publication . Article . Other literature type . Research . Preprint . 2020

StreamFlow: cross-breeding cloud with HPC

Colonnelli, Iacopo; Cantalupo, Barbara; Merelli, Ivan; Aldinucci, Marco;
Open Access
  • Published: 26 Feb 2020 Journal: IEEE Transactions on Emerging Topics in Computing (eissn: 2376-4562, Copyright policy)
  • Publisher: Institute of Electrical and Electronics Engineers (IEEE)
  • Country: Italy
Abstract
Comment: 30 pages - 2020 IEEE Transactions on Emerging Topics in Computing
Subjects
free text keywords: Computer Science (miscellaneous), Human-Computer Interaction, Information Systems, Computer Science Applications, Workflow, High-Performance Computing, Cloud, Bioinformatics, FOS: Computer and information sciences, Computer Science - Distributed, Parallel, and Cluster Computing, D.1.3, D.3.2, C.1.3, Cloud computing, Task analysis, Containers, Tools, Computer architecture, DSL, Pipelines
Funded by
EC| DeepHealth
Project
DeepHealth
Deep-Learning and HPC to Boost Biomedical Applications for Health
  • Funder: European Commission (EC)
  • Project Code: 825111
  • Funding stream: H2020 | IA
Download fromView all 8 versions
Zenodo
Other literature type . 2020
Provider: Datacite
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Research . 2020
Provider: ZENODO
Zenodo
Other literature type . 2020
Provider: Datacite
43 references, page 1 of 3

[1] Why use work ows? https://taverna.incubator.apache.org/ introduction/why-use-workflows. Accessed: 2020-02-16.

[2] E. Afgan, D. Baker, M. van den Beek, D. J. Blankenberg, D. Bouvier, M. Cech, J. Chilton, D. Clements, N. Coraor, C. Eberhard, B. A. Gruning, A. Guerler, J. Hillman-Jackson, G. V. Kuster, E. Rasche, N. Soranzo, N. Turaga, J. Taylor, A. Nekrutenko, and J. Goecks. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research, 44(Webserver-Issue):W3{W10, 2016.

[3] M. Albrecht, P. Donnelly, P. Bui, and D. Thain. Make ow: a portable abstraction for data intensive computing on clusters, clouds, and grids. In Proceedings of the 1st ACM SIGMOD Workshop on Scalable Work ow Execution Engines and Technologies, SWEET@SIGMOD 2012, Scottsdale, AZ, USA, May 20, 2012, page 1, 2012.

[4] M. Aldinucci, S. Bagnasco, S. Lusso, P. Pasteris, and S. Rabellino. Occam: a exible, multi-purpose and extendable HPC cluster. In Journal of Physics: Conf. Series (CHEP 2016), volume 898, page 082039, San Francisco, USA, 2017. [OpenAIRE]

[5] M. Aldinucci, H. L. Bouziane, M. Danelutto, and C. Perez. STKM on SCA: a uni ed framework with components, work ows and algorithmic skeletons. In Proc. of 15th Intl. Euro-Par 2009 Parallel Processing, volume 5704 of LNCS, pages 678{690, Delft, The Netherlands, Aug. 2009. Springer.

[6] M. Aldinucci, S. Rabellino, M. Pironti, F. Spiga, P. Viviani, M. Drocco, M. Guerzoni, G. Boella, M. Mellia, P. Margara, I. Drago, R. Marturano, G. Marchetto, E. Piccolo, S. Bagnasco, S. Lusso, S. Vallero, G. Attardi, A. Barchiesi, A. Colla, and F. Galeazzi. HPC4AI, an AI-on-demand federated platform endeavour. In ACM Computing Frontiers, Ischia, Italy, May 2018. [OpenAIRE]

[7] P. Amstutz, M. R. Crusoe, N. Tijani, B. Chapman, J. Chilton, M. Heuer, A. Kartashov, J. Kern, D. Leehr, H. Mnager, M. Nedeljkovich, M. Scales, S. Soiland-Reyes, and L. Stojanovic. Common work ow language, v1.0, 2016.

