Curr. Vita

Matthew B. Jones

jones@nceas.ucsb.edu

National Center for Ecological Analysis and Synthesis E-mail: jones@nceas.ucsb.edu

University of California Santa Barbara 735 State St., Suite 300 Santa Barbara, CA 93101

Education

Appointments

Grants

Service

Software

Publications

  1. Hallett, L. M., Jones, S. K., MacDonald, A. A. M., Jones, M. B., Flynn, D. F. B., Ripplinger, J., … Collins, S. L. (2016). codyn: An r package of community dynamics metrics. Methods in Ecology and Evolution, 7(10), 1146–1151. http://doi.org/10.1111/2041-210X.12569 [pdf] [link]
  2. Ludaescher, B., Chard, K., Gaffney, N., Jones, M. B., Nabrzyski, J., Stodden, V., & Turk, M. (2016, October 28). Capturing the "Whole Tale" of Computational Research: Reproducibility in Computing Environments. Retrieved from http://arxiv.org/abs/1610.09958 [link]
  3. Cao, Y., Jones, C., Cuevas-Vicenttín, V., Jones, M. B., Ludäscher, B., McPhillips, T., … Wei, Y. (2016). DataONE: A Data Federation with Provenance Support. In M. Mattoso & B. Glavic (Eds.), Provenance and Annotation of Data and Processes (Vol. 9672, pp. 230–234). Cham: Springer International Publishing. Retrieved from http://link.springer.com/10.1007/978-3-319-40593-3_28 [link]
  4. Shepherd, A., Chandler, C., Arko, R. A., Jones, M., Hitzler, P., Janowicz, K., … Rauch, S. (2015). Linked Data: Forming Partnerships at the Data Layer. In 2015 American Geophysical Union Fall Meeting, San Francisco, 14-18 December 2015. Retrieved from http://adsabs.harvard.edu/abs/2015AGUFMIN12A..03S [link]
  5. Jones, M. (2015). Lowering the Barrier to Reproducible Research by Publishing Provenance from Common Analytical Tools. In 2015 AGU Fall Meeting. AGU. Retrieved from http://adsabs.harvard.edu/abs/2015AGUFMIN43D..07J [link]
  6. Jones, M. (2015). Realizing the Living Paper using the ProvONE Model for Reproducible Research. In 2015 AGU Fall Meeting. AGU. Retrieved from http://adsabs.harvard.edu/abs/2015AGUFMIN53B1833J [link]
  7. Krisnadhi, A., Hu, Y., Janowicz, K., Hitzler, P., Arko, R., Carbotte, S., … Wiebe, P. (2015). The GeoLink Modular Oceanography Ontology. In The Semantic Web - ISWC 2015. 14th International Semantic Web Conference, Bethlehem, Pennsylvania, United States, October 11-15, 2015. Springer. Retrieved from http://iswc2015.semanticweb.org/sites/iswc2015.semanticweb.org/files/93670255.pdf [link]
  8. Katz, D. S., Choi, S.-C. T., Wilkins-Diehr, N., Hong, N. C., Venters, C. C., Howison, J., … Littauer, R. (2015). Report on the Second Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2). CoRR, abs/1507.01715. http://doi.org/10.5334/jors.85 [link]
  9. Shepherd, A., Arko, R., Krisnadhi, A., Hitzler, P., Janowicz, K., Chandler, C., … Fils, D. (2015). Ontology Design Patterns: Bridging the Gap Between Local Semantic Use Cases and Large-Scale, Long-Term Data Integration. In European Geosciences Union General Assembly 2015, Vienna, Austria, 12 - 17 April 2015. Retrieved from http://adsabs.harvard.edu/abs/2015EGUGA..17.8413S [link]
  10. Arko, R. A., Carbotte, S., Chandler, C., Cheatham, M., Fils, D., Hitzler, P., … Wiebe, P. (2015). EarthCube GeoLink: Semantics and Linked Data for the Geosciences. In 2015 American Geophysical Union Fall Meeting, San Francisco, 14-18 December 2015. Retrieved from http://adsabs.harvard.edu/abs/2015AGUFMIN41C1710A [link]
