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

• Published in: Community ecology Vol. 20; no. 3; pp. 230 - 237
• Main Authors: Feranchuk, S., Belkova, N., Potapova, U., Ochirov, I., Kuzmin, D., Belikov, S.
• Format: Journal Article
• Language: English
• Published: Cham Akadémiai Kiadó 01.12.2019; Springer International Publishing
• Subjects: Animal Ecology; Biodiversity; bioinformatics; Community & Population Ecology; computer software; Internet; Life Sciences; Marine & Freshwater Sciences; Microbial Ecology; Plant Ecology; Python; Microbial ecology; Data analysis; Interactive visualization; Web server; Graphical presentation; Free software
• ISSN: 1585-8553; 1588-2756; 1588-2756
• DOI: 10.1556/168.2019.20.3.3

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.