Difference between revisions of "Team:Waterloo/Integrated Practices"

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Research relies on the collection and analysis of data to develop explanations about the phenomena it seeks to represent (Borgman, 2015). Currently, many research disciplines are developing new data sharing and data use practices. One of these disciplines is biology, where novel ideas and practices around data are being established.  This paper focuses on data and science within synthetic biology, and specifically on the International Genetically Engineered Machine (iGEM), a leading synthetic biology competition. It begins with a review of open-science as a social and technical movement, then we introduce synthetic biology and the iGEM competition specifically, to show how open-data concepts are being encouraged and meeting resistance in this forum.  
 
Research relies on the collection and analysis of data to develop explanations about the phenomena it seeks to represent (Borgman, 2015). Currently, many research disciplines are developing new data sharing and data use practices. One of these disciplines is biology, where novel ideas and practices around data are being established.  This paper focuses on data and science within synthetic biology, and specifically on the International Genetically Engineered Machine (iGEM), a leading synthetic biology competition. It begins with a review of open-science as a social and technical movement, then we introduce synthetic biology and the iGEM competition specifically, to show how open-data concepts are being encouraged and meeting resistance in this forum.  
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<a href="/OpenScience">Read it here!</a>
 
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<div align="center"><div class=col-md-4>Reviewing our conclusions to the network analysis, recommendations were made for further investigation and specific improvements on our analysis on iGEM collaboration data.</div></div>
 
<div align="center"><div class=col-md-4>Reviewing our conclusions to the network analysis, recommendations were made for further investigation and specific improvements on our analysis on iGEM collaboration data.</div></div>
 
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      References
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<ol>
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<li>Baker, D., Church, G., Collins, J., Endy, D., Jacobson, J., Keasling, J., … Weiss, R. (2006). ENGINEERING LIFE: Building a FAB for Biology. (cover story). Scientific American, 294(6), 44–51.</li>
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<li>The BioBrick™ User Agreement - BioBricks Foundation. (n.d.). Retrieved December 7, 2015, from https://biobricks.org/bpa/users/agreement/ </li>
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Borgman, C. L. (2015). Big Data, Little Data, No Data: Scholarship in the Networked World. Cambridge, Massachusetts: The MIT Press.</li>
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<li>Cai, Y., Wilson, M., & Peccoud, J. (2010). GenoCAD for iGEM: A grammatical approach to the design of standard-compliant constructs. Nucleic Acids Research, 38(8), 2637–2644-2637–2644. doi:10.1093/nar/gkq086</li>
 +
<li>Canton, B., Labno, A., & Endy, D. (2008). Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology, 26(7), 787–793. http://doi.org/10.1038/nbt1413</li>
 +
<li>"Competition." Competition. N.p., n.d. Web. 07 Dec. 2015. <https://igem.org/Competition>.</li>
 +
<li>Endy, D. (2005). Foundations for engineering biology. Nature, 438(7067), 449–453. http://doi.org/10.1038/nature04342</li>
 +
<li>Facets. (n.d.). Retrieved December 5, 2015, from https://igem.org/Facets</li>
