Endy:Notebook/Synthetic Biology Open Language

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====Genetic Engineering (Under Construction)====
====Genetic Engineering (Under Construction)====
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<th>Symbol</th>
<th>Symbol</th>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><span style="font-weight: normal"><b>Forward Primer Site<br>
<td><span style="font-weight: normal"><b>Forward Primer Site<br>
</b>Represents a site for primer binding in the forward strand.</span></td>
</b>Represents a site for primer binding in the forward strand.</span></td>
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</tr>
<tr>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><span style="font-weight: normal"><b>Reverse Primer Site<br>
<td><span style="font-weight: normal"><b>Reverse Primer Site<br>
</b>Represents a site for primer binding in the reverse strand.</span></td>
</b>Represents a site for primer binding in the reverse strand.</span></td>
</tr>
</tr>
<tr>
<tr>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><b>Forward Barcode<br>
<td><b>Forward Barcode<br>
</b><span style="font-weight: normal">Represents a location on a DNA sequence where developer information is encoded on the forward strand. &nbsp;The encoded information can, for example, include the name of the individual or team that developed the standard biological part.<br>
</b><span style="font-weight: normal">Represents a location on a DNA sequence where developer information is encoded on the forward strand. &nbsp;The encoded information can, for example, include the name of the individual or team that developed the standard biological part.<br>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><b>Reverse Barcode<br>
<td><b>Reverse Barcode<br>
</b><span style="font-weight: normal">Represents a location on a DNA sequence where developer information is encoded on the reverse strand. &nbsp;The encoded information can, for example, include the name of the individual or team that developed the standard biological part.</span></td>
</b><span style="font-weight: normal">Represents a location on a DNA sequence where developer information is encoded on the reverse strand. &nbsp;The encoded information can, for example, include the name of the individual or team that developed the standard biological part.</span></td>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><span style=" font-weight: normal"><b>Prefix<br>
<td><span style=" font-weight: normal"><b>Prefix<br>
</b>Represents the prefix sequence of an assembly standard. &nbsp;The identifier of the specific prefix sequence used is OPTIONAL, but it MUST be located in the rectangle.<br>
</b>Represents the prefix sequence of an assembly standard. &nbsp;The identifier of the specific prefix sequence used is OPTIONAL, but it MUST be located in the rectangle.<br>
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<td><span style="font-weight: normal"><b>Shorthand Prefix<br>
<td><span style="font-weight: normal"><b>Shorthand Prefix<br>
</b>Represents the prefix sequence of an assembly standard.&nbsp; The rectangle found in the Prefix symbol is excluded.</span></td>
</b>Represents the prefix sequence of an assembly standard.&nbsp; The rectangle found in the Prefix symbol is excluded.</span></td>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><span style=" font-weight: normal"><b>Suffix</b><b><br>
<td><span style=" font-weight: normal"><b>Suffix</b><b><br>
</b>Represents the suffix sequence of an assembly standard. &nbsp;The identifier of the specific prefix sequence used is OPTIONAL, but it MUST be located in the rectangle.</span></td>
</b>Represents the suffix sequence of an assembly standard. &nbsp;The identifier of the specific prefix sequence used is OPTIONAL, but it MUST be located in the rectangle.</span></td>
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<tr>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><span style="font-weight: normal"><b>Shorthand Suffix<br>
<td><span style="font-weight: normal"><b>Shorthand Suffix<br>
</b>Represents the prefix sequence of an assembly standard.&nbsp; The rectangle found in the Suffix symbol is excluded.</span></td>
</b>Represents the prefix sequence of an assembly standard.&nbsp; The rectangle found in the Suffix symbol is excluded.</span></td>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><span style=" font-weight: normal"><b>Scar</b>&nbsp;<br>
<td><span style=" font-weight: normal"><b>Scar</b>&nbsp;<br>
Represents where a suffix and prefix sequence were ligated.</span></td>
Represents where a suffix and prefix sequence were ligated.</span></td>
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<tr>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><span style=" font-weight: normal"><b>3' Overhang Restriction Site<br>
<td><span style=" font-weight: normal"><b>3' Overhang Restriction Site<br>
</b>Represents a restriction endonuclease site that results in 3' overhangs. &nbsp;The diagonal line indicates the geometry of the cut site and the 3' sticky ends.</span></td>
</b>Represents a restriction endonuclease site that results in 3' overhangs. &nbsp;The diagonal line indicates the geometry of the cut site and the 3' sticky ends.</span></td>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><span style=" font-weight: normal"><b>5</b><b>' Overhang Restriction Site<br>
<td><span style=" font-weight: normal"><b>5</b><b>' Overhang Restriction Site<br>
</b>Represents a restriction endonuclease site that results in 5' overhangs. &nbsp;The diagonal line indicates the geometry of the cut site and the 5' sticky ends.</span></td>
</b>Represents a restriction endonuclease site that results in 5' overhangs. &nbsp;The diagonal line indicates the geometry of the cut site and the 5' sticky ends.</span></td>
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<tr>
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<td>Under Construction</td>
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<td>Coming Soon...</td>
<td><span style=" font-weight: normal"><b>Blunt Restriction Site<br>
<td><span style=" font-weight: normal"><b>Blunt Restriction Site<br>
</b>Represents a restriction endonuclease site that results in no overhangs. &nbsp;The straight line indicates the geometry of the cut site.</span></td>
</b>Represents a restriction endonuclease site that results in no overhangs. &nbsp;The straight line indicates the geometry of the cut site.</span></td>

Revision as of 19:24, 26 October 2009

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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
  • Contributors
    • Lesia Bilitchenko, Jerome Bonnet, Barry Canton, Deepak Chandran, Mackenzie Cowell, Douglas Densmore, Joanna Chen, Eric Fernandez, Tim Ham, Raik Gruenberg, Jason Kelly, Adam Liu, Richard Mar, Lance Martin, Alec Nielsen, Robert Ovadia, Randy Rettberg, Herbert Sauro, Reshma Shetty, Francois St-Pierre, Emma Weeding, and Ming Yan.

