Endy:Notebook/Synthetic Biology Open Language

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|colspan="2" style="background-color: #F2F2F2;" align="right"|[[{{FULLPAGENAME}}/Entry_Base|Customize your entry pages]] [[Help:Notebook/Project_Base/Customize_entry_page|<html><img src="/images/a/aa/Help.png" border="0" /></html>]]
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==Project Description==
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* '''SBOL Visual is the graphical notation component of the [[The_BioBricks_Foundation:Standards/Technical/Exchange | Synthetic Biology Open Language (SBOL)]] being developed by the [http://groups.google.com/group/synbiodex Synthetic Biology Data Exchange Group]'''
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**It is intended for the formal specification of composite parts and devices.   
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**It is targeted for use by biological engineers in forward engineering projects.
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**It encourages and supports [http://en.wikipedia.org/wiki/Model-driven_architecture model-driven engineering].
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* '''SBOL Visual is an open standard.'''
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**Languages emerge from the friction of top-down control (eg. [http://en.wikipedia.org/wiki/History_of_French Preservation of the French Language]) and bottom-up needs to communicate (eg. [http://en.wikipedia.org/wiki/Popular_culture Pop Culture]).  With this in mind, SBOL Visual is flourishing in an environment of open communication while rigorously defining symbols, syntax, and grammar.
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*'''SBOL Visual is an abstract tool for solving concrete problems.'''
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**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.
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==Developers and Contributors==
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*Lead Developers
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**[[User:Suzanne_Bartram | Suzie Bartram]]
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**[[User:Endy | Drew Endy]]
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**Anusuya Ramasubramanian
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**[[User:Cesar A. Rodriguez | Cesar Rodriguez]]
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*Contributors
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**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.
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== Review ==
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=== Survey of Synthetic Biology Diagrams ===
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*http://parts.mit.edu/wiki/index.php/IAP2004:Polkadorks
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=== Graphical Notation Standards/Software Tools ===
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*[http://www.sbgn.org/Main_Page Systems Biology Grahical Notation]
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*[http://ecocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&object=NIL&orgids=ECOLI&chromosome=COLI-K12&bp-range=1/50000 EcoCyc Notation]
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*[http://www.gnsbiotech.com/papers/dac.pdf Diagrammatic Cell Language]
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*[http://www.genocad.org GenoCAD]
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*[http://www.biotapestry.org/ BioTapestry]
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*[http://www.celldesigner.org/ CellDesigner]
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*[http://synbioss.sourceforge.net/ SynBioSS]
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=== DNA Sequence Features ===
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*[http://partsregistry.org/Help:Part_Features Registry of Standard Biological Parts]
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*[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank]
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*[http://www.sequenceontology.org/ Sequence Ontology]
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=== Literature ===
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*Novere, et al. Systems Biology Graphical Notation. Nature Biotechnology 2009 vol. 27 (8) pp. 735-41  [http://www.nature.com/nbt/journal/v27/n8/abs/nbt.1558.html Link]
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*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  [http://rsif.royalsocietypublishing.org/content/6/Suppl_4/S393.full?sid=cba2c56f-dfed-4e76-9fdd-d9d1b87eb02d Link]
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*Shetty, et al. Engineering BioBrick vectors from BioBrick parts. Journal of Biological Engineering. 2008; 2: 5.  [http://www.jbioleng.org/content/2/1/5 Link]
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*Voigt. Genetic parts to program bacteria. Current Opinion in Biotechnology, 17(5):548–57, Oct 2006.  [http://www.scribd.com/doc/8576047/curr-opin-biotechnol-2006-voigt-genetic-parts-to-program-bacteria Link]
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*Hill et al. SynBioSS: The Synthetic Biology Modeling Software Suite. Bioinformatics 24 (21): 2551. (2008)  [http://dx.doi.org/doi:10.1093/bioinformatics/btn468 Link]
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*Andrianantoandro, et al.  Synthetic biology: new engineering rules for an emerging discipline.  Molecular Systems Biology.  2006 vol. 2 pp. 2006.0028.
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*Endy. Foundations for engineering biology. Nature. 2005 vol. 438 (7067) pp. 449-53.
