FAQ

Frequently Asked Questions

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SBOL

What is Synthetic Biology?
Synthetic biology is a new frontier in biological research where scientists and engineers design and create living systems to carry out useful tasks. In the last half century, the fundamental biochemical pieces and processes that comprise the phenomena of life have been isolated and studied by scientists in the laboratory. This reductionist approach to molecular biology has yielded enormous insight into the basic molecular units that govern life, such as genes encoded on DNA. Today, a new approach, synthetic biology, is possible in which basic units of biochemistry are re-assembled into new living systems, using platform technologies such as DNA synthesis, genome engineering, simulation tools, and computer-aided-design. In the future, important technologies like solar energy, biofuels, and medicines may be synthesized out of “wetware.”
What is the role of a standard language in synthetic biology?
Standards decrease friction in markets by reducing the cost of translating data and designs. So commercial entities can concentrate on transacting the goods and services in which they create the most value.
What is SBOL?
The design process is fundamental to synthetic biology. The SBOL standard empowers and enables a design-oriented, forward-engineering approach for synthetic biology in the following ways:

  • Facilitates storage of genetic designs in repositories
  • Helps synthetic biologists and genetic engineers electronically exchange designs with each other and with biofabrication centers
  • Supports development of Genetic Design Automation (GDA) software tools for synthetic biologists
  • Represents hierarchically assembled genetic compositions
  • Represents abstract genetic compositions without an explicit nucleotide sequence
  • Allows expression of genetic designs in publications and thus aids scientific reproducibility
  • Captures elements of a design that move beyond DNA Sequences to include RNA, proteins, small molecules and molecular interactions
  • SBOL is extensible to allow other kinds of data to be attached to the core data model. This includes, for example, experimental data, host information and mathematical models
  • Introductory slides on SBOL can be found here
Is SBOL free?
Yes. SBOL is not patented, has no royalties, and does not cost anything to use.
Is SBOL open?
SBOL is open source and licensed under the Creative Commons Attribution 4.0 International License.
How will SBOL help me?
Using the SBOL data model will let you download sequence designs from published experiments. You can retrieve SBOL designs from repositories like SynBioHub, and JBEI-ICE. Take a look at our applications page to see the software tools that currently support SBOL. If you want to support SBOL data in your tool, take a look at the available programming languages that are available to use in your tool.

You can also express your design using SBOL Visual. If you want to use SBOL visual in your tool, you can download the available SBOL graphical notations here.

What can I do with SBOL?
You can describe the components of a design and the interactions between components like circuit diagrams in the file using SBOL data. And you can draw them to prepare publications using SBOL visual. You can submit genetic designs to include all sequence
information for your paper in one file. You can also attach mathematical models to genetic designs SBOL will let you move your designs and work history between different tools.
What kinds of companies should use SBOL?
SynBio software companies, DNA synthesis companies, DNA design companies, really any company that makes or uses genetic materials.
I’m a small company. Why should I use the SBOL standard?
Use of the SBOL standard promotes ease of data access across applications and devices. Which means faster development time with fewer resources required, so you can get to market quickly.
I’m a large company. Why should I use SBOL?
There are no royalties to pay, and you won’t be sued for using it. Contributes to efficient patent searching. Patented devices can be represented in SBOL, so you can more easily search for comparison to your proposed designs. Use of open standards is also a key element of corporate social responsibility.
Why not just store all my sequence data in Word and Excel?
Designs in these tools become ambiguous to other people and are not easily read by, and swapped between software applications.
Can I use the SBOL logo in my own work/tools?
Yes, the SBOL Logo is free to use. You can get the logo here.

We’d be very flattered if you wanted to use it, but if you like us that much, please consider donating or sponsoring
development of SBOL. We’d love to have you. Note, however, that use of the SBOL logo does not convey any kind of endorsement or certification
by sbolstandard.org.

How is the SBOL standard funded?
SBOL is funded by grants through the National Science Foundation through Collaborative awards #1355909 and #1356401 and EPSRC grant
#EP/J02175X/1. Other sponsorship, support, or endorsements have been provided by the federal agencies, federal research centers,
commercial enterprises, and academic institutions. Please contact the SBOL Editors for donation consideration.
SBOL vs. GenBank
With the emergence of large-scale DNA sequencing technology in the last few decades, there has also emerged a need to manage and share vast amounts of sequence data. For researchers in the biological sciences, the public GenBank database, data standard, and file format has become a familiar friend. However, there are several reasons why the GenBank standard is insufficient for satisfying the needs of synthetic biologists. While the GenBank standard is used to primarily describe sequences that correspond to an existing DNA sample, the SBOL standard promotes forward-engineering of novel sequences. In other words, SBOL makes it easy to assemble novel sequences from DNA components using computer-aided design and genetic design automation. Moreover, SBOL is able to capture elements of intended design about proteins and small molecules for example, as well as the interactions between them.

Genbank is a great file format for sequences and unstructured annotations. What can you do with SBOL that you can’t with Genbank? Genbank isn’t meant for designs. It will not represent interactions between components,
let you specify undefined components, is not modular and won’t describe designs using proteins and small molecules.

