16.04.2009
2
welcomed the number of alternative standards being developed by other researchers. Thefield is currently at a point where a lot of experimentation is needed, and from now on anynew proposed standard for physical assembly will just be assigned a number. Drew notedthat a commercial BioBrick assembly kit for BBa will soon be available. A show of hands inthe room suggested that about half of those in the room whose labs were doing DNAconstruction were using the BBa standard.Drew noted that much of the focus so far has been on physical assembly standards, withsome 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 publicationMore generally, the community should continue to develop standards for construction,measurement, depiction, functional composition, etc. It might be too early to developuniversal standards, but this should not stop researchers from thinking about them, as theymight 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 communityshould be striving for — would this be
useful
in practice, or is it better to have moreinformation? There is a tension between the amount of information that might be useful andthe information that authors are willing to input, e.g. when it comes to describing parts. ThePoBoL (provisional BioBrick language) being developed might be useful for describing partsand linking them to biological knowledge.
3) Publishing
The journals
IET Synthetic Biology
(editor: Jim Haseloff) and
Synthetic Biology
(editor: AdamArkin) 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 andannotating 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. (notprescriptive in terms of the included information, but the review process willdetermine whether it seems appropriate for the given part.)Similar existing examples might include the 1-page papers in
Nucleic Acid Research
, and theefforts 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 partscharacterization.The journals would offer speedy publication turnaround, and published datasheets wouldhave doi numbers and could be cited (in publications and on personal CVs). Any datasheets
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