RT Journal Article
SR Electronic
T1 Pixel: a digital lab assistant to integrate biological data in multi-omics projects
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 427724
DO 10.1101/427724
A1 Thomas Denecker
A1 William Durand
A1 Julien Maupetit
A1 Charles Hébert
A1 Jean-Michel Camadro
A1 Pierre Poulain
A1 Gaëlle Lelandais
YR 2018
UL http://biorxiv.org/content/early/2018/09/27/427724.abstract
AB 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 integrate all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original digital assistant 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. Unlike other bioinformatics platforms like Galaxy, the Pixel Web App does not provide any computational programs to analyze the data. Still, it allows to rapidly integrate existing results and thus holds a strategic position in the management of research data.