E-Science References

From 2010.igem.org


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.
In ACM SIGMOD, pages 745-747.

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.
Scientific Programming, 13, 219-237.

"Department of Defense" (2001).
Number January. The Defense Acquisition University.

DiCaterino, A., Larsen, K., Tang, M.-H., and Wang, W.-L. (1997).
An Introduction to Workflow Management Systems CTG . MFA – 002 Center for Technology in Government University at Albany / SUNY.

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.

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).
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.
Prentice Hall; 2nd edition, 2nd edition.

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.
Nucleic acids research, 34(Web Server issue), W729-32.

Kennard, S. and Stiver, M. C. (2000).
Understanding SOAP.

Knight, T. (2003).
Idempotent Vector Design for Standard Assembly of Biobricks Standard Biobrick Sequence Interface.
Structure, pages 1-11.

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.
Nucleic acids research, pages 1-7.

LESC (2010).
LESC - London e-Science Centre - What is e-Science?
last accesses 22/04/2010.

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.
Current opinion in biotechnology, 20(4), 479-85.

Morgan, H. (1978).
Characteristics of Application Software Maintenance.
Communications of the ACM, 21(6).

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.
Online, (December 2005), 1067-1100.

Pautasso, C. and Leymann, F. (2008).
RESTful Web Services vs . “ Big ” Web Services : Making the Right Architectural Decision.
Technology, pages 805-814.

Pressman, R. S. (1992).
Software Engineering. A Practisioner's Approach.
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.

Royce, W. W. (1970).
Proceedings, IEEE WESCON, (August), 1-9.

Snell, J. (2001).
Programming Web Services with SOAP.