Abstract
This paper proposes High Voltage Electron Microscope (HVEM) DataGrid for biological data management. HVEM DataGrid allows researchers to share the results of their biological experiments using HVEM, so that they can analyze them together to perform good research. The proposed system is for people whose primary work is to access HVEM, to obtain experimental results for biological samples and to store or retrieve them on HVEM DataGrid. The architecture of the HVEM Grid[3] is designed to materialize all the necessary conditions in allowing the user 1) to control every part of HVEM in a fine-grained manner, 2) to check the HVEM and observe various states of the specimen, 3) to manipulate their high resolution 2-D and 3-D images, and 4) to handle the experimental data including storing and searching them. HVEM DataGrid, a subsystem of the HVEM Grid system, is to provide a simple web-based controlling method for remote biological data.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Foster, I., Kesselman, C., Tuecke, S.: The anatomy of the grid: Enabling scalable virtual organizations. Intl. J. Supercomputer Applications (2001)
Korea Basic Science Institute, KBSI Microscopes & facilitates, http://hvem.kbsi.re.kr/eng/index.htm
H. Han, H. Jung, H.Y. Yeom, H.S. Kweon, J. Lee: HVEM Grid: Experiences in constructing an Electron Microscopy Grid. In: The Eighth Asia Pacific Web Conference (2006)
Globus Aliiance, Globus Toolkit 4.0 Release Mannuals, http://www.globus.org/toolkit/docs/4.0
Oxford e-Science Centre, e-Science Definitions, http://e-science.ox.ac.uk/public/general/definitions.xml
Atkins, D.E. et al.: Revolutionizing Science and Engineering Through Cyberinfrastructure: Report of the National Science Foundation Blue-Ribbon Advisory Panel on Cyberinfrastructure. National Science Foundation (2003)
PostgreSQL Global Ddevelopment Grpoup, PostgreSQL 8.0, http://www.postgresql.org
San Diego Supercomputer Center, SDSC Storage Resource Borker(SRB), http://www.sdsc.edu/srb
Martone, M.E., Zhang, S., Gupta, A., Qian, X., He, H., Price, D.L., Wong, M., Santini, S., Ellisman, M.H.: The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics 1(4), 235–245 (2003)
NEESgrid, http://www.neesgrid.org
UK e-science Programme, http://www.nesc.ac.uk
Japan NAREGI project, http://www.naregi.org
Korean Society of Electron Microscopy, http://ksem.com
European Microscopy Society, http://www.eurmicsoc.org
Microscopy Society of America, http://www.microscopy.org
The Royal Microscopical Society, http://www.rms.org.uk
Telescience Project, https://telescience.ucsd.edu
Hadida-Hassan, M., Young, S.J., Peltier, S.T., Wong, M., Lamont, S.P., Ellisman, M.H.: Web-based telemicroscopy. Journal of Structural Biology 125(2–3), 235–245 (1999)
Peltier, S.T. et al.: The Telescience Portal for Advanced Tomography Applications. Journal of Parallel and Distributed Computing: Computational Grid 63(5), 539–550 (2002)
Lin, A.W. et al.:The Telescience Project : Applications to Middleware Interaction Components. In: Proceedings of The 18th IEEE International Symposium on Computer-Based Medical Systems, pp. 543–548 (2005)
Biogrid Project, http://www.biogrid.jp
Chaos Project, http://www.cs.umd.edu/projects/hpsl/chaos
Afework, A., Beynon, M., Bustamante, F., Demarzo, A., Ferreira, R., Miller, R., Silberman, M., Saltz, J., Sussman, A., Tsang, H.: Digital Dynamic Telepathology – the Virtual Microscope. In: Proceedings of the 1998 AMIA Annual Fall Symposium, American Medical Informatics Association, Hanley and Belfus, Inc. (1998)
Ferreira, R., Moon, B., Humphries, J., Sussman, A., Saltz, J., Miller, R., Demarzo, A.: The Virtual Microscope. In: Proceedings of the 1997 AMIA Annual Fall Symposium, American Medical Informatics Association, Hanley and Belfus, Inc. (1997)
CERN Datagrid Project, http://eu-datagrid.web.cern.ch/eu-datagrid
Breton, V., Medina, R., Montagnat, J.: DataGrid, Prototype of a Biomedical Grid. Methods of Information in Medicine 42(2), Schattauer, 143–148 (2003)
Hoschek, W., Jaen-Martinez, J., Samar, A., Stockinger, H., Stockinger, K.: Data Management in an International Data Grid Project. In: IEEE/ACM International Workshop on Grid Computing Grid’2000, Bangalore, India (2000)
Stockinger, H., Dono, F., Laure, E., Muzzafar, S., et al.: Grid Data Management in action, computing in high energy physics. In: CHEP (2003)
Paricle Physics Data Grid, http://www.ppdg.net
Stockinger, K., Stockinger, H., Dutka, L., Slota, R. et al.: Acces Cost Estimation for Unified Grid Storage Systems. In: IEEE/ACM 4th international workshop on grid computing (Grid2003), IEEE Computer Society Press
NERC DataGrid, Web Site, http://ndg.badc.rl.ac.uk
Lawrence B.N., Cramer, R., Gutierrez, M., Kleese van Dam, K., Kondapalli, S., Latham, S., Lowry, R., O’Neill, K., Woolf, A.: The NERC DataGrid Prototype. In: Cox, S.J. (ed.) Proceedings of the U.K. e-science All Hands Meeting, ISBN 1-904425-11-9 (2003)
Stephens, A., Marsh, K.P., Lawrence, B.N.: Presenting a multi-terabyte dataset via the web. In: Proceedings of the ECMWF Ninth Workshop on Meteorological Operational Systems (2003)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Jung, I.Y., Cho, I.S., Yeom, H.Y., Kweon, H.S., Lee, J. (2007). HVEM DataGrid: Implementation of a Biologic Data Management System for Experiments with High Voltage Electron Microscope. In: Dubitzky, W., Schuster, A., Sloot, P.M.A., Schroeder, M., Romberg, M. (eds) Distributed, High-Performance and Grid Computing in Computational Biology. GCCB 2007. Lecture Notes in Computer Science(), vol 4360. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69968-2_13
Download citation
DOI: https://doi.org/10.1007/978-3-540-69968-2_13
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-69841-8
Online ISBN: 978-3-540-69968-2
eBook Packages: Computer ScienceComputer Science (R0)