Toward Reproducible Analysis and Exploration of High-Throughput Biological Datasets

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Date
2019-01-21
Type
Doctoral thesis
Doktorgradsavhandling

Author
Fjukstad, Bjørn
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.
Has part(s)

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]. F1000Research, 4:81. Also available at https://doi.org/10.12688/f1000research.6238.2. Version 1 available at http://hdl.handle.net/10037/8813.

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. ACM-BCB -17: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 556–561. Also available at http://dx.doi.org/10.1145/3107411.3107481.

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. PLoS Computational Biology, 13(9), e1005680. Also available at https://doi.org/10.1371/journal.pcbi.1005680.

Paper IV: Fjukstad, B. & Bongo, L.A. (2017). A review of scalable bioinformatics pipelines. Data Science and Engineering, 2(3), 245–251. Also available at https://doi.org/10.1007/s41019-017-0047-z.

Paper V: Raknes, I.A., Fjukstad, B. & Bongo, L.A. (2017). nsroot: Minimalist process isolation tool implemented with linux namespaces. Norsk Informatikkonferanse. Also available at https://ojs.bibsys.no/index.php/NIK/index.

Paper VI: Fjukstad, B., Dumeaux, V., Hallett, M. & Bongo, L.A. (2018). Reproducible data analysis pipelines for precision medicine. (Manuscript). Also available at https://doi.org/10.1101/354811.

Publisher
UiT Norges arktiske universitet
UiT The Arctic University of Norway
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