Endy:Notebook/Synthetic Biology Open Language

Project Description

• SBOL Visual is the graphical component of the Synthetic Biology Open Language (SBOL) being developed by the Synthetic Biology Data Exchange Group
  • It is intended for the formal specification of composite parts and devices.
  • It is targeted for use by biological engineers in forward engineering projects.
  • It encourages and supports model-driven engineering.
• SBOL Visual is an open standard.
  • Languages emerge from the friction of top-down control (eg. Preservation of the French Language) and bottom-up needs to communicate (eg. Pop Culture). With this in mind, SBOL Visual is flourishing in an environment of open communication while rigorously defining symbols, syntax, and grammar.
• SBOL Visual is an abstract tool for solving concrete problems.
  • Technical languages have an additional challenge of balancing the requirements of providing a philosophically consistent framework while still being useful for solving concrete problems. Balancing this tension is difficult and requires both top-down and bottom-up approaches. With that in mind, SBOL Visual has a rigorous and consistent structure and is being used in concrete software tools while working on concrete Synthetic Biology projects.

Developers and Contributors

• Lead Developers
  • Suzie Bartram
  • Drew Endy
  • Cesar Rodriguez
• Contributors
  • Douglas Densmore
  • Lesia Bilitchenko
  • Joanna Chen
  • Adam Liu
  • Richard Mar
  • Emma Weeding
  • Ming Yan

Review

Survey of Synthetic Biology Diagrams

• http://parts.mit.edu/wiki/index.php/IAP2004:Polkadorks

Graphical Notation Standards/Software Tools

• Systems Biology Grahical Notation
• EcoCyc Notation
• Diagrammatic Cell Language
• BioTapestry
• CellDesigner
• SynBioSS

DNA Sequence Features

• Registry of Standard Biological Parts
• GenBank

Literature

• Novere, et al. Systems Biology Graphical Notation. Nature Biotechnology 2009 vol. 27 (8) pp. 735-41 Link
• Matsuoka, et al. Consistent design schematics for biological systems: standardization of representation in biological engineering. Journal of the Royal Society Interface. EPub June 3 2009 Link
• Shetty, et al. Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering. 2008; 2: 5. Link
• Voigt. Genetic parts to program bacteria. Current Opinion in Biotechnology, 17(5):548–57, Oct 2006. Link
• Hill et al. SynBioSS: The Synthetic Biology Modeling Software Suite. Bioinformatics 24 (21): 2551. (2008) [dx.doi.org/doi:10.1093/bioinformatics/btn468 Link]

Use Cases, Requirements and Comments

Click here to read the ongoing discussions... You are highly encouraged to contribute!

Design

Basic Parts

Concept	Subclass	Status	Forward	Reverse	Bidirectional	Proposed By	Discussion
Promoter	General	Consensus
	Constitutive	Proposed				S. Bartram, A. Endy
	Constitutive	Proposed				S. Bartram, A. Endy
	Inducible	Proposed				Suzie Bartram
	Inducible	Under Development				S. Bartram, A. Endy
	Inducible	Under Development				S. Bartram, A. Endy
	Repressible	Proposed				Suzie Bartram
	Repressible	Under Development				S. Bartram, A. Endy
	Repressible	Under Development				S. Bartram, A. Endy
	?	Under Development				S. Bartram, A. Endy
Ribosome Binding Site	General	Proposed				PartsRegistry.org
	Directional	Proposed				Timothy Ham
	Directional	Proposed				Alec Nielsen
Open Reading Frame		Consensus
Transcription Terminator		Consensus				Jerome Bonnet
Restriction Site	General	Proposed				Jerome Bonnet
	General	Proposed				Raik Gruenberg
	Overhang	Proposed				Raik Gruenberg
	Overhang	Proposed				Raik Gruenberg
	Blunt	Proposed				Raik Gruenberg
Primer Site		Consensus
Assembly	Prefix	Under Development				S. Bartram, A. Endy
	Prefix	Under Development				S. Bartram, A. Endy
	Suffix	Under Development				S. Bartram, A. Endy
	Suffix	Under Development				S. Bartram, A. Endy
	Scar	Under Development				S. Bartram, A. Endy
	Scar	Proposed				Alec Nielsen
	Scar	Proposed				Suzie Bartram
	Scar	Proposed				Multiple
	Scar	Proposed				Alec Nielsen
	Blunt	Proposed				Raik Gruenberg
Protein Degradation Tag		Coming Soon...

Devices

Grammar

Implementation

• Software Tools
  • Clotho-Spectacles
  • BioBrick Studio
• Tutorials
  • Incorporating Symbols into PowerPoint 2004 for Macs
  • Incorporating Symbols into PowerPoint 2007 for Windows
• Symbols
  • Version 0.4
    • Released 8-13-2009
    • 72 dpi PNGs: Download
  • Version 0.3
    • Released on 7-10-2009
    • 300 dpi PNGs: Download
    • 300 dpi JPEGs: Download
  • Prior Releases

Maintenance

• Symbol Status
  • Request for Proposals
  • Under Development
  • Proposed
  • Consensus
  • Included in v.#
  • Deprecated
• Deprecated Symbols
  • Link

Notes

• Request for Comments
  • RFC 16
  • RFC 18
• Related Project
  • BioBuilder Educational Toolkit
• Tiny URL
  • http://tinyurl.com/sbolv

Recent changes