Which tools will allow me to build SBOL?
We have summarize a list of SBOL data and SBOL visual tools that were reported to us here.

SBOL Data

Where can I get detailed information on SBOL Data?
SBOL is described in detail in the current SBOL specification.
What is the difference between SBOL 1.1 and 2.0?
SBOL 1.1 provides users with the ability to specify the structure of their designs. SBOL 2.0 improves upon the expressibility by adding the ability to specify function. More details of the differences can be found by reading the specifications for SBOL 1.1 and SBOL 2.0.
Are there repositories that store SBOL data?
Yes, there are several repositories. For instance, the SynBioHub and JBEI ICE. You can have a look at the current repositories that have been reported to ushere.

SBOL Visual

What is SBOL visual?
SBOL visual is a uniform way to draw diagrams of synthetic biology designs. Currently, these designs are depicted at the genetic level.
How do I draw SBOL visual designs?
There are a couple of SBOL visual software tools that you can use to draw SBOL visual glyphs such as VisBOL, SBOLDesigner and PigeonCAD. You can view a full list of SBOL visual tools that we have recorded here.

SBOL Community

How can I contribute to the community?
You can become a part of the community by emailing the SBOL Editors. More information on joining the SBOL community can be found on the here.
When does the SBOL community meet?
The SBOL community meets approximately every 6 months. A list of previous and upcoming meetings can be found here.
Is there a mailing list for the SBOL community?
Yes, there are three!

Detailed discussions about the SBOL specification are generally conducted through sbol-dev@googlegroups.com. The archives for this list can be accessed here. To join the mailing list, email the SBOL Editors.

Subscribe to sbol-announce@googlegroups.com if you would like to keep informed about developments in the SBOL community. Feel free to post to this email list as well if you have your own SBOL related announcements you would like to make.

Questions related to SBOL Data or SBOL Visual usage can be sent to sbol-users@googlegroups.com.

Citing SBOL

What paper should I cite for SBOL 1.1?
M. Galdzicki, K. Clancy, E. Oberortner, M. Pocock, J. Quinn, C. Rodriguez, N. Roehner, M. L. Wilson, L. Adam, C. Anderson, B. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grünberg, J. Hallinan, N.J. Hillson, J. D. Johnson, A. Kuchinsky,
M. Lux, G. Misirli, J. Peccoud, H. Plahar, E. Sirin, G.B Stan, A. Villalobos, A. Wipat, J. Gennari, C. Myers, and H. Sauro. “The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology,”
Nature Biotechnology, vol. 32, pp. 545-550, Jun. 2014. doi:10.1038/nbt.2891
What paper should I cite for SBOL 2.0?
General description:
N. Roehner, J. Beal, K. Clancy, B. Bartley, G. Misirli, R. Grunberg, E. Oberortner, M. Pocock, M. Bissell, C. Madsen, T. Nguyen, M. Zhang, Z. Zhang, Z. Zundel, D. Densmore, J. Gennari, A. Wipat, H. Sauro, and C. Myers. “Sharing structure and function
in biological design with SBOL 2.0,” ACS Synthetic Biology, vol. 5, no. 6, pp. 498-506, Apr. 2016. doi: 10.1021/acssynbio.5b00215

Detailed specification:
B. Bartley, J. Beal, K. Clancy, N. Hillson, G. Misirli, N. Roehner, H. Sauro, E. Oberortner, C. Madsen, M. Pocock, A. Wipat, T. Nguyen, Z. Zhang, C. Myers, J. Gennari, and M. Bissell. “Synthetic Biology Open Language (SBOL) Version 2.0.0,” Journal of Integrative Bioinformatics, vol.
12, no. 2, pp. 272, Sep. 2015. doi: 10.2390/biecoll-jib-2015-272..

What paper should I cite for SBOL Visual 1.1?
J. Y. Quinn, R. S. Cox, A. Adler, J. Beal, S. Bhatia, Y. Cai, J. Chen, K. Clancy, M. Galdzicki, N. J. Hillson, N. L. Novère, A.J. Maheshwari, J. A. McLaughlin, C. Myers, P. Umesh, M. Pocock, C. Rodriguez, L. Soldatova, G.B. Stan, N. Swainston, A. Wipat,
and H. Sauro. “SBOL Visual: A Graphical Language for Genetic Designs,” PLoS Biol, vol. 13, no. 12, Dec. 2015.doi:10.1371/journal.pbio.1002310
What paper should I cite for libSBOLj?
Z. Zhang, T. Nguyen, N. Roehner, G. Misirli, M. Pocock, E. Oberortner, M. Samineni, Z. Zundel, J. Beal, K. Clancy, A. Wipat, and C. Myers. “libSBOLj 2.0: A Java Library to Support SBOL 2.0,IEEE Life Sciences Letters, vol. 1,
no. 4, pp. 34-37, Mar. 2016. doi:10.1109/LLS.2016.2546546