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Science and Technology Resources on the Internet

Synthetic Biology Resources on the Internet

Dana Antonucci-Durgan
Biology & Chemistry Librarian
Stony Brook University Libraries
Stony Brook, New York
dana.antonucci@stonybrook.edu

Copyright 2010, Dana Antonucci-Durgan. Used with permission.

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Abstract

Synthetic biology, a branch of biotechnology, uses engineering principles to create new biological entities. In addition to literature on current research projects, researchers need to be aware of the social, ethical and security issues surrounding this science. This guide highlights synthetic biology web resources freely available on the Internet.

Introduction

Synthetic biology is one of the latest emerging fields in biotechnology. The term "synthetic biology" has been used in the literature for over 100 years (Campos 2009) to describe a change or alteration of a biological construct, however contemporary definitions differ substantially from the first use of the term. The diverse nature of the research has lead to a wide variety of definitions adopted by scientists to describe the field and some researchers have argued that synthetic biology is not a unique field but rather a "redefinition of biotechnology" (What's in a Name? 2009).

While researchers have not agreed on a standard definition of synthetic biology there are some common elements of the field described in the literature. Some common threads of current synthetic biology definitions include the synthesis or creation of new biological systems or entities (Agapakis & Silver 2009; Deplazes 2009) using engineering principles (Heinemann & Panke 2006) such as modularity and scalability (Agapakis & Silver 2009). Another common element that defines synthetic biology is the use of unnatural elements or parts to create biological entities (Benner & Sismour 2005). Andrianantoandro et al. (2006) state one goal of synthetic biology is to "extend or modify the behavior of organisms and engineer them to perform new tasks."

The breadth of synthetic biology research has been stated to fall into five categories ranging from DNA-based device construction (O'Malley et al. 2008) to the creation of unnatural genetic code (Lam et al. 2009). The research literature, however, traverses many disciplines including mathematics, computer science, molecular biology and engineering.

Synthetic biology research has implications in many fields such as drug discovery, medicine, and fuel production. The interdisciplinary nature of the field may require researchers to search various subject databases. Researchers may find relevant literature in biomedical databases such as PubMed and the Web of Science-Science Citation Index, as well as engineering databases including Compendex and Inspec.

The creation of artificial biological components with natural or enhanced functionality has sparked much debate over security, safety and ethical considerations. The need for information on current protocols and laws governing research is an important aspect of this growing field. Scientists also need to be aware of intellectual property and patent issues surrounding the creation of biological systems.

Scope and Methods

This guide includes many of the free sites available on the Internet to assist researchers in finding synthetic biology information. As synthetic biology is an interdisciplinary field, this list of resources does not include all subject databases containing synthetic biology research as the focus of this webliography is on sites specific to synthetic biology information. The webliography is selective rather than comprehensive as some synthetic biology sites were excluded from the list based on outdated information or broken or misdirecting links.

This webliography was created using results from Google and Microsoft Bing searches as well as literature searches of PubMed, Web of Science, and Compendex. The resources selected for inclusion include free resources, with the exception of the journal titles which may require a subscription, specific to synthetic biology research and issues. The resources are limited to English language sites. Computer modeling programs and other software tools are not included in this webliography.

The resources in this guide were selected for researchers and educators in the field of synthetic biology to learn more about the research community, conference and event information, as well as current policy and ethical debates. The guide includes information on sites focusing on biological parts information and standards which is an important component of synthetic biology research. The author is not aware of other published synthetic biology webliographies in the library literature.

Associations

International Association of Synthetic Biology
{http://synthetic-biology.net/}

The International Association of Synthetic Biology, comprised of commercial companies and organizations, offers many workshops on policy and security issues associated with synthetic biology research. The Code of Conduct for Best Practices in Gene Synthesis outlines "safe and responsible use of synthetic DNA."

Blogs, Wikis and Communities

OpenWetWare
http://openwetware.org/wiki/Main_Page

An online forum for researchers to post course, protocol, and research group information. The site includes blogs on a number of topics including Science in the Open and the OpenWetWare Community.

Synthetic Biology- Royal Society Publishing
http://royalsocietysynbio.blogspot.com/

The Royal Society blog includes links to interviews, current news, and research. The Twitter results list provides links to current communication on synthetic biology.

Synthetic Biology.org
http://syntheticbiology.org/

A collection of news items and resources for synthetic biology researchers. The site includes a list of discussion groups as well as current research initiatives. The conference list includes past and upcoming conferences and events on synthetic biology research.