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==Use Cases, Requirements and Comments ==
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===[[Endy:Notebook/BioBrick_Open_Language_Specification/Comments | Click here]] to read the ongoing discussions...  You are welcome to contribute!===
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== Design ==
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===Basic Parts===
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====Central Dogma====
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<table width="100%" cellpadding="3" cellspacing="0" border="1" class="zeroBorder" bordercolor="#000000">
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<tr>
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<th>Symbol</th>
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<th>Name & Description</th>
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<th>Status</th>
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<th>Proposed By</th>
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</tr>
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<tr>
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<td>[[Image:Sbolv.origin_of_replication.png]]</td>
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<td><span style="font-weight: normal"><b>Origin of Replication</b><br>
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<div style="text-align: left;">The circle represents a plasmid. &nbsp;The rectangle indicates the site of the replication origin on the plasmid. &nbsp;An indication of the plasmid copy number is OPTIONAL but MUST be located in the center of the circle. &nbsp;Molecules per cell is the RECOMMENDED scale.</div>
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</span></td>
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    <td><span style="font-weight: normal">Included in v. 1.0</span></td>
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    <td>
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      <ul>
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        <li>[[User:Suzanne_Bartram | Bartram]]</li>
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        <li>[[User:Endy | Endy]]</li>
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      </ul>
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    </td>
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  </tr>
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  <tr>
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    <td>[[Image:shorthand_origin_of_replication.sbolv.png]]</td>
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  <td><span style=" font-weight: normal"><b>Shorthand Origin of Replication</b><br>
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<div style="text-align: left;">Shorthand version of the Origin of Replication. &nbsp;The rectangle is omitted. This symbol SHOULD be used for rapid drawing and communication. However, the Origin of Replication symbol is RECOMMENDED.</div>
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</span></td>
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    <td><span style="font-weight: normal">Included in v. 1.0</span></td>
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    <td>
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      <ul>
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        <li>[[User:Suzanne_Bartram | Bartram]]</li>
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        <li>[[User:Endy | Endy]]</li>
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      </ul>
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    </td>
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  </tr>
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<tr>
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<td>[[Image:forward_constitutive_promoter.sbolv.png]]</td>
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<td><span style=" font-weight: normal">
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<div id="djzw" style=" text-align: left"><b>Forward Constitutive Promoter</b></div>
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<div id="hpt-" style="text-align: justify;">Represents a DNA sequence that promotes RNA polymerase binding and transcription in the forward strand. &nbsp;The open square indicates constitutive transcription.</div>
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</span></td>
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    <td><span style="font-weight: normal">Included in v. 1.0</span></td>
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    <td>
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      <ul>
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        <li>[[User:Suzanne_Bartram | Bartram]]</li>
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        <li>[[User:Endy | Endy]]</li>
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      </ul>
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    </td>
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</tr>
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<tr>
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<td>[[Image:ReverseConstitutivePromoter.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>Reverse Constitutive Promoter<br>
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</b>Represents a constitutive promoter initiating transcription in the reverse strand.</span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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    <td>
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      <ul>
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        <li>[[User:Suzanne_Bartram | Bartram]]</li>
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        <li>[[User:Endy | Endy]]</li>
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      </ul>
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    </td>
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</tr>
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<tr>
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<td>[[Image:forward_inducible_promoter.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>Forward Inducible Promoter<br>
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<div style="text-align: justify;"><span style="font-weight: normal">Represents a promoter that requires induction before promoting transcription in the forward strand. &nbsp;The "+" symbol in the square indicates that the promoter is inducible.</span></div>
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</b></span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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    <td>
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      <ul>
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        <li>[[User:Suzanne_Bartram | Bartram]]</li>
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        <li>[[User:Endy | Endy]]</li>
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      </ul>
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    </td>
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</tr>
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<tr>
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<td>
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<div style="text-align: left" id="ws13">[[Image:reverse_inducible_promoter.sbolv.png]]</div>
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</td>
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<td><span style=" font-weight: normal"><b>Reverse Inducible Promoter<br>
