Endy:Notebook/Synthetic Biology Open Language

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=== Grammar ===
=== Grammar ===
 +
=== Ideas for Symbols from SBOL semantic Terminology ===
 +
(needs to be converted to wiki table)
 +
[[Image:SBOLsemantic_symbols_figure1.png]]
== Implementation ==
== Implementation ==

Revision as of 18:07, 19 April 2010

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Project Description

  • SBOL Visual is the graphical notation 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 welcome to contribute!

Design

Basic Parts

  • Upcoming Enhancements
    • The symbols will be provided with and without the abstract DNA Strand
    • A subset of the symbols will be provided with color
      • Green Promoters
      • Red Terminators

Central Dogma

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
Image:forward_promoter_with_upstream_operator.sbolv.png Forward Promoter with Upstream Operator
 Represents a forward promoter with an upstream 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 left of the square indicates an upstream operator.  Information about the specific location and function of the operator is OPTIONAL, but MUST be located within the open rectangle. 		 Included in v. 1.0
Image:forward_promoter_with_upstream_and_downstream_operators.sbolv.png Forward Promoter with Upstream and Downstream Operators
 Represents a forward promoter with upstream and downstream operators.  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 rectangles to the left and right of the square indicate upstream and downstream operators, respectively.  Information about the specific location and function of the operators are OPTIONAL, but MUST be located within the rectangles. 		 Included in v. 1.0
Image:forward_open_reading_frame.sbolv.png Forward Open Reading Frame
Represents a forward open reading frame (ORF).  The polygon indicates the single continuous DNA fragment of the ORF.  The angled right wall indicates the forward direction of the reading frame.		 Included in v. 1.0
  • Common Use
Image:reverse_open_reading_frame.sbolv.png Reverse Open Reading Frame
Represents a reverse open reading frame (ORF).  The polygon indicates the single continuous DNA fragment of the ORF.  The angled left wall indicates the reverse direction of the reading frame.		 Included in v. 1.0
  • Common Use
Image:forward_translation_start_site.sbolv.png Forward Translation Start Site
Represents a Shine-Delgarno sequence in the forward strand of prokaryotes, IRES in viruses and ribosome loading structure in eukaryotes.		 Included in v. 1.0
Image:reverse_translation_start_site.sbolv.png Reverse Translation Start Site
Represents a Shine-Delgarno sequence on the reverse strand in prokaryotes and equivalent sites or structures in eukaryotes.		 Included in v. 1.0
Image:forward_terminator.sbolv.png Forward Terminator
Represents the location on a DNA sequence where transcription ends in the forward strand.		 Included in v. 1.0
Image:reverse_terminator.sbolv.png Reverse Terminator
Represents the location on a DNA sequence where transcription ends in the reverse strand.		 Included in v. 1.0
Image:bidirectional_terminator.sbolv.png Bidirectional Terminator
Represents the location on a DNA sequence where transcription ends in both strands.		 Included in v. 1.0
Image:ribonuclease_site.sbolv.png  Ribonuclease Site
Represents the location on a DNA sequence that codes for a ribonuclease cleavage site on the RNA.  The dashed line indicates a functional element located on the RNA. The "x" symbol indicates cleavage of the RNA.		 Included in v. 1.0
Image:rna_stability_element_stable.sbolv.png RNA Stability Element, "Stable" 
Represents a location on a DNA sequence that codes for an RNA secondary structure that effects the stability of the RNA.  The dashed line indicates a functional element located on the RNA.  The diameter of the circle SHOULD indicate the half life of the RNA.  A log scale is RECOMMENDED.  The larger circle indicates qualitatively an RNA molecule with a long half-life.		 Included in v. 1.0
Image:rna_stability_element_intermediate.sbolv.png RNA Stability Element, "Intermediate"
Represents a location on a DNA sequence that codes for an RNA secondary structure that effects the stability of the RNA.  The dashed line indicates a functional element located on the RNA.  The diameter of the circle SHOULD indicate the half life of the RNA.  A log scale is RECOMMENDED.  The smaller circle indicates qualitatively an RNA molecule with an intermediate half-life.		 Included in v. 1.0
Image:rna_stability_element_unstable.sbolv.png RNA Stability Element, "Unstable"
Represents the location on a DNA sequence that codes for an RNA secondary structure that effects the stability of the RNA.  The dashed line indicates a functional element located on the RNA.  The diameter of the circle SHOULD indicate the half-life of the RNA.  A log scale is RECOMMENDED.  The smallest circle indicates qualitatively an RNA molecule with a short life span.		 Included in v. 1.0
Image:protease_site.sbolv.png Protease Site
Represents the location on a DNA sequence that codes for a protease cleavage site.  The solid line indicates a functional element located on a peptide/protein.  The "x" symbol indicates cleavage of a peptide or protein.		 Included in v. 1.0
Image:degradation_element_stable.sbolv.png Protein Degradation Element "Stable" 
Represents a location on a DNA sequence that codes for a degradation-related structure in a peptide/protein .  The solid line indicates a functional element located on the peptide/protein.  The diameter of the circle SHOULD indicate the half-life of the peptide/protein.  A log scale is RECOMMENDED.  The larger circle indicates qualitatively a peptide/protein with a long half-life.		 Included in v. 1.0
Image:degradation_element_intermediate.sbolv.png Protein Degradation Element "Intermediate"
Represents a location on a DNA sequence that codes for a degradation-related structure in a peptide/protein .  The solid line indicates a functional element located on the peptide/protein.  The diameter of the circle SHOULD indicate the half-life of the peptide/protein.  A log scale is RECOMMENDED.  The smaller circle indicates qualitatively a peptide/protein with an intermediate half-life.		 Included in v. 1.0
Image:degradation_element_unstable.sbolv.png Protein Degradation Element "Unstable"
Represents a location on a DNA sequence that codes for a degradation-related structure in a peptide/protein .  The solid line indicates a functional element located on the peptide/protein.  The diameter of the circle SHOULD indicate the half-life of the peptide/protein.  A log scale is RECOMMENDED.  The smallest circle indicates qualitatively a peptide/protein with a short half-life.		 Included in v. 1.0

