Development of a pipeline toolkit
About the client
Cergentis is a leading genomics company in the field of oncology and complete gene sequencing. Cergentis improves the quality of genetic research and human healthcare by empowering precision medicine and advanced genetic engineering. Based on their proprietary and widely published NGS-based Targeted Locus Amplification (TLA) technology, the company provides products and services to leading pharmaceutical companies and research institutes worldwide.
Project overview
Cergentis has multiple in-house bioinformatics pipelines that are used to complement their innovative TLA technology. However, these pipelines are currently only executable via command-line interface and are not accessible to non-technical users.
The objective of the project is to integrate these pipelines into a web application with an intuitive user interface that can be used by everyone in the company. Behind the web application should be a queuing system in place that runs the pipeline and notifies the initiator upon completion. The key requirements for the web application were that it was easy to use, easy to maintain, and would run on an in-house server.
“The lizards are great to work with because of their strong and clear communication skills, their ability to emphasize with the situation, and to provide input and the necessary solutions based on our requirements and needs.” – Cergentis
Our approach
• Develop a web-app interface to be intuitive and display all relevant information needed
• Develop steps framework refactoring of the existing pipeline code to a unified framework that is composed of multiple executable steps.
• Development of a command-line interface (CLI) to run steps.
• Development of the back end architecture for asynchronous execution of steps. Makes use of a Redis server for the queuing system.
• Implementation of a user management system in the web-app.
• Easy deployment on the in-house server
Results
Customisable Pipelines
Delivers experiment results much faster in fully customisable pipelines.
Easy to modify
Easy to modify or extend pipelines, as well as an easy integration of new pipelines or steps.
User-friendly
User-friendly with intuitive interface for non-technical staff.