[8] D. Aran, A. P. Looney, L. Liu, E. Wu, V. Fong, A. Hsu, S. Chak, R. P. Naikawadi, P. J. Wolters, A. R. Abate, A. J. Butte, and M. Bhattacharya. Reference-based analysis of lung single-cell sequencing reveals a transitional pro brotic macrophage. Nature Immunology, 20(2):163{172, 2019. [OpenAIRE]

[9] M. P. Atkinson, S. Gesing, J. Montagnat, and I. J. Taylor. Scienti c workows: Past, present and future. Future Generation Comp. Syst., 75:216{ 227, 2017. [OpenAIRE]

[10] R. Badia, E. Ayguade, and J. Labarta. Work ows for science: A challenge when facing the convergence of HPC and big data. Supercomput. Front. Innov.: Int. J., 4(1):2747, Mar. 2017.

[11] S. C. Boulakia, K. Belhajjame, O. Collin, J. Chopard, C. Froidevaux, A. Gaignard, K. Hinsen, P. Larmande, Y. L. Bras, F. Lemoine, F. Mareuil, H. Menager, C. Pradal, and C. Blanchet. Scienti c work ows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Comp. Syst., 75:284{298, 2017. [OpenAIRE]

[12] A. Butler, P. Ho man, P. Smibert, E. Papalexi, and R. Satija. Integrating single-cell transcriptomic data across di erent conditions, technologies, and species. Nature Biotechnology, 36(5):411{420, 2018.

[13] M. Caballero, J. Gomez, and A. Bantouna. Deep-learning and hpc to boost biomedical applications for health (deephealth). In 2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS), pages 150{155, Los Alamitos, CA, USA, June 2019. IEEE Computer Society.

[14] V. Cima, S. Bohm, J. Martinovic, J. Dvorsky, K. Janurova, T. V. Aa, T. J. Ashby, and V. I. Chupakhin. Hyperloom: A platform for de ning and executing scienti c pipelines in distributed environments. In Proceedings of the 9th Workshop on Parallel Programming and RunTime Management Techniques for Manycore Architectures and 7th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms, PARMA-DITAM@HiPEAC 2018, Manchester, United Kingdom, January 23-23, 2018, pages 1{6, 2018.

[15] R. F. da Silva, R. Filgueira, I. Pietri, M. Jiang, R. Sakellariou, and E. Deelman. A characterization of work ow management systems for extreme-scale applications. Future Generation Comp. Syst., 75:228{238, 2017.

43 references, page 1 of 3
Abstract
Comment: 30 pages - 2020 IEEE Transactions on Emerging Topics in Computing
Subjects
free text keywords: Computer Science (miscellaneous), Human-Computer Interaction, Information Systems, Computer Science Applications, Workflow, High-Performance Computing, Cloud, Bioinformatics, FOS: Computer and information sciences, Computer Science - Distributed, Parallel, and Cluster Computing, D.1.3, D.3.2, C.1.3, Cloud computing, Task analysis, Containers, Tools, Computer architecture, DSL, Pipelines
Funded by
EC| DeepHealth
Project
DeepHealth
Deep-Learning and HPC to Boost Biomedical Applications for Health
  • Funder: European Commission (EC)
  • Project Code: 825111
  • Funding stream: H2020 | IA
Download fromView all 8 versions
Zenodo
Other literature type . 2020
Provider: Datacite
ZENODO
Research . 2020
Provider: ZENODO
Zenodo
Other literature type . 2020
Provider: Datacite
43 references, page 1 of 3

[1] Why use work ows? https://taverna.incubator.apache.org/ introduction/why-use-workflows. Accessed: 2020-02-16.

[2] E. Afgan, D. Baker, M. van den Beek, D. J. Blankenberg, D. Bouvier, M. Cech, J. Chilton, D. Clements, N. Coraor, C. Eberhard, B. A. Gruning, A. Guerler, J. Hillman-Jackson, G. V. Kuster, E. Rasche, N. Soranzo, N. Turaga, J. Taylor, A. Nekrutenko, and J. Goecks. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research, 44(Webserver-Issue):W3{W10, 2016.

[3] M. Albrecht, P. Donnelly, P. Bui, and D. Thain. Make ow: a portable abstraction for data intensive computing on clusters, clouds, and grids. In Proceedings of the 1st ACM SIGMOD Workshop on Scalable Work ow Execution Engines and Technologies, SWEET@SIGMOD 2012, Scottsdale, AZ, USA, May 20, 2012, page 1, 2012.