Genetic Engineering

Symbol Name & Description Status Proposed By
Image:forward_primer_site.sbolv.png Forward Primer Site
Represents a site for primer binding in the forward strand.		 Included in v. 1.0
  • Common Use
Image:reverse_primer_site.sbolv.png Reverse Primer Site
Represents a site for primer binding in the reverse strand.		 Included in v. 1.0
  • Common Use
Image:forward_barcode.sbolv.png 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.

 Included in v. 1.0
Image:reverse_barcode.sbolv.png 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.		 Included in v. 1.0
Image:prefix.sbolv.png 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.

 Included in v. 1.0
Image:shorthand_prefix.sbolv.png Shorthand Prefix
Represents the prefix sequence of an assembly standard.  The rectangle found in the Prefix symbol is excluded.		 Included in v. 1.0
Image:suffix.sbolv.png 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.		 Included in v. 1.0
Image:shorthand_suffix.sbolv.png Shorthand Suffix
Represents the prefix sequence of an assembly standard.  The rectangle found in the Suffix symbol is excluded.		 Included in v. 1.0
Image:scar.sbolv.png Scar 
Represents where a suffix and prefix sequence were ligated.		 Included in v. 1.0
Image:3_prime_overhang_restriction_site.sbolv.png 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.		 Included in v. 1.0
Image:5_prime_overhang_restriction_site.sbolv.png 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.		 Included in v. 1.0
Image:blunt_restriction_site.sbolv.png Blunt Restriction Site
Represents a restriction endonuclease site that results in no overhangs.  The straight line indicates the geometry of the cut site.		 Included in v. 1.0
Image:insulator.png Insulator
Coming Soon...		 Under Development


Devices

Symbol Name & Description Status Proposed By
Reporter
Description...		 Request for Proposals
AND Gate
Description...		 Request for Proposals
OR Gate
Description...		 Request for Proposals
XOR Gate
Description...		 Request for Proposals
NOR Gate
Description...		 Request for Proposals
NOT Gate
Description...		 Request for Proposals

Grammar

Ideas for Symbols from SBOL semantic Terminology

(needs to be converted to wiki table) Image:SBOLsemantic_symbols_figure1.png

Implementation

Maintenance

Symbol Status

Status Definition
Request for Proposals A symbol is needed but their isn't consensus on the appearance of the symbol.
Under Development A rough draft of a symbol was submitted.
Proposed The final version of a symbol was submitted and the author is seeking comments.
Consensus A rough consensus has been reached that the symbol is a candidate for inclusion in an official release of SBOLv.
Included in v. # The version of SBOLv where the symbol was included.
Deprecated A symbol is not being considered for inclusion in SBOLv.

Deprecated Symbols

Notes


Recent changes



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