Bioportainer Workbench: a versatile and user-friendly system that integrates implementation, management, and use of bioinformatics resources in Docker environments

Author(s)

Menegidio, Fabiano B. ; Barbosa, David Aciole ; Goncalves, Rafael dos S. ; Nishime, Marcio M. ; Jabes, Daniela L. ; de Oliveira, Regina Costa ; Nunes, Luiz R.

• Document type: Journal article
• Source: GIGASCIENCE; v. 8, n. 4, p. 9-pg., 2019-04-01.

Abstract

Background: The Docker project is providing a promising strategy for the development of virtualization systems in bioinformatics. However, implementation, management, and launching of Docker containers is not entirely trivial for users not fully familiarized with command line interfaces. This has prompted the development of graphical user interfaces to facilitate the interaction of inexperienced users with Docker environments. Results: We describe the BioPortainer Workbench, an integrated Docker system that assists inexperienced users in interacting with a bioinformatics-dedicated Docker environment at 3 main levels: (i) infrastructure, (ii) platform, and (iii) application. Conclusions: The BioPortainer Workbench represents a pioneering effort in developing a comprehensive and easy-to-use Docker platform focused on bioinformatics, which may greatly assist in the dissemination of Docker virtualization technology in this complex field of research. (AU)

• FAPESP's process: 17/13197-8 - Characterization of promoter elements responsive to the quorum sensing (QS) auto-inducer 2 (AI-2) in Zymomonas mobilis
• Grantee: Luiz Roberto Nunes
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Regular Program Grants
• FAPESP's process: 17/08112-3 - Composition and influence of the intestinal microbiome in mice, during the process of cachexia development, induced by transplantation of Lewis lung carcinoma (LLC) cells
• Grantee: Daniela Leite Jabes
• Support Opportunities: Regular Research Grants