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Capturing and supporting contexts for scientific data sharing via the biological sciences collaboratory

Published: 06 November 2004 Publication History

Abstract

Scientific collaboration is largely focused on the sharing and joint analysis of scientific data and results. Today, a movement is afoot within the scientific computing community to shift "collaboratory" development from traditional tool-centric approaches to more data-centric ones. Yet, to effectively support data sharing means more than providing a common repository for storing and retrieving shared data sets. In order to reasonably comprehend and apply another researcher's data set, the scientist must grasp the various contexts of the data as it relates to the overall data space, applications, experiments, projects, and the scientific community. Under development at the Pacific Northwest National Laboratory, the Biological Sciences Collaboratory (BSC) enables the sharing of biological data and analyses through diverse capabilities such as metadata capture, electronic laboratory notebooks, data organization views, data provenance tracking, analysis notes, task management, and scientific workflow management. Overall, BSC strives to identify and capture the various social and scientific contexts in which data sharing collaborations in biology take place and to provide collaboration tools and capabilities that can effectively support and facilitate these important data sharing contexts.

References

[1]
Apache Software Foundation. Jetspeed. http://jakarta.apache.org/jetspeed/site/index.html.
[2]
Apache Software Foundation. The Jakarta Slide Project. http://jakarta.apache.org/slide.
[3]
Arzberger, P., and Finhold, T.A. 2002. "Data and Collaboratories in the Biomedical Community." National Biomedical Computation Resource at the University of California, San Diego (NIH award RR08605).
[4]
Bhandarkar, M., Budescu, G., Humphrey, W.F., Izaguirre, J.A., Izrailev, S., Kalé, L.V., Kosztin, D., Molnar, F., Phillips, J.C., and Schulten, K. 1999. "BioCoRE: A Collaboratory for Structural Biology." Proceedings of the SCS International Conference on Web-Based Modeling and Simulation, San Francisco, CA, pp. 242--251.
[5]
Birnholtz, J.P. and Bietz, M.J. 2003. "Data at Work: Supporting Sharing in Science and Engineering." Proceedings of the 2003 International ACM SIGGROUP Conference on Supporting Group Work, Sanibel Island, FL, pp. 339--348.
[6]
Bourne, P.E., Gribskov, M., Johnson, G., Moreland, J., and Weissig, H. 1998. "A Prototype Molecular Interactive Collaborative Environment (MICE)." Proceeding of the 1998 Pacific Symposium on Biocomputing, Kapalua, HI, pp.118--129.
[7]
Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., Gaasterland, T., Glenisson, P., Holstege, F.C., Kim, I.F., Markowitz, V., Matese, J.C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., and Vingron, M. 2001. "Minimum Information About a Microarray Experiment (MIAME)-Toward Standards for Microarray Data." Natural Genetics, 29(4), pp. 365--371.
[8]
Brazma, A., Parkinson, H., Sarkans, U., Shojatalab, M., Vilo, J., Abeygunawardena, N., Holloway, E., Kapushesky, M., Kemmeren, P., Lara, G.G., Oezcimen, A., Rocca-Serra, P., and Sansone, S.A. 2003. "ArrayExpress--A Public Repository for Microarray Gene Expression Data at the EBI." Nucleic Acids Research, 31(1), pp. 68--71.
[9]
Edgar, R., Domrachev, M., and Lash, A.E. 2002. "Gene Expression Omnibus: NCBI Gene Expression and Hybridization Array Data Repository." Nucleic Acids Research, 30(1), pp. 207--210.
[10]
IBM. Lotus Instant Messaging (Sametime). http://www.lotus.com/products/lotussametime.nsf/wdocs/homepage.
[11]
Louis, K.S., Jones, L.M., and Campbell, E.G. 2002. "Sharing in Science." American Scientist, 90(4): pp. 304--307.
[12]
