25 June 2013

Reports and Workshops Relating to Biology and Cyberinfrastructure

Over the past several years, a number of reports on cyberinfrastructure particularly relevant to biological research and biological infrastructure have been issued. Links to a sample of some of the reports are listed below, with reports supported by the NSF first and then a list of reports by other organizations.

This is a “best effort” listing, which includes a sample set of reports that have been published. If you would like to identify additional reports that we should list, or have corrections or suggestions to make regarding this list, please send email to pmccartn@nsf.gov.


Documents on this Biological Sciences Reports Page for the General Public are displayed verbatim as submitted by the author(s). Except for clearly designated official Foundation reports or issuances, NSF has not approved or endorsed their content. Any opinions, findings, conclusions or recommendations expressed are those of the contributor and do not necessarily reflect the views of the National Science Foundation.

Reports from workshops sponsored by the National Science Foundation and NSF advisory groups relevant to biology and cyberinfrastructure


Beach, J., J. Cook, L.S. Ford, R. Gropp, J. Hanken, K. Joyce, L.McDate, B. Thiers (eds). 2012. Implementation plan for the network integrated biocollectinos alliance. http://www.aibs.org/public-policy/NIBA_Implementation_Plan.pdf

Losos, J.B., S.J. Arnold, G. Bejerano, E. D. Brodie III, D. Hibbett, H. E. Hoekstra, D. P. Mindell, A. Monteiro, C. Moritz, H. A. Orr, D. A. Petrov, S.S. Renner, R.E. Ricklefs, P.S. Soltis, T.L. Turner. 2013. Evolutionary Biology for the 21st Century. PLoS Biol 11(1): e1001466. http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001466


Gil, Y. and H. Hirsh (eds). 2012. Final Report on the 2012 NSF Workshop on Discovery Informatics. http://www.discoveryinformaticsinitiative.org/diw2012

Kolker, E., E. Stewart, V. Ozdemir. 2012. Opportunities and Challenges
for the Life Sciences Community. OMICS A Journal of Integrative Biology 16: 138-147. http://online.liebertpub.com/doi/pdfplus/10.1089/omi.2011.0152[This, and the 2011 OMICS Volume 15
Number 4 special issue represent the report output of DELSA workshops I and II. See http://www.delsaglobal.org/events/previous-events for more information on DELSA workshops.]


Kolker, E. (ed.) 2011. Special Issue on Data-Intensive Science. OMICS A Journal of Integrative Biology, Volume 15, Number 4, 2011. http://online.liebertpub.com/toc/omi/15/4

Close, T. and R. Last (eds). 2011. Phenomics: Genotype to Phenotype - A report of the Phenomics workshop sponsored by the USDA and NSF. http://www.nsf.gov/bio/pubs/reports/phenomics_workshop_report.pdf

Holsinger, K. , E. Kellogg, M. Smith. 2011. Dimensions of Biodiversity Workshop Report. http://dx.doi.org/10.6084/m9.figshare.695027

NESCent. 2011. Cyberinfrastructure for collaborative science. https://www.nescent.org/wg_collabsci/2011_Workshop/Documents

Norris. C. (ed). 2011. Prospects for a Scientific Software Innovation Institute in Biological Collections Digitization: Interim White Paper, September 2011. http://www.spnhc.org/media/assets/S2I2- RCNCollectionsDigitizationWhitePaper.pdf


Ahalt, S. (ed). 2010. NSF Workshop on Creating Scientific Software Innovation Institutes for Sustained Cyberinfrastructure Achievement and Excellence Workshop Report and Recommendations. http://www.acsu.buffalo.edu/~abani/RENCI_NCSA_NSF_1049273_workshop_report.pdf

Beach, J., L. Ford, R. Guralnick, M. Mares, B. Thiers, M.Westneat, B. Wiegmann,2010. A Strategic Plan for Establishing a Network Integrated Collections Alliance. http://digbiocol.files.wordpress.com/2010/06/digistratplanfinalv1.pdf

Blum, S., M. Donoghue, L. Ford, G. Guala, R. Guralnick, M. Mares, B. Thiers, M. Westneat, Q. Wheeler.
2010. Developing a digital U.S. biological collections national resource: First steps towards a strategic plan. http://digbiocol.wordpress.com/author/robgur/

Casey, R., R. Hooper, J. Myers, M. Parsons. 2008. Cyberinfrastructure for Environmental Observation Networks (CEON) Workshop Report. http://feon.wdfiles.com/local--files/start/Feb2008WorkshopFinalReport.pdf

Duke, C. (ed). 2010. Strategies for Sustainability of Biological Infrastructure: Workshop Report. http://www.esa.org/science_resources/DocumentFiles/Strategies Sustainability Biological Infrastructure-Workshop Report.pdf

Gries, C., A. Rodrigo, M.B. Jones, D. Vieglais. 2010. Cyberinfrastructure and the NSF Dimensions of Biodiversity Program Solicitation Planning for Success. Workshop held Oct. 13-15 2010. Madison, WI. http://lter.limnology.wisc.edu/cidimensions/report


Advisory Committee for Environmental Research and Education. 2009. Transitions and Tipping Points in Complex Environmental Systems. A Report by the NSF Advisory Committee for Environmental Research and Education. http://www.nsf.gov/geo/ere/ereweb/ac-ere/nsf6895_ere_report_090809.pdf