  11. Krisnadhi, A., Hu, Y., Janowicz, K., Hitzler, P., Arko, R., Carbotte, S., … Wiebe, P. (2015). The GeoLink Framework for Pattern-based Linked Data Integration. Proceedings of the ISWC 2015 Posters &Amp; Demonstrations Track. Retrieved from http://ceur-ws.org/Vol-1486/paper_99.pdf [pdf] [link]
  12. Stephanie E Hampton, Sean Anderson, Sarah C Bagby, Corinna Gries, Xueying Han, Edmund Hart, … Naupaka Zimmerman. (2014). The Tao of Open Science for Ecology. http://doi.org/10.7287/peerj.preprints.549v1 [link]
  13. Michener, W. K., & Jones, M. B. (2012). Ecoinformatics: supporting ecology as a data-intensive science. Trends in Ecology &Amp; Evolution, 27(2), 85–93. http://doi.org/10.1016/j.tree.2011.11.016 [link]
  14. Jones, M. B., & Gries, C. (Eds.). (2011). Proceedings of the Environmental Information Management Conference (EIM 2011). In Proceedings of the Environmental Information Management Conference (EIM 2011) (pp. 1–175). Santa Barbara: University of California. http://doi.org/10.5060/D2NC5Z4X [link]
  15. Reichman, O. J., Jones, M. B., & Schildhauer, M. P. (2011). Challenges and opportunities of open data in ecology. Science (New York, N.Y.), 331(6018), 703–5. http://doi.org/10.1126/science.1197962 [link]
  16. Leinfelder, B., Bowers, S., O’Brien, M., Jones, M. B., & Schildhauer., M. (2011). Using Semantic Metadata for Discovery and Integration of Heterogeneous Ecological Data. In M. B. Jones & C. Gries (Eds.), Proceedings of the Environmental Information Management Conference (EIM 2011) (pp. 92–97). Santa Barbara, CA: University of California. http://doi.org/10.5060/D2NC5Z4X
  17. Barseghian, D., Crawl, D., Jones, M. B., Altintas, I., Tao, J., & Riddle, S. (2011). Sensor lifecycle management using scientific workflows. In M. B. Jones & C. Gries (Eds.), Proceedings of the Environmental Information Management Conference (EIM 2011) (pp. 33–38). University of California. http://doi.org/10.5060/D2NC5Z4X [pdf]
  18. Dexter, N. C., Cobb, J. W., Vieglais, D., Jones, M. B., & Lowe, M. (2011). DataONE member node pilot integration with TeraGrid? In Proceedings of the 2011 TeraGrid Conference on Extreme Digital Discovery - TG ’11 (p. 1). New York, New York, USA: ACM Press. http://doi.org/10.1145/2016741.2016756 [link]
  19. Bowers, S., Cao, H., Schildhauer, M., Jones, M., Leinfelder, B., & O’Brien, M. (2010). A semantic annotation framework for retrieving and analyzing observational datasets. In Proceedings of the third workshop on Exploiting semantic annotations in information retrieval - ESAIR ’10 (p. 31). New York, New York, USA: ACM Press. http://doi.org/10.1145/1871962.1871982 [pdf] [link]
  20. Barseghian, D., Altintas, I., Jones, M. B., Crawl, D., Potter, N., Gallagher, J., … Seabloom, E. W. (2010). Workflows and extensions to the Kepler scientific workflow system to support environmental sensor data access and analysis. Ecological Informatics, 5(1), 42–50. http://doi.org/10.1016/j.ecoinf.2009.08.008 [link]
  21. Leinfelder, B., Tao, J., Costa, D., Jones, M. B., Servilla, M., O’Brien, M., & Burt, C. (2010). A metadata-driven approach to loading and querying heterogeneous scientific data. Ecological Informatics, 5(1), 3–8. http://doi.org/10.1016/j.ecoinf.2009.08.006 [pdf] [link]
  22. Jones, M. B., & Gries, C. (2010). Advances in environmental information management. Ecological Informatics, 5(1), 1–2. http://doi.org/10.1016/j.ecoinf.2010.01.001 [link]
  23. Gries, E. C., Rodrigo, A., Jones, M. B., & Vieglais, D. (2010). Cyberinfrastructure and the NSF Dimensions of Biodiversity Program Solicitation Planning for Success. [pdf]
