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Tools and a web server for data analysis and presentation in microbial ecology

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Abstract

The methods for data presentation are important in bioinformatics as data processing algorithms. The article describes the software package for the extensive analysis of tables with estimates of bacterial abundance levels in environmental samples. The package was designed to be executed in a distributed hardware environment, with powerful packages in Python in the backend and interactive front-end forms. Most of microbial ecology-specific functionality is implemented by the scikit-bio Python package, together with the other Python packages intended for big data analysis. Interactive visualisation tools are implemented by the D3.js software library, therefore, the software project is named D3b. The package is a suite of tools for the analysis of microbial ecology data implemented as a web-service and as a desktop application. It supports a substantial part of the graphical and analytical descriptions of microbial communities used in scientific publications. Source codes are available at github (sferanchuk/d3b_charts) and the on-line version of the system is accessible at d3b-charts.bri-shur.com.

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Abbreviations

BIOM:

Biology Observation Matrix

MDS:

Multi-Dimensional Scaling

OTU:

Operational Taxonomic Unit

PCA:

Principal Components Analysis

RDP:

Ribosomal Database Project

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Authors and Affiliations

  1. Scientific Centre for Family Health and Human Reproduction Problems, 664003, Irkutsk, Russia

    S. Feranchuk & N. Belkova

  2. Siberian Branch of Russian Academy of Sciences, Limnological Institute, 664033, Irkutsk, Russia

    U. Potapova & S. Belikov

  3. Regional Medical and Sports Clinic “Zdorovie”, 664003, Irkutsk, Russia

    I. Ochirov

  4. Laboratory of Forest Genomics, Genome Research and Education Center, Siberian Federal University, 660036, Krasnoyarsk, Russia

    D. Kuzmin

  5. Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, 660074, Krasnoyarsk, Russia

    D. Kuzmin

Authors
  1. S. Feranchuk
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  2. N. Belkova
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  3. U. Potapova
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  4. I. Ochirov
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  5. D. Kuzmin
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  6. S. Belikov
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Correspondence to S. Feranchuk.

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Feranchuk, S., Belkova, N., Potapova, U. et al. Tools and a web server for data analysis and presentation in microbial ecology. COMMUNITY ECOLOGY 20, 230–237 (2019). https://doi.org/10.1556/168.2019.20.3.3

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  • DOI: https://doi.org/10.1556/168.2019.20.3.3

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