Journal, conference, book, and workshop papers

  1. Petra ten Hoopen P, Robert D. Finn, Lars Ailo Bongo, Erwan Corre, Bruno Fosso, Folker Meyer, Alex Mitchell, Eric Pelletier, Graziano Pesole, Monica Santamaria, Nils Peder Willassen, and Guy Cochrane. The metagenomics data life-cycle: standards and best practices. GigaScience 2017.
  2. Espen Mikal Robertsen, Hubert Denise, Alex Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen. ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services. F1000Research. 2017.
  3. Edvard Pedersen, Lars Ailo Bongo. Large-scale Biological Meta-Database Management. Future Generation Computer Systems. Vol 67. Feb 2017.
  4. Nils Peder Willassen, Robert D. Finn, Guy Cochrane, Lars Ailo Bongo, Petra Ten Hoppen. Marine metagenomics infrastructure as driver for research and industrial innovation. In Proc. of ECCB. 2016.
  5. Edvard Pedersen, Lars Ailo Bongo. Big Biological Data Management. Book chapter in "Resource Management for Big Data Platforms and Applications” , Springer series on Computer Communications and Networks. 2016.
  6. Ove Kåven, Lars Ailo Bongo. MORTAL - Multiparadigm Optimizing Retargetable Transdisciplinary Abstraction Language. in Proc. of NIK 2015, Ålesund, Norway.
  7. Milan Mihajlovic, Lars Ailo Bongo, Raimondas Ciegis, Neki Frasheri, Dragi Kimovski, Peter Kropf, Svetozar Margenov, Maya Neytcheva, Thomas Rauber, Gudula Runger, Roman Trobec, Roel Wuyts, Roman Wyrzykowski, Jing Gong. Applications for ultrascale computing. Supercomputing Frontiers and Innovations, v. 2, n. 1, June 2015. ISSN 2313-8734.
  8. Bjørn Fjukstad, Karina Standahl Olsen, Mie Jareid, Eiliv Lund, Lars Ailo Bongo. Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies. F1000Research 2015, 4:81.
  9. Lars Ailo Bongo, Edvard Pedersen, and Martin Ernstsen. Data-intensive computing infrastructure systems for unmodified biological data analysis pipelines. Lecture Notes in Bioinformatics, vol. 8623. Springer, 2015.
  10. Qian Zhu, Aaron K Wong, Arjun Krishnan, Miriam R Aure, Alicja Tadych, Ran Zhang, David C Corney, Casey S Greene, Lars A Bongo, Vessela N Kristensen, Moses Charikar, Kai Li, Olga G Troyanskaya. Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nature Methods 12, 211–214. 2015.
  11. Edvard Pedersen, Inge Alexander Raknes, Martin Ernstsen, and Lars Ailo Bongo. Integrating Data-intensive Computing Systems with Biological Data Processing Frameworks. in Proc. of PDP 2015, IEEE. March 2015, Turku, Finland.
  12. Bjørn Fjukstad, Karina Standahl Olsen, Mie Jareid, Eiliv Lund, Lars Ailo Bongo. Kvik: Interactive exploration of genomic data from the NOWAC postgenome biobank. in Proc. of NIK 2014. November 2014, Fredrikstad, Norway.
  13. Giacomo Tartari, Lars Tiede, Einar Jakobsen Holsbø, Kenneth Knudsen, Inge Alexander Raknes, Bjørn Fjukstad, Nicolle Mode, John Markus Bjørndalen, Eiliv Lund, Lars Ailo Bongo. Mr. Clean: a tool for tracking and comparing the lineage of scientific visualization code. in Proc. of 2nd IEEE Working Conference on Software Visualization (VISSOFT 2014). September 2014, Victoria, Canada.
  14. Martin Ernstsen, Erik Kjærner-Semb, Nils P. Willassen, Lars Ailo Bongo. Mario: interactive tuning of biological analysis pipelines using iterative processing. in Proc. of 5th International Workshop on High Performance Bioinformatics and Biomedicine (HiBB). Springer LNCS, vol. 8805, 2014.
  15. Lars Ailo Bongo, Edvard Pedersen, and Martin Ernstsen. Data-intensive computing infrastructure systems for unmodified biological data analysis pipelines. in Proc. of CIBB 2014 – Eleventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics. June 2014, Cambridge, UK.
  16. Edvard Pedersen, Nils P. Willassen, Lars Ailo Bongo. Transparent incremental updates for Genomics Data Analysis Pipelines . in Proc. of HiBB 2013 – 4th Workshop on High Performance Bioinformatics and Biomedicine. Springer LNCS, vol 8374, 2014, pp 311-320.
  17. Christopher Park, Aaron Wong, Casey Greene, Jessica Rowland, Yuanfang Guan, Lars Ailo Bongo, Rebecca D. Burdine, Olga Troyanskaya. Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes. PLoS Computational Biology. vol 9(3), 2013.