  24. Schildhauer, M., Bermudez, L. E., Bowers, S., Dibner, P. C., Gries, C., Jones, M. B., … Madin, J. (2010). A core observational data model for enhancing the interoperability of ontologically annotated environmental data. AGU Fall Meeting Abstracts. Retrieved from http://adsabs.harvard.edu/abs/2010AGUFMIN44B..05S [link]
  25. Gallagher, J., Potter, N., & Jones, M. B. (2010). Common Patterns with End-to-end Interoperability for Data Access. AGU Fall Meeting Abstracts. Retrieved from http://adsabs.harvard.edu/abs/2010AGUFMIN11B1080G [link]
  26. Urban-Lurain, M., Ebert-May, D., Momsen, J., McFall, R., Jones, M. B., Leinfelder, B., & Sticklen, J. (2009). An Assessment Database for Supporting Educational Research. In 2009 39th IEEE Frontiers in Education Conference (pp. M2J–1–6). San Antonio, TX: IEEE Computer Society. http://doi.org/10.1109/FIE.2009.5350595 [link]
  27. Berkley, C., Bowers, S., Jones, M. B., Madin, J. S., & Schildhauer, M. (2009). Improving Data Discovery in Metadata Repositories through Semantic Search. In Proceedings of iSEEK’09. IEEE Computer Society. [pdf]
  28. Borer, E., Seabloom, E., Jones, M. B., & Schildhauer, M. (2009). Some Simple Guidelines for Effective Data Management. Bulletin of the Ecological Society of America, 205–214. http://doi.org/10.1890/0012-9623-90.2.205 [pdf] [link]
  29. Ludaescher, B., Altintas, I., Bowers, S., Cummings, J., Critchlow, T., Deelman, E., … Vouk, M. (2009). Scientific Process Automation and Workflow Management. In A. Shoshani & D. Rotem (Eds.), Scientific Data Management: Challenges, Technology, and Deployment. Chapman & Hall/CRC.
  30. Wang, J., Altintas, I., Hosseini, P. R., Barseghian, D., Crawl, D., Berkley, C., & Jones, M. B. (2009). Accelerating Parameter Sweep Workflows by Utilizing Ad-hoc Network Computing Resources: An Ecological Example. 2009 Congress on Services - I, 267–274. http://doi.org/10.1109/SERVICES-I.2009.9 [link]
  31. Madin, J. S., Bowers, S., Schildhauer, M. P., & Jones, M. B. (2008). Advancing ecological research with ontologies. Trends in Ecology &Amp; Evolution, 23(3), 159–68. http://doi.org/10.1016/j.tree.2007.11.007 [link]
  32. Gries, C., & Jones, M. B. (Eds.). (2008). Proceedings of Environmental Information Management Conference 2008. In Proceedings of Environmental Information Management Conference 2008 (p. 192). Albuquerque, NM. http://doi.org/10.5060/D2S46PV7 [link]
  33. Wang, J., Altintas, I., Berkley, C., Gilbert, L., & Jones, M. B. (2008). A High-Level Distributed Execution Framework for Scientific Workflows. 2008 IEEE Fourth International Conference on EScience, 634–639. http://doi.org/10.1109/eScience.2008.166 [link]
  34. Kruger, J., Jones, M., Schildhauer, M., & Stevens, N. (2008). New technologies for automating the management and analysis of conservation data. Ecological Circuits, 1, 5–8. [pdf]
  35. Barseghian, D., Altintas, I., & Jones, M. B. (2008). Accessing and using sensor data within the Kepler scientific workflow system. In C. Gries & M. B. Jones (Eds.), Proceedings of Environmental Information Management Conference 2008 (pp. 26–32). Albuquerque, NM. http://doi.org/10.5060/D2S46PV7
  36. Leinfelder, B., Tao, J., Costa, D., Jones, M. B., Servilla, M., O’Brien, M., & Burt, C. (2008). Using metadata for loading and querying heterogeneous scientific data. In C. Gries & M. B. Jones (Eds.), Proceedings of Environmental Information Management Conference 2008 (pp. 90–95). Albuquerque, NM. http://doi.org/10.5060/D2S46PV7 [link]
