Toward Reproducible Analysis and Exploration of High-Throughput Biological Datasets

Fjukstad, Bjørn

dc.contributor.advisor	Bongo, Lars Ailo
dc.contributor.author	Fjukstad, Bjørn
dc.date.accessioned	2019-01-31T14:50:30Z
dc.date.available	2019-01-31T14:50:30Z
dc.date.issued	2019-01-21
dc.description.abstract	This dissertation argues that we can develop unified systems for reproducible exploration and analysis of high-throughput biological datasets. We propose an approach, Small Modular Entities (SME), that orchestrates the execution of analysis pipelines and data exploration applications. We realize SMEs using software container technologies together with well-defined interfaces, configuration, and orchestration. It simplifies the development of such applications, and provides detailed information to reproduce the analyses.	en_US
dc.description.doctoraltype	ph.d.	en_US
dc.description.popularabstract	This dissertation argues that we can develop unified systems for reproducible exploration and analysis of high-throughput biological datasets. We propose an approach, Small Modular Entities (SME), that orchestrates the execution of analysis pipelines and data exploration applications. We realize SMEs using software container technologies together with well-defined interfaces, configuration, and orchestration. It simplifies the development of such applications, and provides detailed information to reproduce the analyses.	en_US
dc.description.sponsorship	UiT	en_US
dc.identifier.isbn	978-82-8236-328-0 (trykt) og 978-82-8236-329-7 (pdf)
dc.identifier.uri	https://hdl.handle.net/10037/14576
dc.language.iso	eng	en_US
dc.publisher	UiT Norges arktiske universitet	en_US
dc.publisher	UiT The Arctic University of Norway	en_US
dc.relation.haspart	<p>Paper I: Fjukstad, B., Olsen, K.S., Jareid, M., Lund, E. & Bongo, L.A. (2015). Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies [version 2; referees: 1 approved, 2 approved with reservations]. <i>F1000Research, 4</i>:81. Also available at <a href=https://doi.org/10.12688/f1000research.6238.2>https://doi.org/10.12688/f1000research.6238.2. </a> Version 1 available at <a href=http://hdl.handle.net/10037/8813>http://hdl.handle.net/10037/8813. </a><p> <p>Paper II: Fjukstad, B., Dumeaux, V., Olsen, K.S., Lund, E., Hallett, M. & Bongo, L.A. (2017). Building applications for interactive data exploration in systems biology. <i>ACM-BCB -17: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics</i>, 556–561. Also available at <a href=http://dx.doi.org/10.1145/3107411.3107481>http://dx.doi.org/10.1145/3107411.3107481. </a><p> <p>Paper III: Dumeaux, V., Fjukstad, B., Fjosne, H.E., Frantzen, J-O., Holmen, M.M., Rodegerdts, E. … Hallett, M. (2017). Interactions between the tumor and the blood systemic response of breast cancer patients. <i>PLoS Computational Biology, 13</i>(9), e1005680. Also available at <a href=https://doi.org/10.1371/journal.pcbi.1005680>https://doi.org/10.1371/journal.pcbi.1005680. </a><p> <p>Paper IV: Fjukstad, B. & Bongo, L.A. (2017). A review of scalable bioinformatics pipelines. <i>Data Science and Engineering, 2</i>(3), 245–251. Also available at <a href= https://doi.org/10.1007/s41019-017-0047-z>https://doi.org/10.1007/s41019-017-0047-z. </a><p> <p>Paper V: Raknes, I.A., Fjukstad, B. & Bongo, L.A. (2017). nsroot: Minimalist process isolation tool implemented with linux namespaces.<i> Norsk Informatikkonferanse</i>. Also available at <a href= https://ojs.bibsys.no/index.php/NIK/index>https://ojs.bibsys.no/index.php/NIK/index. </a><p> <p>Paper VI: Fjukstad, B., Dumeaux, V., Hallett, M. & Bongo, L.A. (2018). Reproducible data analysis pipelines for precision medicine. (Manuscript). Also available at <a href=https://doi.org/10.1101/354811>https://doi.org/10.1101/354811. </a><p>	en_US
dc.rights.accessRights	openAccess	en_US
dc.rights.holder	Copyright 2019 The Author(s)
dc.rights.uri	https://creativecommons.org/licenses/by-nc-sa/3.0	en_US
dc.rights	Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)	en_US
dc.subject	VDP::Mathematics and natural science: 400::Information and communication science: 420::System development and system design: 426	en_US
dc.subject	VDP::Matematikk og Naturvitenskap: 400::Informasjons- og kommunikasjonsvitenskap: 420::Systemutvikling og – arbeid: 426	en_US
dc.subject	VDP::Mathematics and natural science: 400::Basic biosciences: 470::Bioinformatics: 475	en_US
dc.subject	VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Bioinformatikk: 475	en_US
dc.title	Toward Reproducible Analysis and Exploration of High-Throughput Biological Datasets	en_US
dc.type	Doctoral thesis	en_US
dc.type	Doktorgradsavhandling	en_US