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Toward Replicability-Aware Modeling and Simulation: Changing the Conduct of M&S in the Information Age

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Book cover Ontology, Epistemology, and Teleology for Modeling and Simulation

Part of the book series: Intelligent Systems Reference Library ((ISRL,volume 44))

Abstract

The use of computational models in science end engineering is increasingly becoming pervasive. However, there is a growing credibility gap due to widespread, relaxed attitudes in communication of experiments, models, and validation of simulations used in computational research. Consequent disputes and article retractions due to unverified code and data suggest a pressing need for greater transparency. We introduce the e Portfolio concept, which is an ensemble documents that interweave the conceptual model, simulator design, experimental frames, and scientific workflow specifications. Strategies and potential mechanisms are delineated to enable authors, publishers, funding agencies, journals, and the broader scientific community to cooperate and establish a sustained model base, simulations, experiments, and documentation, so that scientists can build on each other’s work and achievements.

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References

  • Alberts, B.: Editorial Expression of Concern. Science 327(5962), 144 (2010), http://www.sciencemag.org/content/327/5962/144.1.full

    Article  Google Scholar 

  • Altman, M., King, G.: A Proposed Standard for the Scholarly Citation of Quantitative Data. D-Lib Magazine (March/April 2007), http://www.dlib.org/dlib/march07/altman/03altman.html

  • Anand, M.K., Bowers, S., McPhillips, T., Ludäscher, B.: Exploring Scientific Workflow Provenance Using Hybrid Queries over Nested Data and Lineage Graphs. In: Winslett, M. (ed.) SSDBM 2009. LNCS, vol. 5566, pp. 237–254. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  • Annotea. The Annotea Project (2011), http://www.w3.org/2001/Annotea/

  • Baggerly, K., Coombes, K.: Deriving Chemosensitivity from Cell Lines: Forensic Bioinformatics and Reproducible Research in High-Throughput Biology. Annals Applied Statistics 3(4), 1309–1334 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  • Beck, K.: Test-Driven Development by Example. Addison Wesley (2003)

    Google Scholar 

  • Borgman, C.L.: Scholarship in the Digital Age: Information, Infrastructure, and the Internet. The MIT Press, Cambridge (2007)

    Google Scholar 

  • Chang, C., et al.: Retraction. Science 314(5807), 1875 (2006), http://www.sciencemag.org/cgi/content/full/314/5807/1875b

    Article  Google Scholar 

  • CreativeCommons (2011), http://www.creativecommons.org

  • Cummings, T.P., Glotzer, S.C.: Inventing a New America through Discovery and Innovation in Science, Engineering, and Medicine. World Technology Evaluation Center (2010)

    Google Scholar 

  • David, A.P., Spence, M.: Toward Institutional Infrastructures for e-Science: The Scope of Challenges. Technical Report: Oxford Technical Institute (May 2003)

    Google Scholar 

  • Data Cite (2011), http://thedata.org/citation/tech

  • De Roure, D., Goble, C., Stevens, R.: The Design and Realisation of the myExperiment Virtual Research Environment for Social Sharing of Workflows. Future Generation Computer Systems 25, 561–567 (2009)

    Article  Google Scholar 

  • Donoho, D., Maleki, A., Rahman, I., Shahram, M., Stodden, V.: Reproducible Research in Computational Harmonic Analysis. Computing in Science & Engineering 11(1), 818 (2009)

    Article  Google Scholar 

  • Economist, The Clouds of Unknowing. The Economist (March 18, 2010), http://www.economist.com/node/15719298

  • Edwards, H.S.: Improving Student Performance by Evaluating How Well Students Test Their Own Programs. Journal of Educational Resources in Computing 3(3), 1–24 (2003)

    Google Scholar 

  • Fenton, E.N., Bieman, J.: Software Metrics: A Rigorous and Practical Approach. Chapman & Hall (2010)

    Google Scholar 

  • Fomel, S., Hennenfent, G.: Reproducible Computational Experiments using Scons. In: IEEE International Conference on Acoustics, Speech, and Signal Processing, vol. 4, pp. 1257–1260 (2009)

    Google Scholar 

  • Fomel, S., Claerbout, J.: Guest Editors’ Introduction: Reproducible Research. Computing in Science and Engineering 11(1), 5–7 (2009)

    Article  Google Scholar 

  • Foster, I.: Service-oriented Science. Science 308, 814–817 (2005)

    Article  Google Scholar 

  • Gentleman, R.: Reproducible Research: A Bioinformatics Case Study. Statistical Applications in Genetics and Molecular Biology 4(1), 123–137 (2005)

    Article  MathSciNet  Google Scholar 

  • Kiczales, G., Des Rivieres, J., Bobrow, D.G.: The Art of the Meta-object Protocol. MIT Press (1992)