  18. Otto Anshus, Tor-Magne Stien Hagen, Bård Fjukstad, Lars Ailo Bongo, Yong Liu, Lars Tiede. Nine Years of the Tromsø Display Wall, in POWERWALL: International Workshop on Interactive, Ultra-High-Resolution Displays, part of the ACM SIGCHI Conference on Human Factors in Computing Systems. 2013.
  19. Lars Ailo Bongo. Bulk Synchronous Visualization. in Proc. of the 2013 International Workshop on Programming Models and Applications for Multicores and Manycores. ACM, pp 21-30, Shenzhen, China, 2013.
  20. Edvard Pedersen, Nils Peder Willassen, Lars Ailo Bongo. GeStore – Incremental Computation for Metagenomic Pipelines . in Proceedings of NIK 2012. Tapir. pp. 251-254. Bodø, Norway.
  21. Lars Ailo Bongo. BSV - 1000 Window Visualization System. in Proceedings of NIK 2012. Tapir. pp. 251-254. Bodø, Norway.
  22. Aaron Wong, Christopher Park, Casey Greene, Lars Ailo Bongo, Yuanfang Guan, Olga Troyanskaya. IMP: A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Research. vol 40, 2012.
  23. Terje André Johansen, Daniel Stødle, Lars Ailo Bongo. A Web Application Widget Library for Scalable Interactive Biological Data Visualization. in Proceedings of NIK 2011. Tapir. pp. 109-120. Tromsø, Norway.
  24. William Josephson, Lars Ailo Bongo, David Flynn, Kai Li. DFS: A File System for Virtualized Flash Storage. ACM TOS. Vol. 6, Issue 3. September 2010.
  25. William Josephson, Lars Ailo Bongo, David Flynn, Kai Li. DFS: A File System for Virtualized Flash Storage. Usenix ;login. Vol. 35, Number 2. April 2010.
  26. William Josephson, Lars Ailo Bongo, David Flynn, Kai Li. DFS: A File System for Virtualized Flash Storage. in Proceedings of the 8th USENIX Conference on File and Storage Technologies (FAST '10). February 23–26, 2010.
  27. Lars Ailo Bongo, Grant Wallace, Tore Larsen, Kai Li, and Olga Troyanskaya. System Support for Remote Visualization of Genomics Applications over Wide Area Networks. in Proc. of The International Workshop on Distributed, High-Performance and Grid Computing in Computational Biology. Springer Lecture Notes in Bioinformatics 4360. Pp. 157-174. Eilat, Israel, 2007.
  28. Lars Ailo Bongo, Brian Vinter, Otto J. Anshus, Tore Larsen and John Markus Bjørndalen. Using Overdecomposition to Overlap Communication Latencies with Computation and Take Advantage of SMT Processors. in Proceedings of the 2006 International Conference on Parallel Processing Workshops. IEEE Computer Society. pp 239--247. Columbus, Ohio, USA. August. 2006.
  29. Lars Ailo Bongo, Otto J. Anshus and John Markus Bjørndalen. Low overhead high performance monitoring of collective communication. in Proceedings of the 2005 International Conference on Parallel Processing. IEEE Computer Society. pp 455--464. Oslo, Norway. June. 2005.
  30. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. Collective communication performance analysis within the communication system. in Proceedings of Euro-Par 2004. LNCS 3149, Springer 2004.
  31. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen, Tore Larsen. Extending Collective Operations with Application Semantics for Improving Multi-cluster Performance. in Proceedings of Third International Workshop on Algorithms, Models and Tools for Parallel Computing on Heterogeneous Networks (HeteroPar04). IEEE Computer Society 2004.
  32. Otto Anshus, John Markus Bjørndalen, Lars Ailo Bongo. Experiences Parallelizing, Configuring, and Monitoring of Parallel Applications on Clusters. Parallel computing: Software Technology, Algorithms, Architectures and Applications. Elsevier 2004.
  33. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. EventSpace - Exposing and Observing Communication Behavior of Parallel Cluster Applications. in Euro-Par 2003 Parallel Processing, Proceedings of the 9th International Euro-Par Conference. Springer 2003.
  34. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. Using a Virtual Event Space to Understand Parallel Application Communication Behavior. in Norsk informatikkonferanse NIK'2003. Tapir Akademisk Forlag 2003.
  35. John Markus Bjørndalen, Otto Anshus, Tore Larsen, Lars Ailo Bongo, Brian Vinter. Scalable Processing and Communication Performance in a Multi-Media Related Context. in Proceedings of the 28th EuroMicro Conference. 2002.