 +
<li>Grand, A., Wilkinson, C., Bultitude, K., & Winfield, A. (2012). Open Science: A New “Trust Technology”? Science Communication, 34(5), 679-689. doi:10.1177/1075547012443021</li>
 +
<li>Help:Prefix-Suffix. (n.d.). Retrieved December 7, 2015, from http://parts.igem.org/Help:Prefix-Suffix </li>
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<li>An iGEM Critique. (n.d.). Retrieved December 4, 2015, from https://2015.igem.org/Team:Waterloo/Practices/An_iGEM_Critique</li>
 +
<li>Judging/Medals. (n.d.). Retrieved December 4, 2015, from https://2015.igem.org/Judging/Medals</li>
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<li>Kelwick, R., Bowater, L., Yeoman, K. H., & Bowater, R. P. (2015). Promoting microbiology education through the iGEM </li><li>synthetic biology competition. FEMS Microbiology Letters, 362(16). http://doi.org/10.1093/femsle/fnv129</li>
 +
<li>Kotlarsky, J., & Oshri, I. (2005). Social ties, knowledge sharing and successful collaboration in globally distributed system development projects. European Journal of Information Systems, 14(1), 37. http://doi.org/http://dx.doi.org.proxy.lib.uwaterloo.ca/10.1057/palgrave.ejis.3000520</li>
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<li>Kidisyuk, M. (2015). Fair Use of Genetic Material: An iGEM-Specific Guide. Retrieved from https://static.igem.org/mediawiki/2015/2/23/Fair_Use_of_Genetic_Material_(an_iGEM-specific_guide).pdf </li>
 +
<li>Leduc, S. (1912). La biologie synthétique. A. Poinat.</li>
 +
<li>Ma, S., Tang, N., & Tian, J. (2012). DNA synthesis, assembly and applications in synthetic biology. Current Opinion in Chemical Biology, 16(3–4), 260–267. http://doi.org/10.1016/j.cbpa.2012.05.001</li>
 +
<li>Müller, K. M., & Arndt, K. M. (2012). Standardization in synthetic biology. Methods in Molecular Biology (Clifton, N.J.), 813, 23–43. http://doi.org/10.1007/978-1-61779-412-4_2</li>
 +
<li>Oldham, P., Hall, S., & Burton, G. (2012). Synthetic Biology: Mapping the Scientific Landscape. PLoS ONE, 7(4), e34368. http://doi.org/10.1371/journal.pone.0034368</li>
 +
<li>Osbourn, A. E., O’Maille, P. E., Rosser, S. J., & Lindsey, K. (2012). Synthetic biology. New Phytologist, 196(3), 671–677. http://doi.org/10.1111/j.1469-8137.2012.04374.x
 +
P. J. Turnbaugh, M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan, R. E. Ley, M. L. Sogin, W. J. Jones, B. A. Roe, J. P. Affourtit, M. Egholm, B. Henrissat, A. C. Heath, R. Knight, and J. I. Gordon, “A core gut microbiome in obese and lean twins,” Nature, vol. 457, no. 7228, pp. 480–484, Jan. 2009.</li>
 +
<li>Price, D. D. S. (1986). Little Science, Big Science...and Beyond. New York: Columbia Univ Pr.</li>
 +
<li>Purnick, P. E. M., & Weiss, R. (2009). The second wave of synthetic biology: from modules to systems. Nature Reviews Molecular Cell Biology, 10(6), 410–422. http://doi.org/10.1038/nrm2698</li>
 +
<li>Shetty, R. P., Endy, D., & Jr, T. F. K. (2008). Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering, 2(1), 1–12. http://doi.org/10.1186/1754-1611-2-5 </li>
 +
"IGEM Startups." IGEM Startups. N.p., n.d. Web. 07 Dec. 2015. <https://igem.org/IGEM_Startups>.
 +
<li>University of Oxford iGEM Team. (2014). Intellectual Property Report. Retrieved from https://static.igem.org/mediawiki/2014/8/86/IP_REPORTWEBVER.pdf </li>
 +
<li>Zeleny, M., & Hufford, K. D. (1992). The Application of Autopoiesis in Systems Analysis: Are Autopoietic Systems Also Social Systems? International Journal of General Systems, 21(2), 145–160. http://doi.org/10.1080/03081079208945066</li>
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</ul>
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Revision as of 20:10, 16 October 2016

