LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata

• DOI: 10.1186/s12859-020-03908-5
• Publication Date: 2020-12-02T12:03:16Z
• Authors: Bo Zhao; Luke Bryant; Rebecca Cordell; Michael Wilde; Dahlia Salman; Dorota Ruszkiewicz; Wadah Ibrahim; Amisha Singapuri; Tim Coats; Erol Gaillard; Caroline Beardsmore; Toru Suzuki; Leong Ng; Neil Greening; Paul Thomas; Paul Monks; Christopher Brigh...; Salman Siddiqui; Robert C. Free
• Keywords: USable; Linkage (software); Data mapping

Abstract Background Data handling in clinical bioinformatics is often inadequate. No freely available tools provide straightforward approaches for consistent, flexible metadata collection and linkage of related experimental data generated locally by vendor software. Results To address this problem, we created LabPipe, a toolkit which driven through local client that runs alongside software connects to light-weight server. The allows re-usable configurations be defined experiment collection, handles entry data. LabPipe was piloted multi-site breathomics study. Conclusions provided controlled approach collation the exemplar study enough deal effectively with different challenges.