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  • 1 Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
  • 2 Limnological Institute, 664033 Irkutsk, Russia
  • 3 Regional Medical and Sports Clinic “Zdorovie”, 664003, Irkutsk, Russia
  • 4 Siberian Federal University, 660036 Krasnoyarsk, Russia
  • 5 Siberian Federal University, 660074 Krasnoyarsk, Russia
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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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  • Ecology SJR Quartile Score (2018): Q2
  • Ecology, Evolution, Behavior and Systematics SJR Quartile Score (2018): Q3
  • Scimago Journal Rank (2018): 0.428
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Language: English

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Publication Programme: 2020. Vol. 21.
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Senior editors

Editor(s)-in-Chief: Podani, János

Editor(s)-in-Chief: Jordán, Ferenc

Honorary Editor(s): Orlóci, László

Editorial Board

  • Madhur Anand, CAN (forest ecology, computational ecology, and ecological complexity)
  • S. Bagella, ITA (temporal dynamics, including succession, community level patterns of species richness and diversity, experimental studies of plant, animal and microbial communities, plant communities of the Mediterranean)
  • P. Batáry, HUN (landscape ecology, agroecology, ecosystem services)
  • P. A. V. Borges, PRT (community level patterns of species richness and diversity, sampling in theory and practice)
  • A. Davis, GER (supervised learning, multitrophic interactions, food webs, multivariate analysis, ecological statistics, experimental design, fractals, parasitoids, species diversity, community assembly, ticks, biodiversity, climate change, biological networks, cranes, olfactometry, evolution)
  • Z. Elek, HUN (insect ecology, invertebrate conservation, population dynamics, especially of long-term field studies, insect sampling)
  • T. Kalapos, HUN (community level plant ecophysiology, grassland ecology, vegetation-soil relationship)
  • G. M. Kovács, HUN (microbial ecology, plant-fungus interactions, mycorrhizas)
  • W. C. Liu,TWN (community-based ecological theory and modelling issues, temporal dynamics, including succession, trophic interactions, competition, species response to the environment)
  • L. Mucina, AUS (vegetation survey, syntaxonomy, evolutionary community ecology, assembly rules, global vegetation patterns, mediterranean ecology)
  • P. Ódor, HUN (plant communities, bryophyte ecology, numerical methods)
  • F. Rigal, FRA (island biogeography, macroecology, functional diversity, arthropod ecology)
  • D. Rocchini, ITA (biodiversity, multiple scales, spatial scales, species distribution, spatial ecology, remote sensing, ecological informatics, computational ecology)
  • F. Samu, HUN (landscape ecology, biological control, generalist predators, spiders, arthropods, conservation biology, sampling methods)
  • U. Scharler, ZAF (ecological networks, food webs, estuaries, marine, mangroves, stoichiometry, temperate, subtropical)
  • D. Schmera, HUN (aquatic communities, functional diversity, ecological theory)
  • M. Scotti, GER (community-based ecological theory and modelling issues, trophic interactions, competition, species response to the environment, ecological networks)
  • B. Tóthmérész, HUN (biodiversity, soil zoology, spatial models, macroecology, ecological modeling)
  • S. Wollrab, GER (aquatic ecology, food web dynamics, plankton ecology, predator-prey interactions)

 

Advisory Board

  • S. Bartha, HUN
  • S.L. Collins, USA
  • T. Czárán, HUN
  • E. Feoli, ITA
  • N. Kenkel, CAN
  • J. Lepš, CZE
  • S. Mazzoleni, ITA
  • Cs. Moskát, HUN
  • B. Oborny, HUN
  • M.W. Palmer, USA
  • G.P. Patil, USA
  • V. de Patta Pillar, BRA
  • C. Ricotta, ITA
  • Á. Szentesi, HUN

PODANI, JÁNOS
E-mail: podani@ludens.elte.hu


JORDÁN, FERENC
E-mail: jordan.ferenc@gmail.com

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Manuscript submission: COMEC Manuscript Submission