Waterloo iGEM
Open Science

Research relies on the collection and analysis of data to develop explanations about the phenomena it seeks to represent (Borgman, 2015). Currently, many research disciplines are developing new data sharing and data use practices. One of these disciplines is biology, where novel ideas and practices around data are being established. This paper focuses on data and science within synthetic biology, and specifically on the International Genetically Engineered Machine (iGEM), a leading synthetic biology competition. It begins with a review of open-science as a social and technical movement, then we introduce synthetic biology and the iGEM competition specifically, to show how open-data concepts are being encouraged and meeting resistance in this forum.

Read it here!

Networks
A codebook was created in order to explicitly state the definitions and methods used in collecting, organizing, and analyzing collaboration data from the 2015 iGEM competition.
The data collected on iGEM teams in 2015 was analyzed in order to determine the effect of collaboration on team success.
Reviewing our conclusions to the network analysis, recommendations were made for further investigation and specific improvements on our analysis on iGEM collaboration data.
References
  1. Baker, D., Church, G., Collins, J., Endy, D., Jacobson, J., Keasling, J., … Weiss, R. (2006). ENGINEERING LIFE: Building a FAB for Biology. (cover story). Scientific American, 294(6), 44–51.
  2. The BioBrick™ User Agreement - BioBricks Foundation. (n.d.). Retrieved December 7, 2015, from https://biobricks.org/bpa/users/agreement/
    3. Borgman, C. L. (2015). Big Data, Little Data, No Data: Scholarship in the Networked World. Cambridge, Massachusetts: The MIT Press.
  3. Cai, Y., Wilson, M., & Peccoud, J. (2010). GenoCAD for iGEM: A grammatical approach to the design of standard-compliant constructs. Nucleic Acids Research, 38(8), 2637–2644-2637–2644. doi:10.1093/nar/gkq086
  4. Canton, B., Labno, A., & Endy, D. (2008). Refinement and standardization of synthetic biological parts and devices. Nature Biotechnology, 26(7), 787–793. http://doi.org/10.1038/nbt1413
  5. "Competition." Competition. N.p., n.d. Web. 07 Dec. 2015. .
  6. Endy, D. (2005). Foundations for engineering biology. Nature, 438(7067), 449–453. http://doi.org/10.1038/nature04342
  7. Facets. (n.d.). Retrieved December 5, 2015, from https://igem.org/Facets
  8. Grand, A., Wilkinson, C., Bultitude, K., & Winfield, A. (2012). Open Science: A New “Trust Technology”? Science Communication, 34(5), 679-689. doi:10.1177/1075547012443021
  9. Help:Prefix-Suffix. (n.d.). Retrieved December 7, 2015, from http://parts.igem.org/Help:Prefix-Suffix
  10. An iGEM Critique. (n.d.). Retrieved December 4, 2015, from https://2015.igem.org/Team:Waterloo/Practices/An_iGEM_Critique
  11. Judging/Medals. (n.d.). Retrieved December 4, 2015, from https://2015.igem.org/Judging/Medals
  12. Kelwick, R., Bowater, L., Yeoman, K. H., & Bowater, R. P. (2015). Promoting microbiology education through the iGEM
  13. synthetic biology competition. FEMS Microbiology Letters, 362(16). http://doi.org/10.1093/femsle/fnv129
  14. Kotlarsky, J., & Oshri, I. (2005). Social ties, knowledge sharing and successful collaboration in globally distributed system development projects. European Journal of Information Systems, 14(1), 37. http://doi.org/http://dx.doi.org.proxy.lib.uwaterloo.ca/10.1057/palgrave.ejis.3000520
  15. Kidisyuk, M. (2015). Fair Use of Genetic Material: An iGEM-Specific Guide. Retrieved from https://static.igem.org/mediawiki/2015/2/23/Fair_Use_of_Genetic_Material_(an_iGEM-specific_guide).pdf
  16. Leduc, S. (1912). La biologie synthétique. A. Poinat.
  17. Ma, S., Tang, N., & Tian, J. (2012). DNA synthesis, assembly and applications in synthetic biology. Current Opinion in Chemical Biology, 16(3–4), 260–267. http://doi.org/10.1016/j.cbpa.2012.05.001
  18. Müller, K. M., & Arndt, K. M. (2012). Standardization in synthetic biology. Methods in Molecular Biology (Clifton, N.J.), 813, 23–43. http://doi.org/10.1007/978-1-61779-412-4_2
  19. Oldham, P., Hall, S., & Burton, G. (2012). Synthetic Biology: Mapping the Scientific Landscape. PLoS ONE, 7(4), e34368. http://doi.org/10.1371/journal.pone.0034368
  20. Osbourn, A. E., O’Maille, P. E., Rosser, S. J., & Lindsey, K. (2012). Synthetic biology. New Phytologist, 196(3), 671–677. http://doi.org/10.1111/j.1469-8137.2012.04374.x P. J. Turnbaugh, M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan, R. E. Ley, M. L. Sogin, W. J. Jones, B. A. Roe, J. P. Affourtit, M. Egholm, B. Henrissat, A. C. Heath, R. Knight, and J. I. Gordon, “A core gut microbiome in obese and lean twins,” Nature, vol. 457, no. 7228, pp. 480–484, Jan. 2009.
  21. Price, D. D. S. (1986). Little Science, Big Science...and Beyond. New York: Columbia Univ Pr.
  22. Purnick, P. E. M., & Weiss, R. (2009). The second wave of synthetic biology: from modules to systems. Nature Reviews Molecular Cell Biology, 10(6), 410–422. http://doi.org/10.1038/nrm2698
  23. Shetty, R. P., Endy, D., & Jr, T. F. K. (2008). Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering, 2(1), 1–12. http://doi.org/10.1186/1754-1611-2-5
    24. "IGEM Startups." IGEM Startups. N.p., n.d. Web. 07 Dec. 2015. .
  24. University of Oxford iGEM Team. (2014). Intellectual Property Report. Retrieved from https://static.igem.org/mediawiki/2014/8/86/IP_REPORTWEBVER.pdf
  25. Zeleny, M., & Hufford, K. D. (1992). The Application of Autopoiesis in Systems Analysis: Are Autopoietic Systems Also Social Systems? International Journal of General Systems, 21(2), 145–160. http://doi.org/10.1080/03081079208945066