[4] M. Aldinucci, S. Bagnasco, S. Lusso, P. Pasteris, and S. Rabellino. Occam: a exible, multi-purpose and extendable HPC cluster. In Journal of Physics: Conf. Series (CHEP 2016), volume 898, page 082039, San Francisco, USA, 2017. [OpenAIRE]

[5] M. Aldinucci, H. L. Bouziane, M. Danelutto, and C. Perez. STKM on SCA: a uni ed framework with components, work ows and algorithmic skeletons. In Proc. of 15th Intl. Euro-Par 2009 Parallel Processing, volume 5704 of LNCS, pages 678{690, Delft, The Netherlands, Aug. 2009. Springer.

[6] M. Aldinucci, S. Rabellino, M. Pironti, F. Spiga, P. Viviani, M. Drocco, M. Guerzoni, G. Boella, M. Mellia, P. Margara, I. Drago, R. Marturano, G. Marchetto, E. Piccolo, S. Bagnasco, S. Lusso, S. Vallero, G. Attardi, A. Barchiesi, A. Colla, and F. Galeazzi. HPC4AI, an AI-on-demand federated platform endeavour. In ACM Computing Frontiers, Ischia, Italy, May 2018. [OpenAIRE]

[7] P. Amstutz, M. R. Crusoe, N. Tijani, B. Chapman, J. Chilton, M. Heuer, A. Kartashov, J. Kern, D. Leehr, H. Mnager, M. Nedeljkovich, M. Scales, S. Soiland-Reyes, and L. Stojanovic. Common work ow language, v1.0, 2016.

[8] D. Aran, A. P. Looney, L. Liu, E. Wu, V. Fong, A. Hsu, S. Chak, R. P. Naikawadi, P. J. Wolters, A. R. Abate, A. J. Butte, and M. Bhattacharya. Reference-based analysis of lung single-cell sequencing reveals a transitional pro brotic macrophage. Nature Immunology, 20(2):163{172, 2019. [OpenAIRE]

[9] M. P. Atkinson, S. Gesing, J. Montagnat, and I. J. Taylor. Scienti c workows: Past, present and future. Future Generation Comp. Syst., 75:216{ 227, 2017. [OpenAIRE]

[10] R. Badia, E. Ayguade, and J. Labarta. Work ows for science: A challenge when facing the convergence of HPC and big data. Supercomput. Front. Innov.: Int. J., 4(1):2747, Mar. 2017.

[11] S. C. Boulakia, K. Belhajjame, O. Collin, J. Chopard, C. Froidevaux, A. Gaignard, K. Hinsen, P. Larmande, Y. L. Bras, F. Lemoine, F. Mareuil, H. Menager, C. Pradal, and C. Blanchet. Scienti c work ows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Comp. Syst., 75:284{298, 2017. [OpenAIRE]

[12] A. Butler, P. Ho man, P. Smibert, E. Papalexi, and R. Satija. Integrating single-cell transcriptomic data across di erent conditions, technologies, and species. Nature Biotechnology, 36(5):411{420, 2018.

[13] M. Caballero, J. Gomez, and A. Bantouna. Deep-learning and hpc to boost biomedical applications for health (deephealth). In 2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS), pages 150{155, Los Alamitos, CA, USA, June 2019. IEEE Computer Society.

[14] V. Cima, S. Bohm, J. Martinovic, J. Dvorsky, K. Janurova, T. V. Aa, T. J. Ashby, and V. I. Chupakhin. Hyperloom: A platform for de ning and executing scienti c pipelines in distributed environments. In Proceedings of the 9th Workshop on Parallel Programming and RunTime Management Techniques for Manycore Architectures and 7th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms, PARMA-DITAM@HiPEAC 2018, Manchester, United Kingdom, January 23-23, 2018, pages 1{6, 2018.

[15] R. F. da Silva, R. Filgueira, I. Pietri, M. Jiang, R. Sakellariou, and E. Deelman. A characterization of work ow management systems for extreme-scale applications. Future Generation Comp. Syst., 75:228{238, 2017.

43 references, page 1 of 3
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