    Google Scholar 

  • King, D.R., Turnitsa, C.D.: The Landscape of Assumptions. In: Proceedings of the Spring Simulation Multiconference, pp. 81–88 (2008)

    Google Scholar 

  • Leisch, F.: Sweave and Beyond: Computations on Text Documents. In: Proceedings of the 3rd Intl Workshop on Distributed Statistical Computing, pp. 87–96 (2003)

    Google Scholar 

  • Mesirov, J.: Accessible Reproducible Research. Science 327(5964), 415–416 (2010)

    Article  Google Scholar 

  • NSF. Simulation-Based Engineering Science, Revolutionizing Engineering Science through Simulation. National Science Foundation (2006)

    Google Scholar 

  • NSF. Changing the Conduct of Science in the Information Age. Summary Report of Workshop Held on November 12, 2010. National Science Foundation (June 28, 2011), http://www.nsf.gov/pubs/2011/oise11003/

  • Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K.: Taverna: A Tool for the Composition and Enactment of Bioinformatics Workflows. Bioinformatics 20(17), 3045–3054 (2004)

    Article  Google Scholar 

  • Overstreet, M.C., Nance, R.E., Balci, O.: Issues in Enhancing Model Reuse. In: Proceedings of the First International Conference on Grand Challenges for Modeling and Simulation (2002)

    Google Scholar 

  • Ören, T.I., Zeigler, B.P.: Concepts for Advanced Simulation Methodologies. Simulation 32(3), 69–82 (1979)

    Article  Google Scholar 

  • Ören, T.I.: The Richness of Modeling and Simulation and its Body of Knowledge. In: Proceedings of SIMULTECH 2012, 2nd International Conference on Simulation and Modeling Methodologies, Technologies and Applications, Rome, Italy, July 28-31 (invited keynote paper - in press, 2012)

    Google Scholar 

  • Peng, R.: Reproducible Research and Biostatistics. Biostatistics 10(3), 405–408 (2009)

    Article  Google Scholar 

  • reST. reStructuredText: Markup Syntax and Parser Component of Docutils (2011), http://docutils.sourceforge.net/rst.html

  • Saeki, M., Hiroi, T., Ugai, T.: Reflective Specification: Applying a Reflective Language to Formal Specification. In: Proceedings of the 7th International Workshop on Software Specification and Design, pp. 204–213. IEEE CS Press (1993)

    Google Scholar 

  • Schwab, M., Karrenbach, M., Claerbout, J.: Making Scientific Computations Reproducible. Computing in Science and Engineering 2, 61–67 (2000)

    Google Scholar 

  • SCS. The Code of Professional Ethics for Simulationists (2012), http://www.scs.org/upload/03-Code_0.pdf

  • Stodden, V.: The Legal Framework for Reproducible Scientific Research: Licensing and Copyright. Computing in Science & Engineering 11(1), 35–40 (2009)

    Article  Google Scholar 

  • Stodden, V.: The Scientific Method in Practice: Reproducibility in the Computational Sciences, Technical report, MIT Sloan Research (February 2010)

    Google Scholar 

  • Sphinx. Python Document Generator (2011), http://sphinx.pocoo.org

  • Wilensky, U., Rand, W.: Making Models Match: Replicating an Agent-Based Model. Journal of Artificial Societies and Social Simulation 10(42) (2007), http://jasss.soc.surrey.ac.uk/10/4/2.html

  • WTEC. Panel Report on International Assessment of Research and Development in Simulation-Based Engineering and Science. World Technology Evaluation Center (2009)

    Google Scholar 

  • Yilmaz, L.: On the Need for Contextualized Introspective Simulation Models to Improve Reuse and Composability of Defense Simulations. Journal of Defense Modeling and Simulation 1(3), 135–145 (2005)

    Google Scholar 

  • Yilmaz, L.: Reproducibility in Modeling & Simulation Research. Simulation 87(1), 3–6 (2011a)

    Article  Google Scholar 

  • Yilmaz, L.: Simulation Reproducibility: Implications for Theory, Methodology, and Model Development Environments. In: Epistemology of Modeling & Simulation Conference, Pittsburgh, April 1-3 (2011b), http://www.modelingepistemology.pitt.edu/program/

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Yilmaz, L., Ören, T. (2013). Toward Replicability-Aware Modeling and Simulation: Changing the Conduct of M&S in the Information Age. In: Tolk, A. (eds) Ontology, Epistemology, and Teleology for Modeling and Simulation. Intelligent Systems Reference Library, vol 44. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31140-6_11

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  • DOI: https://doi.org/10.1007/978-3-642-31140-6_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-31139-0

  • Online ISBN: 978-3-642-31140-6

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