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

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 Brightling; Salman Siddiqui; Robert C. Free

doi:10.1186/s12859-020-03908-5

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

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 Brightling, Salman Siddiqui, Robert C. Free^*

^*Corresponding author for this work

School of Geography, Earth and Environmental Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

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 flexible toolkit which is driven through a local client that runs alongside vendor software and connects to a light-weight server. The toolkit allows re-usable configurations to be defined for experiment metadata and local data collection, and handles metadata entry and linkage of data. LabPipe was piloted in a multi-site clinical breathomics study. Conclusions LabPipe provided a consistent, controlled approach for handling metadata and experimental data collection, collation and linkage in the exemplar study and was flexible enough to deal effectively with different data handling challenges.

Original language	English
Number of pages	0
Journal	BMC Bioinformatics
Volume	21
Issue number	1
DOIs	https://doi.org/10.1186/s12859-020-03908-5
Publication status	Published - Dec 2020

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Zhao, B., Bryant, L., Cordell, R., Wilde, M., Salman, D., Ruszkiewicz, D., Ibrahim, W., Singapuri, A., Coats, T., Gaillard, E., Beardsmore, C., Suzuki, T., Ng, L., Greening, N., Thomas, P., Monks, P., Brightling, C., Siddiqui, S., & Free, R. C. (2020). LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata. BMC Bioinformatics, 21(1). https://doi.org/10.1186/s12859-020-03908-5

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title = "LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata",

abstract = "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 flexible toolkit which is driven through a local client that runs alongside vendor software and connects to a light-weight server. The toolkit allows re-usable configurations to be defined for experiment metadata and local data collection, and handles metadata entry and linkage of data. LabPipe was piloted in a multi-site clinical breathomics study. Conclusions LabPipe provided a consistent, controlled approach for handling metadata and experimental data collection, collation and linkage in the exemplar study and was flexible enough to deal effectively with different data handling challenges. ",

author = "Bo Zhao and Luke Bryant and Rebecca Cordell and Michael Wilde and Dahlia Salman and Dorota Ruszkiewicz and Wadah Ibrahim and Amisha Singapuri and Tim Coats and Erol Gaillard and Caroline Beardsmore and Toru Suzuki and Leong Ng and Neil Greening and Paul Thomas and Paul Monks and Christopher Brightling and Salman Siddiqui and Free, {Robert C.}",

year = "2020",

month = dec,

doi = "10.1186/s12859-020-03908-5",

language = "English",

volume = "21",

journal = "BMC Bioinformatics",

issn = "1471-2105",

publisher = "BioMed Central Ltd.",

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Zhao, B, Bryant, L, Cordell, R, Wilde, M, Salman, D, Ruszkiewicz, D, Ibrahim, W, Singapuri, A, Coats, T, Gaillard, E, Beardsmore, C, Suzuki, T, Ng, L, Greening, N, Thomas, P, Monks, P, Brightling, C, Siddiqui, S & Free, RC 2020, 'LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata', BMC Bioinformatics, vol. 21, no. 1. https://doi.org/10.1186/s12859-020-03908-5

TY - JOUR

T1 - LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata

AU - Zhao, Bo

AU - Bryant, Luke

AU - Cordell, Rebecca

AU - Wilde, Michael

AU - Salman, Dahlia

AU - Ruszkiewicz, Dorota

AU - Ibrahim, Wadah

AU - Singapuri, Amisha

AU - Coats, Tim

AU - Gaillard, Erol

AU - Beardsmore, Caroline

AU - Suzuki, Toru

AU - Ng, Leong

AU - Greening, Neil

AU - Thomas, Paul

AU - Monks, Paul

AU - Brightling, Christopher

AU - Siddiqui, Salman

AU - Free, Robert C.

PY - 2020/12

Y1 - 2020/12

N2 - 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 flexible toolkit which is driven through a local client that runs alongside vendor software and connects to a light-weight server. The toolkit allows re-usable configurations to be defined for experiment metadata and local data collection, and handles metadata entry and linkage of data. LabPipe was piloted in a multi-site clinical breathomics study. Conclusions LabPipe provided a consistent, controlled approach for handling metadata and experimental data collection, collation and linkage in the exemplar study and was flexible enough to deal effectively with different data handling challenges.

AB - 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 flexible toolkit which is driven through a local client that runs alongside vendor software and connects to a light-weight server. The toolkit allows re-usable configurations to be defined for experiment metadata and local data collection, and handles metadata entry and linkage of data. LabPipe was piloted in a multi-site clinical breathomics study. Conclusions LabPipe provided a consistent, controlled approach for handling metadata and experimental data collection, collation and linkage in the exemplar study and was flexible enough to deal effectively with different data handling challenges.

U2 - 10.1186/s12859-020-03908-5

DO - 10.1186/s12859-020-03908-5

M3 - Article

SN - 1471-2105

VL - 21

JO - BMC Bioinformatics

JF - BMC Bioinformatics

IS - 1

ER -

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

Abstract

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