Pixel: a content management platform for quantitative omics data - Archive ouverte HAL Access content directly
Journal Articles PeerJ Year : 2019

Pixel: a content management platform for quantitative omics data

(1, 2) , (2) , (2) , (3) , (4) , (4) , (1)
1
2
3
4
William Durand
  • Function : Author
  • PersonId : 778596
  • IdRef : 194119254
Julien Maupetit
  • Function : Author
Charles Hébert
  • Function : Author
Jean-Michel Camadro
Pierre Poulain

Abstract

Background. In biology, high-throughput experimental technologies, also referred as ''omics'' technologies, are increasingly used in research laboratories. Several thousands of gene expression measurements can be obtained in a single experiment. Researchers are routinely facing the challenge to annotate, store, explore and mine all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original content management platform to help people involved in a multi-omics biological project. Methods. The Pixel Web App is built with open source technologies and hosted on the collaborative development platform GitHub (https://github.com/Candihub/pixel). It is written in Python using the Django framework and stores all the data in a PostgreSQL database. It is developed in the open and licensed under the BSD 3-clause license. The Pixel Web App is also heavily tested with both unit and functional tests, a strong code coverage and continuous integration provided by CircleCI. To ease the development and the deployment of the Pixel Web App, Docker and Docker Compose are used to bundle the application as well as its dependencies. Results. The Pixel Web App offers researchers an intuitive way to annotate, store, explore and mine their multi-omics results. It can be installed on a personal computer or on a server to fit the needs of many users. In addition, anyone can enhance the application to better suit their needs, either by contributing directly on GitHub (encouraged) or by extending Pixel on their own. The Pixel Web App does not provide any computational programs to analyze the data. Still, it helps to rapidly explore and mine existing results and holds a strategic position in the management of research data.
Fichier principal
Vignette du fichier
2019_Denecker-T_PeerJ_30944779_(Pixel a content management platform for quantitative omics data).pdf (5.89 Mo) Télécharger le fichier
Origin : Publisher files allowed on an open archive

Dates and versions

hal-03100146 , version 1 (06-01-2021)

Licence

Attribution - CC BY 4.0

Identifiers

Cite

Thomas Denecker, William Durand, Julien Maupetit, Charles Hébert, Jean-Michel Camadro, et al.. Pixel: a content management platform for quantitative omics data. PeerJ, 2019, 7, pp.e6623. ⟨10.7717/peerj.6623⟩. ⟨hal-03100146⟩
119 View
40 Download

Altmetric

Share

Gmail Facebook Twitter LinkedIn More