  37. Pennington, D., Higgins, D., Peterson, A. T., Jones, M. B., Ludaescher, B., & Bowers, S. (2007). Ecological Niche Modeling Using the Kepler Workflow System. In I. J. Taylor, E. Deelman, D. B. Gannon, & M. Shields (Eds.), Workflows for e-Science: Scientific Workflows for Grids (pp. 91–108). Springer. Retrieved from http://www.springer.com/computer/communication+networks/book/978-1-84628-519-6 [link]
  38. Jones, C., Blanchette, C., Brooke, M., Harris, J., Jones, M., & Schildhauer, M. (2007). A metadata-driven framework for generating field data entry interfaces in ecology. Ecological Informatics, 2(3), 270–278. http://doi.org/10.1016/j.ecoinf.2007.06.005 [link]
  39. Michener, W. K., Beach, J. H., Jones, M. B., Ludäscher, B., Pennington, D. D., Pereira, R. S., … Schildhauer, M. (2007). A knowledge environment for the biodiversity and ecological sciences. Journal of Intelligent Information Systems, 29(1), 111–126. http://doi.org/10.1007/s10844-006-0034-8 [pdf] [link]
  40. Jones, M. B. (2007). Meta-information systems and ontologies A special feature from ISEI’06. Ecological Informatics, 2(3), 193–194. http://doi.org/10.1016/j.ecoinf.2007.09.003
  41. Jones, M. B., Schildhauer, M. P., Reichman, O. J., & Bowers, S. (2006). The New Bioinformatics: Integrating Ecological Data from the Gene to the Biosphere. Annual Review of Ecology, Evolution, and Systematics, 37(1), 519–544. http://doi.org/10.1146/annurev.ecolsys.37.091305.110031 [link]
  42. Ludäscher, B., Altintas, I., Berkley, C., Higgins, D., Jaeger, E., Jones, M., … Zhao, Y. (2006). Scientific workflow management and the Kepler system. Concurrency and Computation: Practice and Experience, 18(10), 1039–1065. http://doi.org/10.1002/cpe.994 [link]
  43. Romanello, S., Beach, J., Bowers, S., Jones, M., Ludäscher, B., Michener, W., … Schildhauer, M. (2005). Creating and Providing Data Management Services for the Biological and Ecological Sciences: Science Environment for Ecological Knowledge. In J. Frew (Ed.), Proceedings of the 17th International Conference on Scientific and Statistical Database Management (pp. 28–31). Retrieved from http://2005.ssdbm.org/SSDBM_2005_Proceedings.pdf [link]
  44. Cushing, J., Vanderbilt, K., Brunt, J., Gupta, A., Jones, M., & McCartney, P. (2005). NSF Long Term Ecological Research Sites – Praxis et Theoria. In J. Frew (Ed.), Proceedings of the 17th International Conference on Scientific and Statistical Database Management (pp. 303–306). Retrieved from http://2005.ssdbm.org/SSDBM_2005_Proceedings.pdf [link]
  45. Michener, W., Beach, J., Bowers, S., Downey, L., Jones, M. B., Ludaescher, B., … Zhang, J. (2005). Data Integration and Workflow Solutions for Ecology. Lecture Notes in Computer Science, 3615, 321–324. http://doi.org/10.1007/11530084_32 [link]
  46. Fegraus, E. H., Andelman, S., Jones, M. B., & Schildhauer, M. (2005). Maximizing the Value of Ecological Data with Structured Metadata: An Introduction to Ecological Metadata Language (EML) and Principles for Metadata Creation. Bulletin of the Ecological Society of America, 158–168. [pdf]
  47. Berkley, C., Bowers, S., Jones, M. B., Ludaescher, B., Schildhauer, M., & Tao, J. (2005). Incorporating Semantics in Scientific Workflow Authoring. In J. Frew (Ed.), Proceedings of the 17th International Conference on Scientific and Statistical Database Management (pp. 75–78). Santa Barbara, CA. Retrieved from http://2005.ssdbm.org/SSDBM_2005_Proceedings.pdf. [link]
