Standards for Synthetic Biology (BioSysBio 2009)

Existing Standards for DNA Description

Guy Cochrane

For the EMBL database, they need to provide capability for submission and collaborator data exchange. They use SRS for text search and retrieval, simple sequence retrieval (dbfetch), also dump the whole set of files out. There's been a large amount of growth over the past year or so, as the new technologies allow much faster sequencing.

Personal Comment: I took fewer notes for this section as I used to work on TrEMBL (UniProt as it's called now) and am quite familiar with EMBL, so I didn't feel the need to take as many notes…!

Previous Standards Effort: SBML

Herbert Sauro
University of Washington, Seattle

In 1999 there were 5-6 different simulators, and people wanted to be able to move the models from one tool to the next. SBML was originally created to represent homogeneous multi-compartment biochemical systems. They estimate that this format can cover about 80% of the models out there. The initial version was funded by JST. Over 120 software packages now support SBML including MATLAB and Mathematica. SBML is also acceptable to many journals including Nature, Science, and PLoS. It has also since spawned many other initiatives.

Key contributing factors to its take up: a need from the community; availability of detailed documentation; annual/biannual two-day meetings; portable software libraries to enable developers to incorporate standard capabilities into their software; they deliberately didn't try to do everything, as it covered about 80% of the community's needs at the time. Because the libraries were maintained centrally it ensured that the standard didn't diverge, and extensions/modifications were agreed by the community and could then be easily incorporated by developers.

SBML has been going for 8 years. Significant changes are planned. But, the exciting things are the peripheral results: BioModels (repository), KiSAO (ontology/CV), SBO (ontology/CV), TEDDY (ontology/CV), MIASE (presumptive standard for storage of simulation results), SBRML (presumptive standard), Antimony (human-readable version of SBML).

With a standard format, you can all of a sudden do compliance testing – do all applications produce the same results, or even succeed when simulating all models in BioModels? roadRunner, COPASI, BioUML, SBML ODE Solver perform the best.

Physical Standards and the BioBrick Registry

Randy Rettberg

The idea of the registry came from the TTL Data Book for design engineers. The current registry contains a wiki and more – it looks like a website, not a data book. Each biobrick part was listed, and had its own page. The number of teams in 2003 was less than 10 – in 2008 it was 84, with 1180 people.

The quality of the parts is really important. Starting last year, they did a specific set quality control tests. They're making sure that the top 800 bricks grew, had good sequence, the users said they worked, etc.

They also worked on the overall structure of the registry. He'd like to go in the direction of a more distributed system. Future work includes: extension to DAS interface; uploading parts; external tool hooks for sequence analysis and sequence and feature editors.

This session is a preface session for tomorrow's end-of-meeting standards workshop. Beer and pizza!

Tuesday Standards Session

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else's. I'm happy to correct any errors you may spot – just let me know!

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