Davis, J. (ed.) 2006. Cyberinfrastructure in Chemical and Biological Process Systems: Impact and
Directions. A University – Industry – CI Perspective. http://www.oit.ucla.edu/nsfci/NSFCIFullReport.pdf


Arzberger, P. (ed.). 2004. Sensors for Environmental Observatories: Report of the NSF-Sponsored
Workshop. http://wtec.org/seo/final/SEO_report_final.pdf

Ocean ITI Working Group. 2004. Trends in Information Technology Infrastructure in the Ocean Sciences,
24 pp. http://www.geo-prose.com/oceans_iti_trends/oceans_iti_trends_rpt.pdf


Committee on Frontiers at the Interface of Computing and Biology. 2003. Catalyzing Inquiry at the Interface of Computing and Biology. National Research Council. http://www.nap.edu/openbook.php?isbn=030909612X

Estrin, D., W. Michener, G. Bonito, and the workshop participants. 2003. Environmental
Cyberinfrastructure Needs for Distributed Sensor Networks: A Report from a National Science Foundation Sponsored Workshop. Scripps Institution of Oceanography, La Jolla, CA. 12-14 August 2003. http://intranet2.lternet.edu/sites/intranet2.lternet.edu/files/documents/Scientific_Reports/Cyberinfrastructure/cyberRforWeb.pdf

NSF Advisory Committee for Environmental Research and Education. 2003. Complex Environmental Systems: Synthesis for Earth, Life, and Society in the 21st Century. A report summarizing a ten-year outlook in environmental research and education. National Science Foundation. http://www.nsf.gov/geo/ere/ereweb/acere_synthesis_rpt.cfm

NSF Advisory Committee for Environmental Research and Education. 2003. Environmental CyberInfrastructure (ECI) Tools for the study of complex environmental systems. An Occasional paper of the NSF Advisory Committee for Environmental Research and Education AC-ERE 1. http://www.nsf.gov/geo/ere/ereweb/ac-ere/ac-ere1_ECI.pdf

Allison, L. P. Backlund, J.H. Beach, P. Cornillon, K. Droegemeier, P. Fox, D. Haidvogel,
T. Jordan, T. Killeen, J. L. Schnoor. 2003. Cyberinfrastructure for Environmental Research and Education: Report from a workshop held at the National Center for Atmospheric Research October 30 - November 1,
2002. http://www.ncar.ucar.edu/cyber/cyberreport.pdf


Donoghue, M. , S. Gilbert, V. Irish, T. Kaufmann, T. Kocker, L. Krishtalka, M. Lane,
M. Levine, W. McGinnis, M. Puruggana ,N. Sinha, G. Wray. 2001. Evolution of Development and Tree of
Life Workshop Report. http://www.nsf.gov/pubs/2001/bio012/start.htm

Reports sponsored in whole or part by, or representing working groups of, National Institutes of Health, National Research Council, and other organizations


Data and Informatics Working Group. 2012. Draft Report the Advisory Committee to the Director. National Institutes of Health. http://acd.od.nih.gov/Data and Informatics Working Group Report.pdf

Office of Science and Technology Policy. 2012. National Bioeconomy Blueprint. http://www.whitehouse.gov/sites/default/files/microsites/ostp/national_bioeconomy_blueprint_april_2012.pdf


Grossmann C., B. Powers, J.M. McGinnis (eds). 2011. Digital Infrastructure for the Learning Health System: The Foundation for Continuous Improvement in Health and Health Care: Workshop Series Summary. National Academies Press. https://www.ncbi.nlm.nih.gov/books/NBK83569/

Lupia, A. (ed.). 2011. Genes, Cognition, and Social Behavior: Next Steps for Foundations and Researchers. www.isr.umich.edu/cps/workshop/NSF_Report_Final.pdf

National Research Council (US) Committee on A Framework for Developing a New Taxonomy of Disease.
2011. Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New
Taxonomy of Disease. National Academies Press. https://www.ncbi.nlm.nih.gov/books/NBK91503/


Gowdy, J. and D. S. Wilson. 2010. The Relevance of Evolutionary Science for Economic Theory and Policy. Rensselear working papers in economics 1007. http://www.economics.rpi.edu/workingpapers/rpi1007.pdf


National Research Council (US) Committee on Engaging the Computer Science Research Community in Health Care Informatics; Stead WW, Lin HS, editors. Computational Technology for Effective Health Care: Immediate Steps and Strategic Directions. Washington (DC): National Academies Press (US); 2009. https://www.ncbi.nlm.nih.gov/books/NBK20640/

Research Information Network and the British Library, “Patterns of Information Use and Exchange: case studies of researchers in the life sciences.” http://www.rin.ac.uk/our-work/using-and-accessing-information-resources/patterns-information-use-and-exchange-case-studie


Stein, L. 2008. Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nature Reviews Genetics 9: 678-688. http://www.nature.com/nrg/journal/v9/n9/full/nrg2414.html doi:10.1038/nrg2414


Coalition for Advanced Scientific Computing2003. Opportunities for Biomedical Research and the NIH
through High Performance Computing and Data Management. http://www.casc.org/papers/paper13.pdf


Friedman, C.P., J.G. Ozbolt, D.R. Masys. 2001. Toward a New Culture for Biomedical Informatics: Report of the 2001 ACMI Symposium. J Am Med Inform Assoc. 8: 519–526. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC130062/