Towards Provisioning of Reproducible, Reviewable and Reusable In-Silico Experiments with the GridSpace2 Platform

  • Eryk Ciepiela
  • Bartosz Wilk
  • Daniel Harężlak
  • Marek Kasztelnik
  • Maciej Pawlik
  • Marian Bubak
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8500)

Abstract

The observed paradigm switch towards computational methods in research poses a serious challenge for e-infrastructure providers. Apart from delivering computing power, researchers are expected to create the foundation for complete and viable e-science environments. To address this demand, GridSpace2 was developed as a platform for provisioning reproducible, reviewable and reusable in-silico experiments. The resulting environment was applied in the scope of the PLGrid Plus project. In this work we analyze requirements, which should be met by in-silico experiments and describe how these requirements can be accommodated on the platform level, thus decreasing the costs of acquisition, preservation and curation of in-silico experiments. In order to evaluate our approach, we qualitatively assess how the features of GridSpace2 conform to these requirements and how the platform reduces the costs of provisioning in-silico experiments.

Keywords

e-science in-silico experiments reproducibility problem solving environments distributed computing 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Post, D.E., Votta, L.G.: Computational science demands a new paradigm. Physics Today 58(1), 35–41 (2005)CrossRefGoogle Scholar
  2. 2.
    Bell, G., Hey, T., Szalay, A.: Beyond the data deluge. Science 323(5919), 1297–1298 (2009)CrossRefGoogle Scholar
  3. 3.
    Nelson, M.L.: Data-Driven Science: A New Paradigm? EDUCAUSE Review 44(4), 6–7 (2009)Google Scholar
  4. 4.
    PLGrid Plus project web site, http://www.plgrid.pl/plus
  5. 5.
    Bubak, M., Szepieniec, T., Wiatr, K. (eds.): PL-Grid 2011. LNCS, vol. 7136. Springer, Heidelberg (2012)Google Scholar
  6. 6.
    Ciepiela, E., et al.: Managing Entire Lifecycles of e-Science Applications in the GridSpace2 Virtual Laboratory – From Motivation through Idea to Operable Web-Accessible Environment Built on Top of PL-Grid e-Infrastructure. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds.) PL-Grid 2011. LNCS, vol. 7136, pp. 228–239. Springer, Heidelberg (2012)CrossRefGoogle Scholar
  7. 7.
    Ciepiela, E., Harezlak, D., Kocot, J., Bartynski, T., Kasztelnik, M., Nowakowski, P., Bubak, M.: Exploratory programming in the virtual laboratory. In: Proceedings of the 2010 International Multiconference on Computer Science and Information Technology (IMCSIT), pp. 621–628. IEEE (2010)Google Scholar
  8. 8.
    Boulton, G., Campbell, P., Collins, B., Elias, P., Hall, W., Laurie, G., Walport, M.: Science as an open enterprise. The Royal Society (2012)Google Scholar
  9. 9.
    Retraction Watch, Archive for the “not reproducible” Category, http://retractionwatch.com/
  10. 10.
    Merali, Z.: Computational science: Error, why scientific programming does not compute. Nature 467(7317), 775–777 (2010)CrossRefGoogle Scholar
  11. 11.
    Mervis, J.: NSF to ask every grant applicant for data management plan. ScienceInsider (2010), http://news.sciencemag.org/2010/05/
  12. 12.
    The Software Sustainability Institute, http://www.software.ac.uk/
  13. 13.
    Aalbersberg, I.J., Atzeni, S., Koers, H., Specker, B., Zudilova-Seinstra, E.: Bringing Digital Science Deep Inside the Scientific Article: the Elsevier Article of the Future Project. LIBER Quarterly 22 (2013)Google Scholar
  14. 14.
    Nowakowski, P., Ciepiela, E., Harezlak, D., Kocot, J., Kasztelnik, M., Bartynski, T., Meizner, J., Dyk, G., Malawski, M.: The Collage Authoring Environment. In: Proceedings of the International Conference on Computational Science, ICCS 2011. Procedia Computer Science, vol. 4, pp. 608–617 (2011), http://www.sciencedirect.com/science/article/pii/S1877050911001220
  15. 15.
    Ciepiela, E., Harezlak, D., Kasztelnik, M., Meizner, J., Dyk, G., Nowakowski, P., Bubak, M.: The Collage Authoring Environment: From Proof-of-Concept Prototype to Pilot Service. In: ICCS 2013. Procedia Computer Science, vol. 18, pp. 769–778 (2013), http://www.sciencedirect.com/science/article/pii/S1877050913003840
