E-Science References

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References

Agapakis, C. M. and Silver, P. a. (2009).: Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks.
Molecular bioSystems, 5(7), 704-13.
Andrianantoandro, E., Basu, S., Karig, D. K., and Weiss, R. (2006).: Synthetic biology: new engineering rules for an emerging discipline.
Molecular systems biology, 2, 2006.0028.
Antonucci-Durgan and Dana (2010).: Synthetic Biology Resources on the Internet.
Baker, D., Church, G., Collins, J., Endy, D., Jacobson, J., Keasling, J., Modrich, P., Smolke, C., and Weiss, R. (2006).: Engineering Life: Building a FAB for Biology.
Scientific American, (June).
Bateman, A. and Wood, M. (2009).: Cloud computing.
Bioinformatics (Oxford, England), 25(12), 1475.
Benner, S. a. and Sismour, A. M. (2005).: Synthetic biology.
Nature reviews. Genetics, 6(7), 533-43.
Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., Wolstencroft, K., Aleksejevs, S., Stevens, R., Pettifer, S., Lopez, R., and Goble, C. a. (2010).: BioCatalogue: a universal catalogue of web services for the life sciences.
Nucleic acids research, 38 Suppl(May), W689-94.
Booch, G., Maksimchuk, R. A., Engle, M. W., Bobbi J. Young, P., Conallen, J., and Houston, K. A. (2007).: Object-Oriented Analysis and Design with Applications.
Callahan, S. P., Freire, J., Santos, E., Scheidegger, C. E., and Vo, T. S. H. T. (2006).: VisTrails : Visualization meets Data Management.
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Chopra, P. and Kamma, A. (2006).: Engineering life through Synthetic Biology.
In Silico Biology, 0038, 2006-2006.
Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J., and Wipat, A. (2010).: Standard virtual biological parts: a repository of modular modeling components for synthetic biology.
Bioinformatics (Oxford, England), 26(7), 925-31.
Coveney, P. V. (2005).: Scientific Grid computing.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, 363(1833), 1707-13.
Craddock, T., Harwood, C. R., Hallinan, J., and Wipat, A. (2008).: e-Science : relieving bottlenecks in large-scale genome analyses.
Nature, 6(December), 948-954.
Cuellar, A. A., Lloyd, C. M., Nielsen, P. F., Bullivant, D. P., Nickerson, D. P., and Hunter, P. J. (2003).: An Overview of CellML 1.1, a Biological Model Description Language.
Simulation, 79(12), 740-747.
Deelman, E. (2009).: Grids and Clouds: Making Workflow Applications Work in Heterogeneous Distributed Environments.
International Journal of High Performance Computing Applications, 24(3), 284-298.
Deelman, E., Singh, G., Su, M.-h., Blythe, J., Gil, Y., and Kesselman, C. (2005).: Pegasus : A framework for mapping complex scientific workflows onto distributed systems.
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Endler, L., Rodriguez, N., Juty, N., Chelliah, V., Laibe, C., Li, C., and Le Novère, N. (2009).: Designing and encoding models for synthetic biology.
Journal of the Royal Society, Interface / the Royal Society, 6 Suppl 4(April), S405-17.
Endy, D. (2005).: Foundations for engineering biology.
Nature, 438, 449-453.
Fielding, R. T. and Fielding, K. (2000).: Architectural Styles and the Design of Network-based Software Architectures.
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Finney, A., Hucka, M., Bornstein, B. J., Keating, S. M., Shapiro, E., Matthews, J., Kovitz, B. L., Schilstra, M. J., Funahashi, A., Doyle, J., and Kitano, H. (2006).: Software Infrastructure for Effective Communication and Reuse of Computational Models, pages 355-378.
Fox, G. C. and Gannon, D. (2006).: Special Issue: Workflow in Grid Systems.
Concurrency and Computation: Practice and Experience, 18(10), 1009-1019.
Garny, A., Kohl, P., Noble, D., Road, P., Interface, A. P., and Mechanics, C. (2003).: CELLULAR OPEN RESOURCE ( COR ): A PUBLIC C ELL ML BASED ENVIRONMENT FOR MODELING BIOLOGICAL FUNCTION.
International Journal of Bifurcation and Chaos, 13(12), 3579-3590.
Grünberg, R., Nilges, M., and Leckner, J. (2007).: Biskit-a software platform for structural bioinformatics.
Bioinformatics (Oxford, England), 23(6), 769-70.
Heinemann, M. and Panke, S. (2006).: Synthetic biology-putting engineering into biology.
Bioinformatics (Oxford, England), 22(22), 2790-9.
Henderson-Sellers, B. (1997).: A book of Object-Oriented Knowledge: An Introduction to Object-Oriented Software Engineering.
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Hucka, M. (2003).: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Bioinformatics, 19(4), 524-531.
Hull, D., Wolstencroft, K., Stevens, R., Goble, C., Pocock, M. R., Li, P., and Oinn, T. (2006).: Taverna: a tool for building and running workflows of services.
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Kennard, S. and Stiver, M. C. (2000).: Understanding SOAP.
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Knight, T. (2003).: Idempotent Vector Design for Standard Assembly of Biobricks Standard Biobrick Sequence Interface.
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Lee, P. a., Dymond, J. S., Scheifele, L. Z., Richardson, S. M., Foelber, K. J., Boeke, J. D., and Bader, J. S. (2010).: CLONEQC: lightweight sequence verification for synthetic biology.
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Ludäscher, B., Altintas, I., Berkley, C., Higgins, D., Jaeger, E., Jones, M., Lee, E. a., Tao, J., and Zhao, Y. (2006).: Scientific workflow management and the Kepler system.
Concurrency and Computation: Practice and Experience, 18(10), 1039-1065.
Marchisio, M. a. and Stelling, J. (2009).: Computational design tools for synthetic biology.
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Oinn, T., Greenwood, M., Addis, M., Alpdemir, M. N., Ferris, J., Glover, K., Goble, C., Goderis, A., Hull, D., Marvin, D., Li, P., Lord, P., Pocock, M. R., Senger, M., Stevens, R., Wipat, A., and Wroe, C. (2006).: Taverna : lessons in creating a workflow environment for the life sciences.
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Pautasso, C. and Leymann, F. (2008).: RESTful Web Services vs . â€œ Big â€ Web Services : Making the Right Architectural Decision.
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McGraw Hill, first edition.
Richardson, L. and Ruby, S. (2007).: RESTful Web Serivces.
Rios-Velazquez, C. (2006).: "Constructing Knowledge" Actively in Bacterial Genetics Using Synthetic Biology.
Roure, D. D. (2004).: E-Science : The Grid.
IEEE Intelligent Systems, pages 65-71.
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Snell, J. (2001).: Programming Web Services with SOAP.