Advertisement

InSilicoLab – Managing Complexity of Chemistry Computations

  • Joanna Kocot
  • Tomasz Szepieniec
  • Daniel Harężlak
  • Klemens Noga
  • Mariusz Sterzel
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7136)

Abstract

InSilicoLab is an application portal designed to support in silico experiments by easily running computational software on Grids. Unlike manual job submission or grid portals, InSilicoLab enables its users to run complex computations without technical knowledge of how to operate the grid resources. Instead, the users may focus only on the information and activities relevant to their research. This paper is a result of a feasibility study of applying the InSilicoLab concept to the domain of computational chemistry. It, therefore, includes a study of chemistry computations and their realisation in InSilicoLab, as well as a description of the generic architecture of the environment.

Keywords

in silico experiment computational chemistry PSE computional resources e-science 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    InSilicoLab – an application portal supporting in silico experiments on e-Infrastructures, http://insilicolab.grid.cyfronet.pl
  2. 2.
    Frisch, M.J., et al.: Gaussian 09. Gaussian, Inc., Wallingford CT (2009)Google Scholar
  3. 3.
    Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S., Jensen, J.H., Koseki, S., Matsunaga, N., Nguyen, K.A., Su, S., Windus, T.L., Dupuis, M., Montgomery, J.A.: General Atomic and Molecular Electronic Structure System. J. Comput. Chem. 14, 1347–1363 (1993)CrossRefGoogle Scholar
  4. 4.
    TURBOMOLE – Program Package for ab initio Electronic Structure Calculations, http://www.turbomole.com/
  5. 5.
    Open Babel: The Open Source Chemistry Toolbox, http://openbabel.org
  6. 6.
    Gubala, T., Bubak, M., Sloot, P.M.A.: A Semantic Integration of Collaborative Research Environments. In: Cannataro, M. (ed.) A Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare, ch. 26, pp. 514–530. Information Science Reference, IGI Global (2009)Google Scholar
  7. 7.
    Jmol: an open-source Java viewer for chemical structures in 3D, http://www.jmol.org/
  8. 8.
    Zhou, Z., Wang, F., Todd, B.D.: Development of Chemistry Portal for Grid-enabled Molecular Science. In: Proceedings of the First International Conference on e-Science and Grid Computing, pp. 48–55 (2005)Google Scholar
  9. 9.
    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
  10. 10.
    WebMO – a free World Wide Web-based interface to computational chemistry packages, http://www.webmo.net
  11. 11.
    ECCE – Extensible Computational Chemistry Environment, http://ecce.pnl.gov
  12. 12.
    Materials Studio – a comprehensive materials modeling and simulation application, http://accelrys.com/products/materials-studio/index.html
  13. 13.
  14. 14.
    PL-Grid – Polish Infrastructure for Supporting Computational Science in the European Research Space, http://www.plgrid.pl/
  15. 15.
    The Gromacs application, http://www.gromacs.org/
  16. 16.
    Barnacka, A., Bogacz, L., Gochna, M., Janiak, M., Komin, N., Lamanna, G., Moderski, R., Siudek, M.: PL-Grid e-Infrastructure for the Cherenkov Telescope Array Observatory. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds.) PL-Grid 2011. LNCS, vol. 7136, pp. 301–313. Springer, Heidelberg (2012)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Joanna Kocot
    • 1
  • Tomasz Szepieniec
    • 1
  • Daniel Harężlak
    • 1
  • Klemens Noga
    • 1
  • Mariusz Sterzel
    • 1
  1. 1.ACC Cyfronet AGHAGH University of Science and TechnologyKrakówPoland

Personalised recommendations