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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Post, D.E., Votta, L.G.: Computational science demands a new paradigm. Physics Today 58(1), 35–41 (2005)
Bell, G., Hey, T., Szalay, A.: Beyond the data deluge. Science 323(5919), 1297–1298 (2009)
Nelson, M.L.: Data-Driven Science: A New Paradigm? EDUCAUSE Review 44(4), 6–7 (2009)
PLGrid Plus project web site, http://www.plgrid.pl/plus
Bubak, M., Szepieniec, T., Wiatr, K. (eds.): PL-Grid 2011. LNCS, vol. 7136. Springer, Heidelberg (2012)
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)
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)
Boulton, G., Campbell, P., Collins, B., Elias, P., Hall, W., Laurie, G., Walport, M.: Science as an open enterprise. The Royal Society (2012)
Retraction Watch, Archive for the “not reproducible” Category, http://retractionwatch.com/
Merali, Z.: Computational science: Error, why scientific programming does not compute. Nature 467(7317), 775–777 (2010)
Mervis, J.: NSF to ask every grant applicant for data management plan. ScienceInsider (2010), http://news.sciencemag.org/2010/05/
The Software Sustainability Institute, http://www.software.ac.uk/
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)
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
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
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
Baggerly, K.A., Coombes, K.R.: What Information Should Be Required to Support Clinical “Omics” Publications? Clinical Chemistry 57, 688–690 (2011)
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
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
Department of Defense Documentation of Verification: Validation & Accreditation (VV&A) for Models and Simulations. Missile Defense Agency (2008)
Reese, R., Wyatt, D.L.: Software reuse and simulation. In: Proceedings of the 19th Conference on Winter Simulation, pp. 185–192. ACM (1987)
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)
GridSpace2 platform installation in the PL-Grid Infrastructure, https://gs2.plgrid.pl
GridSpace2 project home page, https://dice.cyfronet.pl/gridspace
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)
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)
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)
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)
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)
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)
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)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Ciepiela, E., Wilk, B., Harężlak, D., Kasztelnik, M., Pawlik, M., Bubak, M. (2014). Towards Provisioning of Reproducible, Reviewable and Reusable In-Silico Experiments with the GridSpace2 Platform. In: Bubak, M., Kitowski, J., Wiatr, K. (eds) eScience on Distributed Computing Infrastructure. Lecture Notes in Computer Science, vol 8500. Springer, Cham. https://doi.org/10.1007/978-3-319-10894-0_9
Download citation
DOI: https://doi.org/10.1007/978-3-319-10894-0_9
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-10893-3
Online ISBN: 978-3-319-10894-0
eBook Packages: Computer ScienceComputer Science (R0)