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<div style="text-align: justify;"><span style="font-weight: normal">Represents a promoter that requires induction before promoting transcription in the reverse strand. &nbsp;The "+" symbol in the square indicates that the promoter is inducible.</span></div>
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</b></span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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    <td>
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      <ul>
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        <li>[[User:Suzanne_Bartram | Bartram]]</li>
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        <li>[[User:Endy | Endy]]</li>
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      </ul>
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    </td>
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</tr>
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<tr>
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<td>[[Image:forward_repressible_promoter.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>Forward Repressible Promoter<br>
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<div style="text-align: left;"><span style="font-weight: normal">Represents a promoter where transcription in the forward strand can be repressed. &nbsp;The "-" symbol in the square indicates that the promoter is repressible.</span></div>
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</b></span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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    <td>
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      <ul>
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        <li>[[User:Suzanne_Bartram | Bartram]]</li>
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        <li>[[User:Endy | Endy]]</li>
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      </ul>
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    </td>
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</tr>
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<tr>
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<td>
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<div style="text-align: left">[[Image:reverse_repressible_promoter.sbolv.png]]</div>
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</td>
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<td><span style=" font-weight: normal"><b>Reverse Repressible Promoter<br></b>
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Represents a promoter where transcription in the reverse strand can be repressed. The "-" symbol in the square indicates that the promoter is repressible.</span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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    <td>
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      <ul>
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        <li>[[User:Suzanne_Bartram | Bartram]]</li>
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        <li>[[User:Endy | Endy]]</li>
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      </ul>
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    </td>
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</tr>
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<tr>
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<td>
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<div style="text-align: left">[[Image:forward_promoter_with_downstream_operator.sbolv.png]]</div>
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<br>
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</td>
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<td><span style=" font-weight: normal"><b>Forward Promoter with Downstream Operator<br>
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<span style="font-weight: normal">Represents a forward promoter with a downstream operator. &nbsp;The OPTIONAL "+" symbol MUST be located in the square and indicates an inducible promoter. &nbsp;The OPTIONAL "-" symbol MUST be located in the square and indicates a repressible promoter. &nbsp;</span></b>The rectangle to the right of the square indicates a downstream operator. &nbsp;Information about the specific location and function of the operator is OPTIONAL, but MUST be located within the rectangle.&nbsp;</span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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    <td>
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      <ul>
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        <li>[[User:Suzanne_Bartram | Bartram]]</li>
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        <li>[[User:Endy | Endy]]</li>
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      </ul>
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    </td>
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</tr>
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<tr>
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<td>[[Image:forward_promoter_with_upstream_operator.sbolv.png]]</td>
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<td><b>Forward Promoter with Upstream Operator<br></b>
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<span style="font-weight: normal">Represents a forward promoter with an upstream operator. &nbsp;The OPTIONAL "+" symbol MUST be located in the square and indicates an inducible promoter. &nbsp;The OPTIONAL "-" symbol MUST be located in the square and indicates a repressible promoter.&nbsp;&nbsp;The rectangle to the left of the square indicates an upstream operator. &nbsp;Information about the specific location and function of the operator is OPTIONAL, but MUST be located within the open rectangle.&nbsp;</span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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<td>
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<ul>
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<li>[[User:Suzanne_Bartram | Bartram]]</li>
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<li>[[User:Endy | Endy]]</li>
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</ul>
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</td>
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</tr>
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<tr>
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<td>[[Image:forward_promoter_with_upstream_and_downstream_operators.sbolv.png]]</td>
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<td><b>Forward Promoter with Upstream and Downstream Operators<br></b>
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<span style="font-weight: normal"><b><span style="font-weight: normal">Represents a forward promoter with upstream and downstream operators. &nbsp;The OPTIONAL "+" symbol MUST be located in the square and indicates an inducible promoter. &nbsp;The OPTIONAL "-" symbol MUST be located in the square and indicates a repressible promoter. &nbsp;</span></b>The rectangles to the left and right of the square indicate upstream and downstream operators, respectively. &nbsp;Information about the specific location and function of the operators are OPTIONAL, but MUST be located within the rectangles.&nbsp;</span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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<td>
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<ul>
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<li>[[User:Suzanne_Bartram | Bartram]]</li>
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<li>[[User:Endy | Endy]]</li>
