1887

Research, Collaboration, and Open Science Using Web 2.0

    Authors: Kevin Shee1,+,*, Michael Strong2,3,+,*, Nicholas J. Guido2, Robert A. Lue1, George M. Church2, Alain Viel1
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    Affiliations: 1: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138; 2: Department of Genetics, Harvard Medical School, Boston, MA 02115; 3: National Jewish Health, Denver, CO 80206
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 20 December 2010
    • *Corresponding authors. Mailing addresses:Department of Molecular and Cellular Biology, Harvard University, 440 Winthrop Mail Center, Cambridge, MA 02138. Phone: (916) 294-5316. E-mail: [email protected]. Center for Genes, Environment, and Health, National Jewish Health, Smith Building A656, 1400 Jackson St., Denver, CO 80206. Phone: (303) 270-2782. Fax: (303) 270-2136. E-mail: [email protected].
    • + These authors contributed equally to this manuscript.
    • Copyright © 2010 American Society for Microbiology
    Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 130-134. doi:10.1128/jmbe.v11i2.219
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    Abstract:

    There is little doubt that the Internet has transformed the world in which we live. Information that was once archived in bricks and mortar libraries is now only a click away, and people across the globe have become connected in a manner inconceivable only 20 years ago. Although many scientists and educators have embraced the Internet as an invaluable tool for research, education and data sharing, some have been somewhat slower to take full advantage of emerging Web 2.0 technologies. Here we discuss the benefits and challenges of integrating Web 2.0 applications into undergraduate research and education programs, based on our experience utilizing these technologies in a summer undergraduate research program in synthetic biology at Harvard University. We discuss the use of applications including wiki-based documentation, digital brainstorming, and open data sharing via the Web, to facilitate the educational aspects and collaborative progress of undergraduate research projects. We hope to inspire others to integrate these technologies into their own coursework or research projects.

References & Citations

1. Butler D 2005 Electronic notebooks: a new leaf Nature 436 20 21 10.1038/436020a 16001034 http://dx.doi.org/10.1038/436020a
2. Carson S 2007 A new paradigm for mentored undergraduate research in molecular microbiology CBE Life Sci Educ 6 343 349 10.1187/cbe.07-05-0027 18056305 http://dx.doi.org/10.1187/cbe.07-05-0027
3. Chen J, Call GB, Beyer E, Bai C, Cespedes A, Chan A, et al 2005 Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers PLoS Biol 3 e59 10.1371/journal.pbio.0030059 15719063 548953 http://dx.doi.org/10.1371/journal.pbio.0030059
4. Goodman C 2008 Engineering ingenuity at iGEM Nat Chem Biol 4 108 113 10.1038/nchembio0108-13 http://dx.doi.org/10.1038/nchembio0108-13
5. Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon RM, Foley A, Ford ME, et al 2006 Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform PLoS Genetics 2 e92 10.1371/journal.pgen.0020092 16789831 1475703 http://dx.doi.org/10.1371/journal.pgen.0020092
6. Kerfeld CA, Simons RW 2007 The undergraduate genomics research initiative PLoS Biol 5 e141 10.1371/journal.pbio.0050141 17503966 1868073 http://dx.doi.org/10.1371/journal.pbio.0050141
7. Kihlén M 2005 Electronic lab notebooks do they work in reality? Drug Discovery Today 10 1205 1207 10.1016/S1359-6446(05)03576-2 16213407 http://dx.doi.org/10.1016/S1359-6446(05)03576-2
8. Kuldell N 2007 Authentic teaching and learning through synthetic biology J Biol Eng 1 8 10.1186/1754-1611-1-8 http://dx.doi.org/10.1186/1754-1611-1-8
9. Leuf B, Cunningham W 2001 The wiki way, Chapter 2: Whats a Wiki? Addison-Wesley Professional Boston, MA
10. McLean R, Richards BH, Wardman JI 2007 The effect of Web 2.0 on the future of medical practice and education: Darwikinian evolution or folksonomic revolution? Med J Australia 187 174 177 17680746
11. National Research Council 2003 Bio2010: transforming undergraduate education for future research biologists National Academies Press Washington, DC
12. Phillips ML 2006 Do you need an electronic lab notebook? The Scientist 20 74
13. Russell SH, Hancock MP, McCullough J 2007 Benefits of undergraduate research experiences Science 316 548 549 10.1126/science.1140384 17463273 http://dx.doi.org/10.1126/science.1140384

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/content/journal/jmbe/10.1128/jmbe.v11i2.219
2010-12-20
2020-04-06

Abstract:

There is little doubt that the Internet has transformed the world in which we live. Information that was once archived in bricks and mortar libraries is now only a click away, and people across the globe have become connected in a manner inconceivable only 20 years ago. Although many scientists and educators have embraced the Internet as an invaluable tool for research, education and data sharing, some have been somewhat slower to take full advantage of emerging Web 2.0 technologies. Here we discuss the benefits and challenges of integrating Web 2.0 applications into undergraduate research and education programs, based on our experience utilizing these technologies in a summer undergraduate research program in synthetic biology at Harvard University. We discuss the use of applications including wiki-based documentation, digital brainstorming, and open data sharing via the Web, to facilitate the educational aspects and collaborative progress of undergraduate research projects. We hope to inspire others to integrate these technologies into their own coursework or research projects.