Kellogg, W. A. 1990. "Qualitative Artifact Analysis." Proceedings of INTERACT 90 http://www.hcirn.com/res/event/interact.php, Amsterdam, The Netherlands, pp. 193--198.
[13]
Macedonia, M.R. and Brutzman, D.P., "MBone Provides Audio and Video Across the Internet." IEEE Computer, 27(4), pp. 30--36.
[14]
Mangalam, H., Stewart, J., Zhou, J., Schlauch, K., Waugh, M., Chen, G., Farmer, A.D., Colello, G., and Weller, J.W. 2001. "GeneX: An Open Source Gene Expression Database and Integrated Tool Set." IBM Systems Journal, 40(2), pp. 552--569.
[15]
Merton, R.K. 1968. Social Theory and Social Structure. Free Press, New York.
[16]
Microarray Gene Expression Data Society. MGED - International Meetings on Microarray Gene Expression Databases Group. http://www.mged.org/index.html.
[17]
Microsoft Corporation. NetMeeting. http://www.microsoft.com/windows/netmeeting/default.asp.
[18]
Michigan State University. Shewanella Federation. http://www.shewanella.org/home.sjsp.
[19]
Myers, J.D., Allison, T.C., Bittner, S., Didier, B., Frenklach, M., Green, W.H., Ho, Y., Hewson, J., Koegler, W., Lansing, C., Leahy, D., Lee, M., McCoy, R., Minkoff, M., Nijsure, S., von Laszewski, G., Montoya, D., Pancerella, C., Pinzon, R., Pitz, W., Rahn, L.A., Ruscic, B., Schuchardt, K., Stephan, E., Wagner, A., Windus, T., and Yang, C. 2004. "A Collaborative Informatics Infrastructure for Multi-scale Science." Proceedings of the Challenges of Large Applications in Distributed Environments (CLADE) Workshop, Honolulu, HI
[20]
Myers, J.D., Chappell, A.R., Elder, M., Geist, A., and Schwidder, J. 2003. "Re-Integrating the Research Record." Computing in Science and Engineering, May/June, pp 44--50.
[21]
Olson, G.M., Finholt, T.A., and Teasley, S.D. 2000. "Behavioral Aspects of Collaboratories." In Koslow, S.H. and Huerta, M.F. (eds.), Electronic Collaboration in Science, Lawrence Erlbaum Associates, Mahwah, NJ.
[22]
Peltier, S.T. and Ellisman, M.H. 2003. "The Biomedical Informatics Research Network." In Foster, I. and Kesselman, C. (eds.), The Grid 2, Morgan Kaufmann, San Francisco.
[23]
Shortliffe, E.H., Barnett, O., Cimino, J.J., Greenes, R.A., and Patel, V.L. 1996. "InterMed: An Internet-Based Medical Collaboratory." Proceedings of INET '96, the Annual Meeting of the Internet Society, Montreal, Canada.
[24]
University of California, San Francisco. Molecular Modeling "Collaboratory." http://www.cgl.ucsf.edu/Research/collaboratory.
[25]
University of Michigan. CHEF Information Site. http://chefproject.org/portal.
[26]
University of Michigan. Science of Collaboratories. http://www.scienceofcollaboratories.org.
[27]
Whitehead, E.J. and M. Wiggins. 1998. "WebDAV: IETF standard for collaborative authoring on the Web." IEEE Internet Computing, 2(5): pp. 34--40.
[28]
Wouters, P. and Schröder, P. (eds.). 2003. Promise and Practice in Data Sharing. Book series: Wouters, P. and Schröder, P. (eds.), The Public Domain of Digital Research Data, NIWI-KNAW, Amsterdam.
[29]
Wulf, W. 1993. "The Collaboratory Opportunity." Science 261, (13 Aug 1993), pp. 854--855.

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        cover image ACM Conferences
        CSCW '04: Proceedings of the 2004 ACM conference on Computer supported cooperative work
        November 2004
        644 pages
        ISBN:1581138105
        DOI:10.1145/1031607
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        Published: 06 November 2004

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        Author Tags

        1. collaboratory
        2. data provenance
        3. data sharing
        4. data sharing contexts
        5. data-centric collaboration
        6. metadata
        7. scientific workflow
        8. tool-centric collaboration

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        November 6 - 10, 2004
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