Review

Survey of Synthetic Biology Diagrams

Graphical Notation Standards/Software Tools

DNA Sequence Features

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) Link
  • Andrianantoandro, et al. Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology. 2006 vol. 2 pp. 2006.0028.
  • Endy. Foundations for engineering biology. Nature. 2005 vol. 438 (7067) pp. 449-53.

Use Cases, Requirements and Comments

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

Design

Basic Parts

Central Dogma (Under Construction)

Symbol Name & Description Status Proposed By
Image:Sbolv.origin_of_replication.png Origin of Replication
The circle represents a plasmid.  The rectangle indicates the site of the replication origin on the plasmid.  An indication of the plasmid copy number is OPTIONAL but MUST be located in the center of the circle.  Molecules per cell is the RECOMMENDED scale.
 Included in v. 1.0
Image:shorthand_origin_of_replication.sbolv.png Shorthand Origin of Replication
Shorthand version of the Origin of Replication.  The rectangle is omitted. This symbol SHOULD be used for rapid drawing and communication. However, the Origin of Replication symbol is RECOMMENDED.
 Included in v. 1.0
Image:forward_constitutive_promoter.sbolv.png
Forward Constitutive Promoter
Represents a DNA sequence that promotes RNA polymerase binding and transcription in the forward strand.  The open square indicates constitutive transcription.
 Included in v. 1.0
Image:ReverseConstitutivePromoter.sbolv.png Reverse Constitutive Promoter
Represents a constitutive promoter initiating transcription in the reverse strand.		 Included in v. 1.0
Image:forward_inducible_promoter.sbolv.png Forward Inducible Promoter
Represents a promoter that requires induction before promoting transcription in the forward strand.  The "+" symbol in the square indicates that the promoter is inducible.
 Included in v. 1.0
Image:reverse_inducible_promoter.sbolv.png
 Reverse Inducible Promoter
Represents a promoter that requires induction before promoting transcription in the reverse strand.  The "+" symbol in the square indicates that the promoter is inducible.
 Included in v. 1.0
Image:forward_repressible_promoter.sbolv.png Forward Repressible Promoter
Represents a promoter where transcription in the forward strand can be repressed.  The "-" symbol in the square indicates that the promoter is repressible.
 Included in v. 1.0
Image:reverse_repressible_promoter.sbolv.png
 Reverse Repressible Promoter
 Represents a promoter where transcription in the reverse strand can be repressed. The "-" symbol in the square indicates that the promoter is repressible.		 Included in v. 1.0
Image:forward_promoter_with_downstream_operator.sbolv.png


 Forward Promoter with Downstream Operator
Represents a forward promoter with a downstream operator.  The OPTIONAL "+" symbol MUST be located in the square and indicates an inducible promoter.  The OPTIONAL "-" symbol MUST be located in the square and indicates a repressible promoter.  The rectangle to the right of the square indicates a downstream operator.  Information about the specific location and function of the operator is OPTIONAL, but MUST be located within the rectangle. 		 Included in v. 1.0

Genetic Engineering (Under Construction)

Symbol Name & Description Status Proposed By
Coming Soon... Forward Primer Site
Represents a site for primer binding in the forward strand.
Coming Soon... Reverse Primer Site
Represents a site for primer binding in the reverse strand.
Coming Soon... Forward Barcode

Represents a location on a DNA sequence where developer information is encoded on the forward strand.  The encoded information can, for example, include the name of the individual or team that developed the standard biological part.
Coming Soon... Reverse Barcode
Represents a location on a DNA sequence where developer information is encoded on the reverse strand.  The encoded information can, for example, include the name of the individual or team that developed the standard biological part.
Coming Soon... Prefix

Represents the prefix sequence of an assembly standard.  The identifier of the specific prefix sequence used is OPTIONAL, but it MUST be located in the rectangle.
Coming Soon... Shorthand Prefix
Represents the prefix sequence of an assembly standard.  The rectangle found in the Prefix symbol is excluded.
Coming Soon... Suffix
Represents the suffix sequence of an assembly standard.  The identifier of the specific prefix sequence used is OPTIONAL, but it MUST be located in the rectangle.
Coming Soon... Shorthand Suffix
Represents the prefix sequence of an assembly standard.  The rectangle found in the Suffix symbol is excluded.
Coming Soon... Scar 
Represents where a suffix and prefix sequence were ligated.
Coming Soon... 3' Overhang Restriction Site
Represents a restriction endonuclease site that results in 3' overhangs.  The diagonal line indicates the geometry of the cut site and the 3' sticky ends.
Coming Soon... 5' Overhang Restriction Site
Represents a restriction endonuclease site that results in 5' overhangs.  The diagonal line indicates the geometry of the cut site and the 5' sticky ends.
Coming Soon... Blunt Restriction Site
Represents a restriction endonuclease site that results in no overhangs.  The straight line indicates the geometry of the cut site.

Prior Table

Devices

Concept Subclass Status Symbol
Reporter Request for Proposals
AND Gate Request for Proposals
OR Gate Request for Proposals
XOR Gate Request for Proposals
NOR Gate Request for Proposals

Grammar

Implementation

Maintenance

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

Notes


Recent changes



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