Abstract
BackgroundIn 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.MethodsThe 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.ResultsThe 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.
Highlights
In biology, high throughput (HT) experimental technologies— referred as ‘‘omics’’— are routinely used in an increasing number of research teams
We provide a simple case study, emblematic of our daily use of the Pixel Web App, with the exploration of results issued from transcriptomics and proteomics experiments performed in the pathogenic yeast Candida glabrata
Source code is hosted on the collaborative development platform GitHub and continuous integration is provided by CircleCI
Summary
High throughput (HT) experimental technologies— referred as ‘‘omics’’— are routinely used in an increasing number of research teams. 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. 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. 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
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