LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata
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,...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-12-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-020-03908-5 |
| _version_ | 1818646556871491584 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Bo Zhao |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T00:48:31Z |
| format | Article |
| id | doaj.art-d9acf65666e54bc3a5c97de82ca2c9e2 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-17T00:48:31Z |
| publishDate | 2020-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-d9acf65666e54bc3a5c97de82ca2c9e22022-12-21T22:09:50ZengBMCBMC Bioinformatics1471-21052020-12-012111710.1186/s12859-020-03908-5LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadataBo Zhao0Luke Bryant1Rebecca Cordell2Michael Wilde3Dahlia Salman4Dorota Ruszkiewicz5Wadah Ibrahim6Amisha Singapuri7Tim Coats8Erol Gaillard9Caroline Beardsmore10Toru Suzuki11Leong Ng12Neil Greening13Paul Thomas14Paul Monks15Christopher Brightling16Salman Siddiqui17Robert C. Free18Department of Respiratory Sciences, University of LeicesterNIHR Leicester Biomedical Research Centre, University of LeicesterNIHR Leicester Biomedical Research Centre, University of LeicesterNIHR Leicester Biomedical Research Centre, University of LeicesterDepartment of Chemistry, Loughborough UniversityDepartment of Chemistry, Loughborough UniversityDepartment of Respiratory Sciences, University of LeicesterNIHR Leicester Biomedical Research Centre, University of LeicesterDepartment of Chemistry, University of LeicesterDepartment of Respiratory Sciences, University of LeicesterDepartment of Respiratory Sciences, University of LeicesterNIHR Leicester Biomedical Research Centre, University of LeicesterNIHR Leicester Biomedical Research Centre, University of LeicesterNIHR Leicester Biomedical Research Centre, University of LeicesterDepartment of Chemistry, Loughborough UniversityDepartment of Chemistry, University of LeicesterDepartment of Respiratory Sciences, University of LeicesterDepartment of Respiratory Sciences, University of LeicesterDepartment of Respiratory Sciences, University of LeicesterAbstract 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.https://doi.org/10.1186/s12859-020-03908-5MetadataData managementBiomedicalBreathomics |
| spellingShingle | 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 LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata BMC Bioinformatics Metadata Data management Biomedical Breathomics |
| title | LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata |
| title_full | LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata |
| title_fullStr | LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata |
| title_full_unstemmed | LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata |
| title_short | LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata |
| title_sort | labpipe an extensible bioinformatics toolkit to manage experimental data and metadata |
| topic | Metadata Data management Biomedical Breathomics |
| url | https://doi.org/10.1186/s12859-020-03908-5 |
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