ArXiv, abstracts, and reports

  1. Hege Marie Bøvelstad, Einar Holsbø, Lars Ailo Bongo, and Eiliv Lund, A standard operating procedure for outlier removal in large‐sample epidemiological transcriptomics datasets. bioRxiv, 2017.
  2. E. Holsbø, V. Perduca, L. A. Bongo, E. Lund, and E. Birmelé, Curve Selection For Predicting Breast Cancer Metastasis From Prospective Gene Expression In Blood. bioRxiv, 2017.
  3. Bjørn Fjukstad, Vanessa Dumeaux, Karina Standahl Olsen, Michael Hallett, Eiliv Lund, Lars Ailo Bongo. Building Applications For Interactive Data Exploration In Systems Biology, bioRxiv 2017.
  4. Inge Alexander Raknes, Bjørn Fjukstad, Lars Ailo Bongo. nsroot: Minimalist Process Isolation Tool Implemented With Linux Namespaces. ArXiv. 2016.
  5. Lars Ailo Bongo, Mikael Borg, Amelie Cornelis, Montserrat Gonzalez, Luis Gracia, Rob Hooft, Jarno Laitinen, Ilkka Lappalainen, Mikael Linden, Ludek Matyska, Steven Newhouse, Tommi Nyrönen, Michael Prochazka, Mirek Ruda, Harri Salminen, Christine Staiger, Tony Wildish. The ELIXIR Compute Platform: A Technical Services Roadmap for supporting Life Science Research in Europe. 2016.
  6. Espen Mikal Robertsen, Tim Kahlke, Inge Alexander Raknes, Edvard Pedersen, Erik Kjærner Semb, Martin Ernstsen, Lars Ailo Bongo, Nils Peder Willassen. META-pipe - Pipeline Annotation, Analysis and Visualization of Marine Metagenomic Sequence Data. ArXiv. 2016.
  7. Karina Standahl Olsen, Einar Holsbø, Kamilla Rognmo, Sanda Krum-Hansen, Eiliv Lund. Stress related to a suspicious mammogram - potential transcriptomic effects. Norsk Epidemiologi, Supplement 2015; Volume 25.
  8. Bjørn Fjukstad, Karina Standahl Olsen, Mie Jareid, Eiliv Lund, Lars Ailo Bongo. Interactive omics data exploration in epidemiological studies. Norsk Epidemiologi, Supplement 2015; Volume 25.
  9. Lars Ailo Bongo. Reducing the network latency and bandwidth requirements of distributed and parallel applications. PhD. Thesis. University of Tromsø. July 2007.
  10. Lars Ailo Bongo. The Longcut Wide Area Network Emulator: Design and Evaluation. IFI-UITØ Technical Report(53). 2005.
  11. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. Evaluating the Performance of the Allreduce Collective Operation on Clusters: Approach and Results. IFI-UITØ Technical Report(48). 2004.
  12. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. Performance Monitoring. A Report for the NOTUR Project Emerging Technologies: Cluster. 2003.
  13. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. Using a Virtual Event Space to Understand Parallel Application Communication Behavior. IFI-UITØ Technical Report(44). 2003.
  14. Espen S. Johnsen, Otto Anshus, John Markus Bjørndalen, Lars Ailo Bongo. Survey of execution monitoring tools for computer clusters. A Report for the NOTUR Project Emerging Technologies: Cluster. 2003.
  15. Espen S. Johnsen, Otto Anshus, John Markus Bjørndalen, Lars Ailo Bongo. Survey of optimizing techniques for parallel programs running on computer clusters. A Report for the NOTUR Project Emerging Technologies: Cluster. 2003.

