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.
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.
References
InSilicoLab – an application portal supporting in silico experiments on e-Infrastructures, http://insilicolab.grid.cyfronet.pl
Frisch, M.J., et al.: Gaussian 09. Gaussian, Inc., Wallingford CT (2009)
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)
TURBOMOLE – Program Package for ab initio Electronic Structure Calculations, http://www.turbomole.com/
Open Babel: The Open Source Chemistry Toolbox, http://openbabel.org
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)
Jmol: an open-source Java viewer for chemical structures in 3D, http://www.jmol.org/
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)
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)
WebMO – a free World Wide Web-based interface to computational chemistry packages, http://www.webmo.net
ECCE – Extensible Computational Chemistry Environment, http://ecce.pnl.gov
Materials Studio – a comprehensive materials modeling and simulation application, http://accelrys.com/products/materials-studio/index.html
Gaussian VO, http://egee.grid.cyfronet.pl/Applications/gaussian-vo/
PL-Grid – Polish Infrastructure for Supporting Computational Science in the European Research Space, http://www.plgrid.pl/
The Gromacs application, http://www.gromacs.org/
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)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Kocot, J., Szepieniec, T., Harężlak, D., Noga, K., Sterzel, M. (2012). InSilicoLab – Managing Complexity of Chemistry Computations. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds) Building a National Distributed e-Infrastructure–PL-Grid. Lecture Notes in Computer Science, vol 7136. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28267-6_21
Download citation
DOI: https://doi.org/10.1007/978-3-642-28267-6_21
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-28266-9
Online ISBN: 978-3-642-28267-6
eBook Packages: Computer ScienceComputer Science (R0)