Online Web-Based Science Gateway for Nanotechnology Research

  • Piotr Dziubecki
  • Piotr Grabowski
  • Michał Krysiński
  • Tomasz Kuczyński
  • Krzysztof Kurowski
  • Tomasz Piontek
  • Dawid Szejnfeld
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7136)


The main objective of Science Gateways is to give users remote access to supercomputers and large-scale computing environments in an interactive, web-based and graphical manner. We present a tool, called Vine Toolkit, that has been successfully used as a core web platform for various Science Gateways. Vine Toolkit is a modular, extensible and easy-to-use tool as well as a high-level Application Programming Interface (API) for various applications, visualization components and building blocks. In a nutshell, it allows interoperability between many different HPC and grid technologies within the service layer. As a result, Vine Toolkit provides an ability to build a portal upon different HPC technologies working together to deliver a complete solution to the users. In this article, we briefly describe our most complex and feature-rich project – the Nanotechnology Gateway, as well as a set of tools relevant to advanced scientific portals, development of which was driven by various requirements defined by scientists and gathered in scope of the PL-Grid project.


Science Gateway Web2.0 ABINIT Vine Toolkit Liferay Java Adobe Flex Material Science Nanotechnology 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Russell, M., Dziubecki, P., Grabowski, P., Krysinśki, M., Kuczyński, T., Szjenfeld, D., Tarnawczyk, D., Wolniewicz, G., Nabrzyski, J.: The Vine Toolkit: A Java Framework for Developing Grid Applications. In: Wyrzykowski, R., Dongarra, J., Karczewski, K., Wasniewski, J. (eds.) PPAM 2007. LNCS, vol. 4967, pp. 331–340. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  2. 2.
    Szejnfeld, D., Dziubecki, P., Kopta, P., Krysinski, M., Kuczynski, T., Kurowski, K., Ludwiczak, B., Piontek, T., Tarnawczyk, D., Wolniewicz, M., Domagalski, P., Nabrzyski, J., Witkowski, K.: Vine Toolkit – Towards Portal Based Production Solutions for Scientific and Engineering Communities with Grid-Enabled Resources Support. Scalable Computing: Practice and Experience 11(2), 161–172 (2011)Google Scholar
  3. 3.
    Dziubecki, P., Grabowski, P., Krysinski, M., Kuczynski, T., Kurowski, K., Szejnfeld, D.: Nano-Science Gateway development with Vine Toolkit and Adobe Flex. In: Barbera, R., Andronico, G., La Rocca, G. (eds.) Proceedings of the International Workshop on Science Gateways (IWSG 2010). Consorzio COMETA, Catania (2010)Google Scholar
  4. 4.
    Agullo, E., Coti, C., Herault, T., Langou, J., Peyronnet, S., Rezmerita, A., Cappello, F., Dongarra, J.: QCG-OMPI: MPI applications on grids. Future Generation Computer Systems 27(4), 357–369 (2011) ISSN 0167-739X, doi:10.1016/j.future.2010.11.015 CrossRefGoogle Scholar
  5. 5.
    Kurowski, K., de Back, W., Dubitzky, W., Gulyás, L., Kampis, G., Mamonski, M., Szemes, G., Swain, M.: Complex System Simulations with QosCosGrid. In: Allen, G., Nabrzyski, J., Seidel, E., van Albada, G.D., Dongarra, J., Sloot, P.M.A. (eds.) ICCS 2009, Part I. LNCS, vol. 5544, pp. 387–396. Springer, Heidelberg (2009), doi:10.1007/978-3-642-01970-8_38CrossRefGoogle Scholar
  6. 6.
    Streit, A., Bala, P., Beck-Ratzka, A., Benedyczak, K., Bergmann, S., Breu, R., Daivandy, J. M., Demuth, B., Eifer, A., Giesler, A., Hagemeier, B., Holl, S., Huber, V., Lamla, N., Mallmann, D., Memon, A. S., Memon, M. S., Rambadt, M., Riedel, M., Romberg, M., Schuller, B., Schlauch, T., Schreiber, A., Soddemann, T., Ziegler, W.: UNICORE 6 – Recent and Future Advancements. JUEL-4319 (2010) ISSN 0944-2952Google Scholar
  7. 7.
  8. 8.
  9. 9.
    Foster, I.: Globus Toolkit Version 4: Software for Service-Oriented Systems. In: Jin, H., Reed, D., Jiang, W. (eds.) NPC 2005. LNCS, vol. 3779, pp. 2–13. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  10. 10.
    Moor, R.: Towards a Theory of Digital Preservation. The International Journal of Digital Curation 3(1) (2008)Google Scholar
  11. 11.
    Rajasekar, A., Wan, M., Moore, R., Schroeder, W., Kremenek, G., Jagatheesan, A., Cowart, C., Zhu, B., Chen, S., Olschanowsky, R.: Storage Resource Broker – Managing Distributed Data in a Grid. Computer Society of India Journal, Special Issue on SAN 33(4), 42–54 (2003)Google Scholar