Design documents

  1. Note! These documents are often work in progress
  2. Inge Alexander Raknes, Giacomo Tartari, Aleksandr Agafonov, Lars Ailo Bongo. META-pipe design document. ELIXIR-EXCELERATE design document. Under preparation.
  3. Inge Alexander Raknes, Lars Ailo Bongo. META-pipe authorization server. ELIXIR-EXCELERATE design document. Under preparation.
  4. Aleksandr Agafonov, Lars Ailo Bongo. MMG cluster setup. ELIXIR-EXCELERATE design document. Under preparation.
  5. Inge Alexander Raknes, Lars Ailo Bongo. Marine reference database - technical specification. ELIXIR-EXCELERATE design document. Under preparation.

Theses

  1. Espen Mikal Robertsen. META-pipe – Distributed Pipeline Analysis of Marine Metagenomic Sequence Data. Ph. D. thesis. Dept. of Chemistry. University of Tromsø. February 2017.
  2. Edvard Pedersen. A Data Management Model For Large-Scale Bioinformatics Analysis. Ph. D. thesis. Dept. of Computer Science, University of Tromsø. September 2016.
  3. Jarl Fagerli. COMBUSTI/O. Abstractions facilitating parallel execution of programs implementing common I/O patterns in a pipelined fashion as workflows in Spark. Master thesis. Dept. of Computer Science, University of Tromsø. December 2015.
  4. Kenneth Knudsen. Freia: Exploring Biological Pathways Using Unity3D. Master thesis. Dept. of Computer Science, University of Tromsø. November 2015.
  5. Morten Grønnesby. Automated Lung Sound Analysis. Master’s thesis. Dept. of Computer Science. University of Tromsø. June 2016.
  6. Ove Kåven. Multiparadigm optimizing retargetable transdisciplinary abstraction language. Master thesis. Dept. of Computer Science, University of Tromsø. April 2015.
  7. Inge Alexander Raknes. Spark-SPELL: low-latency query-based search for gene expression compendia on cluster computers. Master thesis. Dept. of Computer Science, University of Tromsø. June 2014.
  8. Kenneth Knudsen. Amdex: automated meta-data extraction from KEGG pathways. Bachelor thesis. Dept. of Computer Science, University of Tromsø. June 2014.
  9. Bjørn Fjukstad. Kvik: interactive exploration of genomic data from the NOWAC postgenome biobank. Master thesis. Dept. of Computer Science, University of Tromsø. Mai 2014.
  10. Martin Ernstsen. Mario - A system for iterative and interactive processing of biological data. Master thesis. Dept. of Computer Science, University of Tromsø. December 2013.
  11. Edvard Pedersen. GeStore : incremental computation for metagenomic pipelines. Master thesis. Dept. of Computer Science, University of Tromsø. June 2012.
  12. Terje André Johansen. A scalable, interactive widget library for visualizing biological data. Master thesis. Dept. of Computer Science, University of Tromsø. June 2011.
  13. Daniel R. Barrett. Undergraduate thesis. Dept. of Computer Science. Princeton University.
  14. Torje Henriksen. Efficient intra-node Communication for Chip Multiprocessors.. Master thesis. Dept. of Computer Science, University of Tromsø. October 2008.
  15. Espen S. Johnsen. Configuration of collective operations in LAM/MPI by use of scripting. Master thesis. Dept. of Computer Science, University of Tromsø. October 2008.

