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.
- Apache Software Foundation. Jetspeed. http://jakarta.apache.org/jetspeed/site/index.html.Google Scholar
- Apache Software Foundation. The Jakarta Slide Project. http://jakarta.apache.org/slide.Google Scholar
- 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).Google Scholar
- 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.Google Scholar
- 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. Google ScholarDigital Library
- 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.Google Scholar
- 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.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- 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.Google ScholarCross Ref
- IBM. Lotus Instant Messaging (Sametime). http://www.lotus.com/products/lotussametime.nsf/wdocs/homepage.Google Scholar
- Louis, K.S., Jones, L.M., and Campbell, E.G. 2002. "Sharing in Science." American Scientist, 90(4): pp. 304--307.Google ScholarCross Ref
- 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. Google ScholarDigital Library
- Macedonia, M.R. and Brutzman, D.P., "MBone Provides Audio and Video Across the Internet." IEEE Computer, 27(4), pp. 30--36. Google ScholarDigital Library
- 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. Google ScholarDigital Library
- Merton, R.K. 1968. Social Theory and Social Structure. Free Press, New York.Google Scholar
- Microarray Gene Expression Data Society. MGED - International Meetings on Microarray Gene Expression Databases Group. http://www.mged.org/index.html.Google Scholar
- Microsoft Corporation. NetMeeting. http://www.microsoft.com/windows/netmeeting/default.asp.Google Scholar
- Michigan State University. Shewanella Federation. http://www.shewanella.org/home.sjsp.Google Scholar
- 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 Google ScholarDigital Library
- 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. Google ScholarDigital Library
- 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.Google Scholar
- 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.Google Scholar
- 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.Google Scholar
- University of California, San Francisco. Molecular Modeling "Collaboratory." http://www.cgl.ucsf.edu/Research/collaboratory.Google Scholar
- University of Michigan. CHEF Information Site. http://chefproject.org/portal.Google Scholar
- University of Michigan. Science of Collaboratories. http://www.scienceofcollaboratories.org.Google Scholar
- Whitehead, E.J. and M. Wiggins. 1998. "WebDAV: IETF standard for collaborative authoring on the Web." IEEE Internet Computing, 2(5): pp. 34--40. Google ScholarDigital Library
- 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.Google Scholar
- Wulf, W. 1993. "The Collaboratory Opportunity." Science 261, (13 Aug 1993), pp. 854--855.Google Scholar
Index Terms
- Capturing and supporting contexts for scientific data sharing via the biological sciences collaboratory
Recommendations
Expectations for a scientific collaboratory: a case study
GROUP '03: Proceedings of the 2003 ACM International Conference on Supporting Group WorkIn the past decade, a number of scientific collaboratories have emerged, yet adoption of scientific collaboratories remains limited. Meeting expectations is one factor that influences adoption of innovations, including scientific collaboratories. This ...
An examination of research data sharing and re-use: implications for data citation practice
This study examines characteristics of data sharing and data re-use in Genetics and Heredity, where data citation is most common. This study applies an exploratory method because data citation is a relatively new area. The Data Citation Index (DCI) on ...
Norms of data sharing in biological sciences
Institutional environments, comprising regulative pressures by funding agencies and journal publishers, and institutional resources, including the availabilities of data repositories and standards for metadata, function as important determinants in ...
Comments