platform for web-based dissemination.
  • Selected and packaged software through a community "Contribution Fest".

Main Results:

  • Created easily accessible and documented metaproteomics software tools and workflows.
  • Resources are available on GitHub, Galaxy Toolshed, and a public Galaxy instance.
  • Workflows are suitable for training novice researchers via online resources and workshops.

Conclusions:

  • The Galaxy-P platform provides essential metaproteomics informatics resources.
  • These tools increase access to and utilization of metaproteomics software.
  • The community-driven approach facilitates ongoing development and dissemination of tools.