  48. Altintas, I., Berkley, C., Jaeger, E., Jones, M., Ludäscher, B., & Mock, S. (2004). Kepler: An Extensible System for Design and Execution of Scientific Workflows. In Proceedings of the 16th International Conference on Scientific and Statistical Database Management (SSDBM’04). IEEE Computer Society. http://doi.org/10.1109/SSDM.2004.1311241 [link]
  49. McCartney, P. H., & Jones, M. B. (2002). Using XML-encoded Metadata as a Basis for Advanced Information Systems for Ecological Research. In Proceedings of the 2002 System Cybernetics and Informatics Conference. Retrieved from http://intranet2.lternet.edu/documents/symposia-and-paper-sessions/2002-system-cybernetics-and-informatics-conference [pdf] [link]
  50. Higgins, D., Berkley, C., & Jones, M. B. (2002). Managing Heterogeneous Ecological Data Using Morpho. In Proceedings of the 14th International Conference on Scientific and Statistical Database Management (SSDBM’02) (pp. 69–76). IEEE Computer Society. http://doi.org/10.1109/SSDM.2002.1029707 [link]
  51. Jones, M. B., Berkley, C., Bojilova, J., & Schildhauer, M. (2001). Managing scientific metadata. IEEE Internet Computing, 5(5), 59–68. http://doi.org/10.1109/4236.957896 [link]
  52. Berkley, C., Jones, M., Bojilova, J., & Higgins, D. (2001). Metacat: a Schema-IndependentXML Database System. In Proceedings of the Thirteenth International Conference on Scientific and Statistical Database Management, SSDBM 2001. (pp. 171–179). IEEE Computer Society. http://doi.org/10.1109/SSDM.2001.938549 [link]
  53. Frondorf, A., Jones, M. B., & Stitt., S. (1999). Linking the FGDC geospatial metadata content standard to the biological/ecological sciences. In Proceedings of the Third IEEE Computer Society Metadata Conference. Bethesda, MD: IEEE Computer Society. Retrieved from http://computer.org/conferen/proceed/meta/1999/papers/4/afrondorf.html [link]
  54. Nottrott, R., Jones, M. B., & Schildhauer, M. (1999). Using XML-structured metadata to automate quality assurance processing for ecological data. In Proceedings of the Third IEEE Computer Society Metadata Conference. Bethesda, MD: IEEE Computer Society. Retrieved from http://computer.org/conferen/proceed/meta/1999/papers/64/rnottrott.html [link]
  55. Jones, M. B. (1998). Web-based Data Management. In W. K. Michener, J. H. Porter, & S. G. Stafford (Eds.), Data and Information Management in the Ecological Sciences: A Resource Guide. Albuquerque, New Mexico: LTER Network Office, University of New Mexico. Retrieved from http://www.ecoinformatics.org/pubs/guide/jones.fv2.htm [link]
  56. Peart, D. R., Poage, N. J., & Jones, M. B. (1992). Winter injury to subalpine red spruce: influence of prior vigor and effects on subsequent growth. Canadian Journal of Forest Research, 22(6), 888–892. http://doi.org/10.1139/x92-118 [link]
  57. Peart, D. R., Jones, M. B., & Palmiotto, P. A. (1991). Winter injury to red spruce at Mt. Moosilauke, New Hampshire. Canadian Journal of Forest Research, 21(9), 1380–1389. http://doi.org/10.1139/x91-195
  58. Jones, M., Folt, C., & Guarda, S. (1991). Characterizing Individual, Population and Community Effects of Sublethal Levels of Aquatic Toxicants - an Experimental Case-Study Using Daphnia. Freshwater Biology, 26(1), 35–44. http://doi.org/10.1111/j.1365-2427.1991.tb00506.x [link]