  12. 12.
    Antonioletti, M., Atkinson, M.P., Baxter, R., Borley, A., Chue Hong, N.P., Collins, B., Hardman, N., Hume, A., Knox, A., Jackson, M., Krause, A., Laws, S., Magowan, J., Paton, N.W., Pearson, D., Sugden, T., Watson, P., Westhead, M.: The Design and Implementation of Grid Database Services in OGSA-DAI. Concurrency and Computation: Practice and Experience 17(2-4), 357–376 (2005)CrossRefGoogle Scholar
  13. 13.
    Foster, I., Grimshaw, A., Lane, P., Lee, W., Morgan, M., Newhouse, S., Pickles, S., Pulsipher, D., Smith, C., Theimer, M.: Open Grid Services Architecture Basic Execution Service Version 1.0 GFD-R.108 (2008),
  14. 14.
    Anjomshoaa, A., Brisard, F., Drescher, M., Fellows, D., Ly, A., McGough, S., Pulsipher, D., Savva, A.: Job Submission Description Language (JSDL) Specification, Version 1.0. GFD-R.056 (2005),
  15. 15.
    OGSA Resource Usage Service,
  16. 16.
  17. 17.
    Oleksiak, A., Tullo, A., Graham, P., Kuczynski, T., Nabrzyski, J., Szejnfeld, D., Sloan, T.: HPC-Europa single point of access as a framework for building science gateways: Research Articles. Concurrency and Computation: Practice & Experience 19(6), 851–866 (2007)CrossRefGoogle Scholar
  18. 18.
  19. 19.
  20. 20.
  21. 21.
    Klimeck, G., McLennan, M., Brophy, S.P., Adams III, G.B., Lundstrom, M.S.: Advancing Education and Research in Nanotechnology. Computing in Science and Engineering 10(5), 17–23 (2008), doi:10.1109/MCSE.2008.120CrossRefGoogle Scholar
  22. 22.
  23. 23.
    Guim, F., Rodero, I., Corbalan, J., Labarta, J., Oleksiak, A., Kuczynski, T., Szejnfeld, D., Nabrzyski, J.: Uniform job monitoring in the HPC-Europa project: data model, API and services. International Journal of Web and Grid Services 3(3), 333–353 (2007)CrossRefGoogle Scholar
  24. 24.
    Gonze, X., Amadon, B., Anglade, P.-M., Beuken, J.-M., Bottin, F., Boulanger, P., Bruneval, F., Caliste, D., Caracas, R., Cote, M., Deutsch, T., Genovese, L., Ghosez, P., Giantomassi, M., Goedecker, S., Hamann, D.R., Hermet, P., Jollet, F., Jomard, G., Leroux, S., Mancini, M., Mazevet, S., Oliveira, M.J.T., Onida, G., Pouillon, Y., Rangel, T., Rignanese, G.-M., Sangalli, D., Shaltaf, R., Torrent, M., Verstraete, M.J., Zerah, G., Zwanziger, J.W.: ABINIT: First-principles approach of materials and nanosystem properties. Computer Phys. Commun. 180, 2582–2615 (2009)CrossRefGoogle Scholar
  25. 25.
    Gonze, X., Rignanese, G.-M., Verstraete, M., Beuken, J.-M., Pouillon, Y., Caracas, R., Jollet, F., Torrent, M., Zerah, G., Mikami, M., Ghosez, P., Veithen, M., Raty, J.-Y., Olevano, V., Bruneval, F., Reining, L., Godby, R., Onida, G., Hamann, D.R., Allan, D.C.: A brief introduction to the ABINIT software package. Zeit. Kristallogr. 220, 558–562 (2005)Google Scholar
  26. 26.
  27. 27.
    Kokalj, A.: Computer graphics and graphical user interfaces as tools in simulations of matter at the atomic scale. Comp. Mat. Sci. 28, 155–168 (2003)CrossRefGoogle Scholar
  28. 28.
  29. 29.
    Karanastasis, E., Varvarigou, T., Grabowski, P.: Portals for Service Oriented Infrastructures. In: Dimitrakos, T., Martrat, J., Wesner, S. (eds.) Service Oriented Infrastructures and Cloud Service Platforms for the Enterprise, pp. 159–177. Springer, Heidelberg (2010) ISBN 978-3-642-04085-6CrossRefGoogle Scholar
  30. 30.
  31. 31.
    Kocot, J., Szepieniec, T., Noga, K., Harężlak, D., Sterzel, M.: InSilicoLab – Managing Complexity of Chemistry Computations. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds.) PL-Grid 2011. LNCS, vol. 7136, pp. 265–275. Springer, Heidelberg (2012)Google Scholar
  32. 32.
    Ciepiela, E., Nowakowski, P., Kocot, J., Harężlak, D., Gubała, T., Meizner, J., Kasztelnik, M., Bartyński, T., Malawski, M., Bubak, M.: 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)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Piotr Dziubecki
    • 1
  • Piotr Grabowski
    • 1
  • Michał Krysiński
    • 1
  • Tomasz Kuczyński
    • 1
  • Krzysztof Kurowski
    • 1
  • Tomasz Piontek
    • 1
  • Dawid Szejnfeld
    • 1
  1. 1.Poznań Supercomputing and Networking CenterPoznańPoland

Personalised recommendations