Centers of Research

Institute of Systems and Synthetic Biology. Imperial College, London.
http://www3.imperial.ac.uk/systemsbiology/

The site highlights the research conducted at the Institute including technology facilities available to researchers.

SynBERC -- Synthetic Biology Engineering Research Center
http://www.synberc.org/

SynBERC is a National Science Foundation Engineering Research Center aimed at conducting research, training scientists and educating the public. The SynBERC site includes links to educational programs in synthetic biology and current research in the field.

Synthetic Biology Maps
http://www.nanotechproject.org/inventories/synthetic_biology_maps/

The Project on Emerging Nanotechnologies, a collaboration of the Woodrow Wilson International Center for Scholars and the Pew Charitable Trusts, created an interactive map of synthetic biology research centers. The search interface, on the Synthetic Biology Project site, allows users to search for research facilities by city and state.

Journals

Synthetic biology research is published in a wide variety of journals including many bioscience, medical, computer science, engineering, and physics journals. The following list of titles includes journals specifically created to publish articles on synthetic biology research.

IET Synthetic Biology
http://ieeexplore.ieee.org/servlet/opac?punumber=4290605

The journal publishes original research as well as review articles and educational material in the field of synthetic biology. A subscription is required to access content. The Systems and Synthetic Biology Network ({http://kn.theiet.org/communities/biology/index.cfm}) provides readers with latest industry news and upcoming events.

Systems and Synthetic Biology
http://www.springerlink.com/content/1872-5325

Systems and Synthetic Biology began publication in 2007. The journal publishes both experimental and computational studies in the field of systems and synthetic biology. Many of the articles are available in full-text via the open access option, however, a subscription is required to view all other articles.

Safety, Security and Ethics

In 2002, the synthesis of the poliovirus from publically available data (Cello, Paul, & Wimmer 2002) sparked debate over security and safety issues in genetic research. The nature of synthetic biology research requires scientists to be aware of current safety protocols and security measures. The following list of web resources addresses the issues surrounding safety, ethics and security in the field.

Ars Synthetica
http://www.ars-synthetica.net

An online forum for researchers and non-professionals to engage in debate and view the current issues surrounding synthetic biology research. The debate section includes links to PBS programs, interviews, cartoons and other interesting exhibits.

Synbiosafe
http://www.synbiosafe.eu/

Synbiosafe is a scientific research project aimed at investigating ethical and safety aspects of synthetic biology research. A bibliography of popular press as well as scholarly articles highlights some of the top research and discussions on ethical issues. The e-conference site includes posts of the discussion from the Synbiosafe open online conference.

Synthetic Biology Project
http://www.synbioproject.org/

The Synthetic Biology Project is a policy group of the Woodrow Wilson International Center for Scholars. The site includes information about reports, conferences and presentations focusing on current social and ethical issues. The "topics" area of the site provides background information and selected publications on various ethical issues.

The Hastings Center- Synthetic Biology
http://www.thehastingscenter.org/Issues/Default.aspx?v=2392

This Hastings Center site posts many news features and articles about the ethical issues surrounding synthetic biology research. In additional to news items, the site includes lists of resources, a discussion forum, and expert links.

Synthetic Biology and Systems Biology Gateway
{http://rsif.royalsocietypublishing.org/site/misc/syntheticbiology.xhtml}

This gateway includes a bibliography of freely available influential synthetic biology articles. The site, hosted by the Royal Society, includes lists of research labs, policy reports and upcoming events and conferences.

Training, Conferences and Educational Resources

Biobuilder
http://www.biobuilder.org/

A teaching resource for synthetic biology information. Each module includes an animated lesson and links to additional synthetic biology resources. The subject area content is not complete as there are many modules which do not contain any information.

European Science Foundation- European Conference on Synthetic Biology (ECSB) II: Design, Programming and Optimisation of Biological Systems
{https://web.archive.org/web/20160417172312/http://www.esf.org/index.php?id=5386}

The site includes abstracts and presentation slides from the 2009 ECSB II. The conference was the second European Conference on Synthetic Biology. The papers and abstracts from the first conference in 2007 can be found at http://www.esf.org/activities/esf-conferences/details/2007/confdetail241.html.

