SBOL – the beginning

Speaker: Raik Gruenberg

This is a presentation given on 20 January, 2016, at the Open Tools and Infrastructure for Biology 2016 held at Newcastle University.

2007 saw the fourth year of the iGEM competition. Everyone was talking about and making use of BioBricks, which allowed you to put together pieces of DNA. There were 54 teams and over 800 new parts during iGEM 2007. All new parts were deposited in the online Registry of Standard Biological Parts. Although this was good for the competition, he determined that it was very difficult to manage your data and the info coming from the lab. Therefore he helped build a set of web servers which would push and pull the data from the local servers to the Registry.

iGEM and the BioBricks Foundation (BBF, set up by Pam Silver and Drew Endy) then started developing the standard itself. They invited David Clark, co-inventor of TCP/IP. Clark suggested that you quickly create a rough consensus and get code up and running ASAP, and to avoid voting. It was also suggested that RFCs (Request for Comments) were used. Endy set up an RFC site for the BBF. With the RFC, anyone could propose a standard which had to include a description of best practices and protocols. Further, it was required that at least two different organizations made use of the proposal before submitting it.

Then, in 2008, Herbert Sauro and Michael Hucka became more involved while at a meeting in Seattle. Gruenberg had a web server setup where local data and BioBricks could be stored. At the 2008, he (together with others) started drafting the data exchange architecture. They settled on PoBOL, the Biobrick Provisional Language. Later that year, no-one had done any RFC’s yet so simply asked for ideas, which were then given an RFC number. BBF RFC #31 was PoBOL.

There was an informal meeting in Stanford in 2009 to further discuss PoBOL. It was in August of 2009 where “SBOL” was first used as the name. 2001 saw SBOL version 1.0, and 2012 saw the release of libSBOLj. Last year, SBOL 2.0 was released.

There was a move away from biobricks with SBOL, and they decided on a mixture of RDF/XML. They also got some dedicated funding and the mailing list discussions were very popular, very much a part of the culture of the SBOL community.

SBOL is a dommunity-driven standardization model which is driven by ideas and visions, (rather than starting with a lot of tools which then require a standard format) and is really a community of developers. It is the only serious standardization effort in synthetic biology.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

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