  16. 16.
    Bardi, A., Manghi, P.: A Rationale for Enhanced Publications. LIBER Quarterly 22 (2014), https://liber.library.uu.nl/index.php/lq/article/view/8445/9825
  17. 17.
    Baggerly, K.A., Coombes, K.R.: What Information Should Be Required to Support Clinical “Omics” Publications? Clinical Chemistry 57, 688–690 (2011)CrossRefGoogle Scholar
  18. 18.
    ASTM Standard E177-13: Standard Practice for Use of the Terms Precision and Bias in ASTM Test Methods. ASTM International, West Conshohocken, PA (2003), http://www.astm.org, doi:10.1520/C0033-03E01
  19. 19.
    McNaught, A.D., Wilkinson, A.: IUPAC. Compendium of Chemical Terminology, 2nd edn. (the “Gold Book”). Blackwell Scientific Publications, Oxford (1997), XML on-line corrected version, http://goldbook.iupac.org, doi:10.1520/E0177-13, created by Nic, M., Jirat, J., Kosata, B.; updates compiled by Jenkins, A. (2006), doi:10.1520/E0177-13, ISBN 0-9678550-9-8
  20. 20.
    Department of Defense Documentation of Verification: Validation & Accreditation (VV&A) for Models and Simulations. Missile Defense Agency (2008)Google Scholar
  21. 21.
    Reese, R., Wyatt, D.L.: Software reuse and simulation. In: Proceedings of the 19th Conference on Winter Simulation, pp. 185–192. ACM (1987)Google Scholar
  22. 22.
    Robinson, S., Nance, R.E., Paul, R.J., Pidd, M., Taylor, S.J.: Simulation model reuse: definitions, benefits and obstacles. Simulation Modelling Practice and Theory 12(7), 479–494 (2004)CrossRefGoogle Scholar
  23. 23.
    GridSpace2 platform installation in the PL-Grid Infrastructure, https://gs2.plgrid.pl
  24. 24.
    GridSpace2 project home page, https://dice.cyfronet.pl/gridspace
  25. 25.
    Ciepiela, E., Jadczyk, T., Harezlak, D., Kasztelnik, M., Nowakowski, P., Dyk, G., Bubak, M., Roterman, I.: Computations of protein hydrophobicity profile as virtual experiment in gridspace virtual laboratory. Bio-Algorithms and Medical-Systems 8(4), 361–372 (2011)Google Scholar
  26. 26.
    Zaraska, L., Stepniowski, W.J., Sulka, G.D., Ciepiela, E., Jaskula, M.: Analysis of nanopore arrangement and structural features of anodic alumina layers formed by two-step anodizing in oxalic acid using the dedicated executable software. Applied Physics A 114(2), 571–577 (2014)CrossRefGoogle Scholar
  27. 27.
    Brzychczy, E.: A Modern Tool for Modelling and Optimisation of Production in Underground Coal Mine. In: Bubak, M., Kitowski, J., Wiatr, K. (eds.) PLGrid Plus. LNCS, vol. 8500, pp. 317–334. Springer, Heidelberg (2014)Google Scholar
  28. 28.
    Rycerz, K., Bubak, M., Ciepiela, E., Pawlik, M., Hoenen, O., Harężlak, D., Wilk, B., Gubała, T., Meizner, J., Coster, D.: Enabling Multiscale Fusion Simulations on Distributed Computing Resources. In: Bubak, M., Kitowski, J., Wiatr, K. (eds.) PLGrid Plus. LNCS, vol. 8500, pp. 195–210. Springer, Heidelberg (2014)Google Scholar
  29. 29.
    Borgdorff, J., Bona-Casas, C., Mamoński, M., Kurowski, K., Piontek, T., Bosak, B., Hoekstra, A.G.: A distributed multiscale computation of a tightly coupled model using the multiscale modeling language. Procedia Computer Science 9, 596–605 (2012)CrossRefGoogle Scholar
  30. 30.
    Borgdorff, J., Mamoński, M., Bosak, B., Kurowski, K., Belgacem, M.B., Chopard, B., Hoekstra, A.G.: Distributed Multiscale Computing with MUSCLE 2, the Multiscale Coupling Library and Environment. arXiv preprint, arXiv:1311.5740 (2013)Google Scholar
  31. 31.
    Rycerz, K., Ciepiela, E., Dyk, G., Groen, D., Gubala, T., Harezlak, D., Bubak, M.: Support for Multiscale Simulations with Molecular Dynamics. Procedia Computer Science 18, 1116–1125 (2013)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Eryk Ciepiela
    • 1
  • Bartosz Wilk
    • 1
  • Daniel Harężlak
    • 1
  • Marek Kasztelnik
    • 1
  • Maciej Pawlik
    • 1
  • Marian Bubak
    • 1
    • 2
    • 3
  1. 1.ACC Cyfronet AGHAGH University of Science and TechnologyKrakówPoland
  2. 2.Faculty of Computer Science, Electronics and Telecommunications, Department of Computer ScienceAGH University of Science and TechnologyKrakówPoland
  3. 3.Institute for Informatics, Faculty of ScienceUniversity of AmsterdamAmsterdamThe Netherlands

Personalised recommendations