FAQ

General

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?

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

For Biologists

What is SBOL?

SBOL is a file format for exchanging synthetic biology designs

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 will SBOL help me?

SBOL will let you download sequence designs from published experiments. You can retrieve SBOL designs from repositories like SynBioHub (http://synbiohub.org/), and JBEI-ICE (https://acs-registry.jbei.org/).

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. And you can draw them to prepare publications. 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.

Genbank versus SBOL

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?

There is a list of SBOL tools at:

http://sbolstandard.org/software/tools/

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.

How do I draw SBOL visual designs?

Use VisBOL, SBOL Designer and PigeonCAD. See http://sbolstandard.org/software/tools/.

For Developers

Is SBOL free?

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.

Where can I get detailed information on SBOL?

SBOL is described in detail in the current SBOL specification: SBOL2.0 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.

Can I use the SBOL logo in my own work/tools?

Yes, the SBOL Logo is free to use.

Are there repositories that store SBOL data?

Yes, there are several repositories. For instance, the SBOL Stack and JBEI ICE.

How can I contribute to the community?

You can become a part of the community by emailing the editors: sbol-editors@googlegroups.com. More information on joining the SBOL community can be found on the Contact page: .

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. 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 editors: sbol-editors@googlegroups.com.

For Companies

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.

Is it free?

Yes! Using the SBOL standard is free to everyone.

Is it licensed?

The SBOL standard is released under Creative Commons 4.0 with Attribution.

Is it safe?

The SBOL standard is simply a specification. SBOL does not spy on anything.

Yes, you can use the SBOL logo. And 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.

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.

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.

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 consider joining the growing list of SBOL sponsors.


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