Skip to main content

Enabling Data Sharing and Collaboration in Complex Systems Applications

  • Conference paper
Distributed, High-Performance and Grid Computing in Computational Biology (GCCB 2007)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4360))

Included in the following conference series:

Abstract

We describe a model for the data storage, retrieval and manipulation requirements of complex system applications based on pervasive, integrated, application specific databases shared over a peer to peer network. Such a model can significannotly increase productivity through transparent data sharing and querying as well as aid collaborations. We show a proof of concept of this approach as implemented in the Adun molecular simulation application together with a discussion of its limitations and possible extensions.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. NIH:NIH Data Sharing Policy and Implementation Guidance (2003)

    Google Scholar 

  2. Venugopal, S., Buyya, R., Ramamohanarao, K.: A taxonomy of data grids for distributed data sharing, management, and processing. ACM Comput. Surv. 38(1), 1–53 (2006)

    Article  Google Scholar 

  3. Lebrun, P.: The large hadron collider, a megascience project. In: Proceedings of the 38th INFN Eloisatron Project Workshop on Superconducting Materials for High Energy Colliders (1999)

    Google Scholar 

  4. Oram, A.: Peer to Peer: Harnessing the Power of Disruptive Technology. O’Reilly and Associates Inc., Sebastopal, CA (2001)

    Google Scholar 

  5. Anderson, D., Cobb, J., Korpela, E., Lebofsky, M., Werthimer, D.: Seti@home: An experiment in public-resource computing. Comm. ACM 45(11), 56–61 (2002)

    Article  Google Scholar 

  6. Gnutella: The gnutella website, http://gnutella.wego.com

  7. Mark, W.L.L., Roussopoulos, N.: Interoperability of mulitple autonomous databases. ACM Comput. Surv. 22(3), 267–293 (1990)

    Article  Google Scholar 

  8. Model: A database of molecular dynamics simulations, http://mmb.pcb.ub.es/MODEL

  9. Giese, T.J., Gregersena, B.A., Liua, Y., Nama, K., Mayaana, E., Mosera, A., Rangea, K.: Nieto Fazaa, O., Silva Lopez, C., de Rodriguez Lerab, A., Schaftenaare, G., Lopez, X., Leea, T.S., Karypisc, G., York, D.M.: QCRNA 1.0: A database of quantum calculations for RNA catalysis. Journal of Molecular Graphics and Modelling 1, in press (2006)

    Google Scholar 

  10. Johnston, M., Fdez. Galván, I., Villà-Freixa, J.: Framework based design of a new all-purpose molecular simulation application: The Adun Simulator. J. Comput. Chem. 26, 1647–1659 (2005)

    Article  Google Scholar 

  11. Sánchez, M.L., Aguilar, M.A., Olivares del Valle, F.J.: Study of solvent effects by means of averaged solvent electrostatic potentials obtained from molecular dynamics data. J. Comput. Chem. 18, 313 (1997)

    Article  Google Scholar 

  12. Aqvist, J., Marelius, J.: The Linear Interation energy Method for Predictiong Ligand Binding Free Energies. Combinatorial Chemistry and High Throughput Screening 4, 613–626 (2001)

    Google Scholar 

  13. Androutsellis-Theotokis, S., Spinellis, D.: A survey of peer-to-peer content distribution technologies. ACM Comput. Surv. 36(4), 335–371 (2004)

    Article  Google Scholar 

  14. Chirita, P.A., Damian, A., Nejdl, W., Siberski, W.: Search strategies for scientific collaboration networks. In: P2PIR’05: Proceedings of the 2005 ACM workshop on Information retrieval in peer-to-peer networks, pp. 33–40. ACM Press, New York, NY, USA (2005)

    Chapter  Google Scholar 

  15. Rodrigues, R., Liskov, B., Shrira, L.: The design of a robust peer-to-peer system. In: EW10: Proceedings of the 10th workshop on ACM SIGOPS European workshop: beyond the PC, pp. 117–124. ACM Press, New York, NY, USA (2002)

    Chapter  Google Scholar 

  16. Ooi, B.C., Shu, Y., Tan, K.L.: Relational data sharing in peer-based data management systems. SIGMOD Rec. 32(3), 59–64 (2003)

    Article  Google Scholar 

  17. Chawathe, Y., Ratnasamy, S., Breslau, L., Lanham, N., Shenker, S.: Making gnutella-like p2p systems scalable. In: SIGCOMM ’03: Proceedings of the 2003 conference on Applications, technologies, architectures, and protocols for computer communications, pp. 407–418. ACM Press, New York, NY, USA (2003)

    Chapter  Google Scholar 

  18. Nejdl, W., Siberski, W., Sintek, M.: Design issues and challenges for rdf- and schema-based peer-to-peer systems. SIGMOD Rec. 32(3), 41–46 (2003)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Werner Dubitzky Assaf Schuster Peter M. A. Sloot Michael Schroeder Mathilde Romberg

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer Berlin Heidelberg

About this paper

Cite this paper

Johnston, M.A., Villà-Freixa, J. (2007). Enabling Data Sharing and Collaboration in Complex Systems Applications. 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_10

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-69968-2_10

  • 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)

Publish with us

Policies and ethics