Project Reports

  1. Johan Ravn. Wheeze Detection using Deep Convolutional Neural Network. Capstone Project. Dept. of Computer Science, University of Tromsø. December 2016.
  2. Frode Opdahl. Virtual reality. Capstone Project. Dept. of Computer Science, University of Tromsø. December 2016.
  3. Nina Angelvik. Low-cost portable air quality sensor kit and cloud service. Capstone Project. Dept. of Computer Science, University of Tromsø. December 2016.
  4. Morten Grønnesby. Pulmonary Crackle Detection Using Signal Processing and Machine Learning. Capstone Project. Dept. of Computer Science, University of Tromsø. December 2015.
  5. Jarl Fagerli. Big Data Facilitation and Management. Capstone Project. Dept. of Computer Science, University of Tromsø. December 2015.
  6. Inge Alexander Raknes. Data cleaning for biological data. Capstone Project. Dept. of Computer Science, University of Tromsø. December 2013.
  7. Bjørn Fjukstad. NOWAC Data Exploration. Capstone Project. Dept. of Computer Science, University of Tromsø. June 2013.
  8. Edvard Pedersen. Big data analysis for metagenomics. Capstone Project. Dept. of Computer Science, University of Tromsø. June 2013.

Posters

  1. Terje Klemetsen, et al. Novel Marine Reference Databases, The Marine Metagenomics Portal (MMP). Poster at the Elixir all-hands meeting. Rome, Italy. April 2017.
  2. Espen M. Robertsen, et al. META-pipe 2.0. Poster at the Elixir all-hands meeting. Rome, Italy. April 2017.
  3. Einar Holsbø. Predicting breast cancer metastasis from blood gene expression using time-to-diagnosis data to derive signature estimates. Poster presented at the 2017 Statistical Methods for Postgenomic Data workshop. London, UK. January 2017.
  4. Espen M. Robertsen, et al. Elixir Pilot Action: Marine metagenomics - towards user centric services. Poster at the Elixir all-hands meeting. Barcelona, Spain. March 2016.
  5. ELIXIR.NO team. ELIXIR.NO - The national technology platform for bioinformatics. Poster at NBS meeting. Tromsø, Norway. January 2016.
  6. Espen Mikal Robertsen, Edvard Pedersen, Martin Ernstsen, Tim Kalhke, Lars Ailo Bongo, Nils Peder Willassen. META-pipe – Pipeline annotation, analysis and visualization of metagenomic data. Poster at NBS meeting. Tromsø, Norway. January 2016.
  7. NeLS team. NeLS: Norwegian e-Infrastructure for Life Sciences. Poster at 2015 Galaxy Community Conference (GCC2015). Norwich, UK. July 2015.
  8. Espen M. Robertsen, et al. Elixir Pilot Action: Marine metagenomics - towards user centric services. Poster at the Elixir all-hands meeting. Hinxton, UK. March 2015.
  9. Giacomo Tartari, Lars Tiede, Einar Jakobsen Holsbø, Kenneth Knudsen, Inge Alexander Raknes, Bjørn Fjukstad, Nicolle Mode, John Markus Bjørndalen, Eiliv Lund, Lars Ailo Bongo. Mr. Clean: a tool for tracking and comparing the lineage of scientific visualization code. Poster at 2nd IEEE Working Conference on Software Visualization (VISSOFT 2014). September 2014, Victoria, Canada.
  10. Lars Ailo Bongo. Bulk Synchronous Visualization. Poster at the 2nd IEEE Symposium on Biological Data Visualization. Seattle, WA, USA. October 2012. (extended abstract, poster).
  11. Edvard Pedersen, Nils Peder Willassen, Lars Ailo Bongo. GeStore - Incremental Computations for Metagenomic Pipelines. Poster at Norsk Bioinformatikk Forum. Bergen, Norway. October 2012. (poster)
  12. Edvard Pedersen, Nils Peder Willassen, Lars Ailo Bongo. GeStore - Incremental Computations for Metagenomic Pipelines. Poster at the 11th Annual Meeting on High Performance Computing and Infrastructure in Norway - NOTUR 2012. Tromsø, Norway. June 2012.(poster)
  13. Lars Ailo Bongo, Daniel Stødle, Grant Wallace, Tore Larsen, Kai Li and Olga Troyanskaya. System Support for Collaborative Genomics Visualizations. Poster at the 16th International Conference on Intelligent Systems for Molecular Biology. Toronto, Canada. July 2008. (poster).
  14. Lars Ailo Bongo. Dynamically adapting communication behavior of parallel applications. NOTUR gathering. Oslo, Norway. May 2003.