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Author and Article Information

  • Published 20 December 2010
  • *Corresponding authors. Mailing addresses:Department of Molecular and Cellular Biology, Harvard University, 440 Winthrop Mail Center, Cambridge, MA 02138. Phone: (916) 294-5316. E-mail: [email protected]. Center for Genes, Environment, and Health, National Jewish Health, Smith Building A656, 1400 Jackson St., Denver, CO 80206. Phone: (303) 270-2782. Fax: (303) 270-2136. E-mail: [email protected].
  • + These authors contributed equally to this manuscript.
  • Copyright © 2010 American Society for Microbiology

Figures

Research, Collaboration, and Open Science Using Web 2.0
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Citation: Shee K, Strong M, Guido N, Lue R, Church G, Viel A. 2010. Research, collaboration, and open science using web 2.0. J. Microbiol. Biol. Educ. 11(2):130-134 doi:10.1128/jmbe.v11i2.219
/content/jmbe/10.1128/jmbe.v11i2.219.f1-jmbe-11-2-130
FIGURE 1

Virtual brainstorming sessions. (A) An example of the shared electronic notebook page used by the students for brainstorming summer project ideas. This method of online brainstorming complemented in-person brainstorming sessions and allowed the students to document, discuss and archive project ideas leading to the formulation of the summer project. (B) A portion of the source code for the brainstorming page is shown to demonstrate the intuitive nature of wiki code. Students can include hyperlinks to relevant websites, images and other e-notebook pages in a user-friendly manner using the wiki.

jmbe/11/2/jmbe-11-2-130f1_thmb.gif
jmbe/11/2/jmbe-11-2-130f1.gif
Image of FIGURE 1

Click to view

FIGURE 1

Virtual brainstorming sessions. (A) An example of the shared electronic notebook page used by the students for brainstorming summer project ideas. This method of online brainstorming complemented in-person brainstorming sessions and allowed the students to document, discuss and archive project ideas leading to the formulation of the summer project. (B) A portion of the source code for the brainstorming page is shown to demonstrate the intuitive nature of wiki code. Students can include hyperlinks to relevant websites, images and other e-notebook pages in a user-friendly manner using the wiki.

Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 130-134. doi:10.1128/jmbe.v11i2.219
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v11i2.219.f2-jmbe-11-2-130
FIGURE 2

The lab wiki. Our wiki contains student-contributed information including laboratory protocols, reagents used, gene sequence information, literature references, student presentations, digital pictures, primary data and archives of virtual brainstorming sessions (http://openwetware.org/wiki/IGEM:Harvard/2007).

jmbe/11/2/jmbe-11-2-130f2_thmb.gif
jmbe/11/2/jmbe-11-2-130f2.gif
Image of FIGURE 2

Click to view

FIGURE 2

The lab wiki. Our wiki contains student-contributed information including laboratory protocols, reagents used, gene sequence information, literature references, student presentations, digital pictures, primary data and archives of virtual brainstorming sessions (http://openwetware.org/wiki/IGEM:Harvard/2007).

Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 130-134. doi:10.1128/jmbe.v11i2.219
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v11i2.219.f3-jmbe-11-2-130
FIGURE 3

The electronic open notebook. (A) An example of a page from the electronic notebook relating to work performed on bacterial targeting. The wiki-based electronic lab notebook contains protocols, data, results, discussions and hyperlinks to other relevant experimental information including (B) sequence information and (C) gel electrophoresis results.

jmbe/11/2/jmbe-11-2-130f3_thmb.gif
jmbe/11/2/jmbe-11-2-130f3.gif
Image of FIGURE 3

Click to view

FIGURE 3

The electronic open notebook. (A) An example of a page from the electronic notebook relating to work performed on bacterial targeting. The wiki-based electronic lab notebook contains protocols, data, results, discussions and hyperlinks to other relevant experimental information including (B) sequence information and (C) gel electrophoresis results.

Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 130-134. doi:10.1128/jmbe.v11i2.219
Download as Powerpoint

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