| 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.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 |
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