Literature DB >> 33625229

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers.

Jingwen Bai1, Chakradhar Bandla1, Jiaxin Guo2, Roberto Vera Alvarez3, Mingze Bai4, Juan Antonio Vizcaíno1, Pablo Moreno1, Björn Grüning5, Olivier Sallou6, Yasset Perez-Riverol1.   

Abstract

BioContainers is an open-source project that aims to create, store, and distribute bioinformatics software containers and packages. The BioContainers community has developed a set of guidelines to standardize software containers including the metadata, versions, licenses, and software dependencies. BioContainers supports multiple packaging and container technologies such as Conda, Docker, and Singularity. The BioContainers provide over 9000 bioinformatics tools, including more than 200 proteomics and mass spectrometry tools. Here we introduce the BioContainers Registry and Restful API to make containerized bioinformatics tools more findable, accessible, interoperable, and reusable (FAIR). The BioContainers Registry provides a fast and convenient way to find and retrieve bioinformatics tool packages and containers. By doing so, it will increase the use of bioinformatics packages and containers while promoting replicability and reproducibility in research.

Entities:  

Keywords:  BioContainers; cloud; computational proteomics; high-performance computing; large-scale data analysis

Year:  2021        PMID: 33625229     DOI: 10.1021/acs.jproteome.0c00904

Source DB:  PubMed          Journal:  J Proteome Res        ISSN: 1535-3893            Impact factor:   4.466


  6 in total

Review 1.  A proteomics sample metadata representation for multiomics integration and big data analysis.

Authors:  Chengxin Dai; Anja Füllgrabe; Julianus Pfeuffer; Elizaveta M Solovyeva; Jingwen Deng; Pablo Moreno; Selvakumar Kamatchinathan; Deepti Jaiswal Kundu; Nancy George; Silvie Fexova; Björn Grüning; Melanie Christine Föll; Johannes Griss; Marc Vaudel; Enrique Audain; Marie Locard-Paulet; Michael Turewicz; Martin Eisenacher; Julian Uszkoreit; Tim Van Den Bossche; Veit Schwämmle; Henry Webel; Stefan Schulze; David Bouyssié; Savita Jayaram; Vinay Kumar Duggineni; Patroklos Samaras; Mathias Wilhelm; Meena Choi; Mingxun Wang; Oliver Kohlbacher; Alvis Brazma; Irene Papatheodorou; Nuno Bandeira; Eric W Deutsch; Juan Antonio Vizcaíno; Mingze Bai; Timo Sachsenberg; Lev I Levitsky; Yasset Perez-Riverol
Journal:  Nat Commun       Date:  2021-10-06       Impact factor: 14.919

2.  FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow.

Authors:  Anna Vlasova; Toni Hermoso Pulido; Francisco Camara; Julia Ponomarenko; Roderic Guigó
Journal:  Genes (Basel)       Date:  2021-10-19       Impact factor: 4.096

3.  Perspectives on automated composition of workflows in the life sciences.

Authors:  Anna-Lena Lamprecht; Magnus Palmblad; Jon Ison; Veit Schwämmle; Mohammad Sadnan Al Manir; Ilkay Altintas; Christopher J O Baker; Ammar Ben Hadj Amor; Salvador Capella-Gutierrez; Paulos Charonyktakis; Michael R Crusoe; Yolanda Gil; Carole Goble; Timothy J Griffin; Paul Groth; Hans Ienasescu; Pratik Jagtap; Matúš Kalaš; Vedran Kasalica; Alireza Khanteymoori; Tobias Kuhn; Hailiang Mei; Hervé Ménager; Steffen Möller; Robin A Richardson; Vincent Robert; Stian Soiland-Reyes; Robert Stevens; Szoke Szaniszlo; Suzan Verberne; Aswin Verhoeven; Katherine Wolstencroft
Journal:  F1000Res       Date:  2021-09-07

4.  Phage Genes Induce Quorum Sensing Signal Release through Membrane Vesicle Formation.

Authors:  Marina Yasuda; Tatsuya Yamamoto; Toshiki Nagakubo; Kana Morinaga; Nozomu Obana; Nobuhiko Nomura; Masanori Toyofuku
Journal:  Microbes Environ       Date:  2022       Impact factor: 2.912

5.  Bioinformatics analysis of the potential regulatory mechanisms of renal fibrosis and the screening and identification of factors related to human renal fibrosis.

Authors:  Cixiao Wang; Shaobo Wu; Jiang Li; Yuexian Ma; Youqun Huang; Na Fang
Journal:  Transl Androl Urol       Date:  2022-06

6.  The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.

Authors:  Yasset Perez-Riverol; Jingwen Bai; Chakradhar Bandla; David García-Seisdedos; Suresh Hewapathirana; Selvakumar Kamatchinathan; Deepti J Kundu; Ananth Prakash; Anika Frericks-Zipper; Martin Eisenacher; Mathias Walzer; Shengbo Wang; Alvis Brazma; Juan Antonio Vizcaíno
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

  6 in total

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