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2009

SynBioStandards Network — Standards workshop 25 March 2009

Meeting organised by: Jim Haseloff Rapporteur: Emma Frow In attendance: about 40 people, including SynBioStandards Network members James Brown, Jane Calvert , James Chappell, Kim de Mora, Alistair Elfick, Fernan Federici, Emma Frow, Jim Haseloff, Chris Hirst, Dick Kitney, Matt Pocock, Peter Robbins, Vincent Rouilly Invited guests: Adam Arkin, Drew Endy, Randy Rettberg, Christina Smolke

****** Immediately after the close of BioSysBio 2009, the SynBioStandards Network sponsored an informal discussion on standards over beer + pizza. This was intended to continue the series of meetings that have taken place in the US (in Seattle and Boston) and during SB4.0 in Hong Kong. Conversation revolved around the following themes:

1)

Update from the BioBricks Foundation (BBF)

Drew Endy updated the group on recent efforts of the BioBrick Foundation (BBF). Although they initiated an RFC process about 2 years ago, the fact that a year later no standards had been submitted suggested that the bar had been set too high. (Initially, RFCs had to be validated / tested by an independent second party before submission.) The submission criteria have now been relaxed, and anyone who has an idea they would like comments on can submit an RFC. Over 20 RFC numbers have been assigned since November 2008, about half of which are currently accompanied by a document. It looks like a viable open standards process is emerging. RFC contributors will have their name associated with the RFC, which will also be assigned a doi number and be stored on the MIT server. BBF_RFC_0 contains instructions for anyone wishing to submit an RFC. Over the past couple of years, the BBF has also been working on developing a legal framework for the open sharing of parts — BioBrick Public Agreements. An advanced draft should be available for public comment by the end of April 2009.

2)

Types of standards needed

When asked about the current state of play for BioBrick standards, Drew Endy replied that the BBa standard initially proposed by Tom Knight has recognized limitations, and

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welcomed the number of alternative standards being developed by other researchers. The field is currently at a point where a lot of experimentation is needed, and from now on any new proposed standard for physical assembly will just be assigned a number. Drew noted that a commercial BioBrick assembly kit for BBa will soon be available. A show of hands in the room suggested that about half of those in the room whose labs were doing DNA construction were using the BBa standard. Drew noted that much of the focus so far has been on physical assembly standards, with some attention to functional composition. As for what should be prioritized / focused on, this is tricky to delimit. The following specific standards were mentioned over the course of the discussion: • Interoperability standards, allowing parts to be used as data objects • Standards for placing DNA synthesis orders • Guidelines / standards for publication More generally, the community should continue to develop standards for construction, measurement, depiction, functional composition, etc. It might be too early to develop universal standards, but this should not stop researchers from thinking about them, as they might productively guide research. A number of ‘minimum information’ standards were mentioned as examples (e.g. MIAME), which resulted in a lively discussion about whether the ‘minimum’ was what the community should be striving for — would this be useful in practice, or is it better to have more information? There is a tension between the amount of information that might be useful and the information that authors are willing to input, e.g. when it comes to describing parts. The PoBoL (provisional BioBrick language) being developed might be useful for describing parts and linking them to biological knowledge.

3)

Publishing

The journals IET Synthetic Biology (editor: Jim Haseloff) and Synthetic Biology (editor: Adam Arkin) are keen to explore publishing standards (in the form of datasheets) for the synthetic biology community. In part, the aim is to increase the reward for checking, documenting and annotating parts — important tasks at this stage of the field. The current proposal for a parts datasheet would include the following sections: 1 – historical record (including any citations, etc) 2 – physical composition (linking to existing information, eg. from GenBank) 3 – validation of sequence (sequence traces) 4 – open-ended section, for authors to describe use, measurements etc. (not prescriptive in terms of the included information, but the review process will determine whether it seems appropriate for the given part.) Similar existing examples might include the 1-page papers in Nucleic Acid Research, and the efforts by Standards in Genome Science. The Canton paper published in Nature Biotechnology also offers a model for the type of information that might be included with parts characterization. The journals would offer speedy publication turnaround, and published datasheets would have doi numbers and could be cited (in publications and on personal CVs). Any datasheets

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will also be sent / linked to the Registry. Would this scheme provide enough motivation for researchers to make their data available? It was noted that some form of centralization is desirable, e.g. one or two journals and the Registry, so that parts characterization information can be usefully linked and built upon.

4)

A professional society for synthetic biologists?

Christina Smolke gave a brief overview of the Institute of Biological Engineering, a professional society in the US. The group seemed to agree that it was important to develop a community of synthetic biologists beyond iGEM, but no formal consensus emerged as to whether it was important to have a dedicated and separate professional society for synthetic biologists at this point — fairly strong opinions were voiced in favour and against. Is the synthetic biology field at a point where dedicated curriculum materials, safety standards, ethical codes, certification schemes, etc. would be possible and useful? What effect might the development of a professional society have on public perception of the field? During the discussion, Randy Rettberg emerged as the strongest advocate for a professional synthetic biology society — other interested parties may wish to contact him in the first instance.

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THE END — of the event report but not the discussion! Please contribute to ongoing developments in the following ways :
• • •

Propose and write RFCs — these can be circulated for comments on the SynBioStandards Network wiki or submitted straight to the BBF Comment on the BBF BioBrick Public Agreement when it is made public in April 2009 Contact Jim Haseloff and Adam Arkin with thoughts or suggestions for publishing synthetic biology datasheets — and submit datasheets to IET Synthetic Biology and Synthetic Biology Keep contributing to the development of community standards!

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