International Genetically Engineered Machine Competition (iGEM)
http://2010.igem.org/Main_Page

The International Genetically Engineered Machine Competition is an international event where students compete to assemble biological components. The iGEM wiki includes information on registering for the competition, team pages as well as teaching resources. The teaching resources include links to lectures and presentations as well as introductory material on synthetic biology. The following are links to previous IGEM competition sites:
IGEM 2009.
http://2009.igem.org/Main_Page
IGEM 2008
http://2008.igem.org/Main_Page
IGEM 2007
{http://2007.igem.org/}
IGEM 2006
{http://2006.igem.org/}
IGEM 2005
{http://2006.igem.org/Igem_2005}
IGEM 2004
{http://2004.igem.org/index.cgi}

Synthetic Biology x.0
http://sb4.biobricks.org/

The Synthetic Biology x.0 conference includes presentations on building biological parts, new technologies in the field as well as social issues and concerns. The date and location for the 5th conference, Synthetic Biology 5.0, has yet to be determined. The link above is to the 4th conference and the following are the links to past conferences:
Synthetic Biology 3.0. Zurich, Switzerland. 2007
http://www.syntheticbiology3.ethz.ch/
Second International Conference on Synthetic Biology. Berkeley, California. 2006.
{http://web.archive.org/web/20081221164338/http://webcast.berkeley.edu/event_details.php?webcastid=15766}
The First International Meeting on Synthetic Biology. Cambridge, Massachusetts. 2004
http://syntheticbiology.org/Synthetic_Biology_1.0.html

Intellectual Property

BioBricks Foundation
http://bbf.openwetware.org/

The BioBricks Foundation aims to keep biological parts freely available to researchers. The drafts of many of the Requests for Comments (RFC) on protocols or standards are found on this site.

BioFab: International Open Facility Advancing Biotechnology
http://www.biofab.org/

The University of California, Berkeley, and Stanford University launched an initiative in December 2009 aimed at producing standardized DNA parts. The site includes a link to readings on the standardization of biological parts as well as lists of current BioFab projects.

Registry of Biological Parts
http://partsregistry.org/Main_Page

An open access repository of biological parts hosted at the Massachusetts Institute of Technology (MIT). Researchers can use or deposit information into the registry. The registry includes a search by parts query that helps researchers locate a specific biological component.

References

Agapakis, C.M., & Silver, P.A. 2009. Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks. Molecular Biosystems 5(7): 704-713. [Internet]. [Cited October 5, 2009]. Available from: http://www.rsc.org/Publishing/Journals/MB/article.asp?doi=b901484e

Andrianantoandro, E., Basu, S., Karig, D.K., & Weiss, R. 2006. Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology 2:2006.0028. [Internet]. [Cited February 10, 2010]. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681505/

Benner, S.A. & Sismour, A.M. 2005. Synthetic biology. [Review]. Nature Reviews Genetics 6(7): 533-543. [Internet]. [Cited February 1, 2010]. Available from: http://www.nature.com/nrg/journal/v6/n7/abs/nrg1637.html

Campos, L. 2009. That was the synthetic biology that was. In: Schmidt, M., et al., editors. Synthetic biology: the technoscience and its societal consequences.; London: Springer, p 5-21. [Internet]. [Cited November 1, 2009]. Available: http://www.springerlink.com/content/978-90-481-2677-4

Cello, J., Paul, A. V., & Wimmer, E. 2002. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 297(5583):1016-1018. [Internet]. [Cited November 12, 2009]. Available from: http://www.sciencemag.org/cgi/content/full/297/5583/1016

Deplazes, Anna. 2009. Piecing together a puzzle: an exposition of synthetic biology. EMBO Reports 10(5):428-32. [Internet]. [Cited February 16, 2010]. Available from: {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680885/}

Heinemann, M. & Panke, S. 2006. Synthetic biology -- putting engineering into biology. Bioinformatics 22(22):2790-2799. [Internet]. [Cited February 20, 2010]. Available from: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/22/2790

Lam, C., Godinho, M., & Martins dos Santos, V. 2009. An Introduction to synthetic biology. In: Schmidt, M., et al., editors. Synthetic biology: the technoscience and its societal consequences. London: Springer. p. 25. [Internet]. [Cited November 1, 2009]. Available from: http://www.springerlink.com/content/978-90-481-2677-4

O'Malley, M. A., Powell, A., Davies, J. F., & Calvert, J. 2008. Knowledge-making distinctions in synthetic biology. Bioessays 30(1):57-65. [Internet]. [Cited November 21, 2009]. Available from: http://www3.interscience.wiley.com/cgi-bin/fulltext/117865239/PDFSTART

What's in a name? 2009. Nature Biotechnology 27(12):1071-73. [Internet]. [Cited January 25, 1010]. Available from: http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1071.html

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