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</ul>
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</td>
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</tr>
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<tr>
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<td>[[Image:forward_open_reading_frame.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>Forward Open Reading Frame<br>
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</b>Represents a forward open reading frame (ORF). &nbsp;The polygon indicates the single continuous DNA fragment of the ORF. &nbsp;The angled right wall indicates the forward direction of the reading frame.</span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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<td>
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<ul>
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<li>Common Use</li>
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</ul>
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</td>
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</tr>
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<tr>
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<td>[[Image:reverse_open_reading_frame.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>Reverse Open Reading Frame<br>
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</b>Represents a reverse open reading frame (ORF). &nbsp;The polygon indicates the single continuous DNA fragment of the ORF. &nbsp;The angled left wall indicates the reverse direction of the reading frame.</span></td>
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-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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<td>
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<ul>
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<li>Common Use</li>
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</ul>
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</td>
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</tr>
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<tr>
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<td>[[Image:forward_translation_start_site.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>Forward&nbsp;</b><b>Translation Start Site<br>
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</b>Represents a Shine-Delgarno sequence in the forward strand of prokaryotes, IRES in viruses and ribosome loading structure in eukaryotes.</span></td>
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-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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-
<td>
+
-
<ul>
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<li>[[User:THam | Ham]]</li>
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</ul>
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</td>
+
-
</tr>
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-
<tr>
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<td>[[Image:reverse_translation_start_site.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>Reverse&nbsp;</b><b>Translation Start Site<br>
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</b>Represents a Shine-Delgarno sequence on the reverse strand in prokaryotes and equivalent sites or structures in eukaryotes.</span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
<td>
+
-
<ul>
+
-
<li>[[User:THam | Ham]]</li>
+
-
</ul>
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</td>
+
-
</tr>
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<tr>
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<td>[[Image:forward_terminator.sbolv.png]]</td>
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<td><span style=" font-weight: normal;"><b>Forward Terminator<br>
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</b>Represents the location on a DNA sequence where transcription ends in the forward strand.</span></td>
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-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
<td>
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-
<ul>
+
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<li>[[User:Jerome_Bonnet | Bonnet]]</li>
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<li>Fernandez</li>
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</ul>
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</td>
+
-
</tr>
+
-
<tr>
+
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<td>[[Image:reverse_terminator.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>Reverse Terminator<br>
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<span style="font-weight: normal">Represents the location on a DNA sequence where transcription ends in the reverse strand.</span></b></span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
<td>
+
-
<ul>
+
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<li>[[User:Jerome_Bonnet | Bonnet]]</li>
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</ul>
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</td>
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</tr>
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<tr>
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<td>[[Image:bidirectional_terminator.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>Bidirectional Terminator<br>
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</b>Represents the location on a DNA sequence where transcription ends in both strands.</span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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<td>
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<ul>
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<li>[[User:Jerome_Bonnet | Bonnet]]</li>
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</ul>
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</td>
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</tr>
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<tr>
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<td>[[Image:ribonuclease_site.sbolv.png]]</td>
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<td><span style=" font-weight: normal">&nbsp;<b>Ribonuclease Site<br>
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</b>Represents the location on a DNA sequence that codes for a ribonuclease cleavage site on the RNA. &nbsp;The dashed line indicates a functional element located on the RNA. The "x" symbol indicates cleavage of the RNA.</span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
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<td>
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<ul>
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<li>[[User:Suzanne_Bartram | Bartram]]</li>
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<li>[[User:Endy | Endy]]</li>
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</ul>
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</td>
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</tr>
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<tr>
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<td>[[Image:rna_stability_element_stable.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>RNA Stability Element, "Stable"&nbsp;<br>
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</b>Represents a location on a DNA sequence that codes for an RNA secondary structure that effects the stability of the RNA. &nbsp;The dashed line indicates a functional element located on the RNA. &nbsp;The diameter of the circle SHOULD indicate the half life of the RNA. &nbsp;A log scale is RECOMMENDED. &nbsp;The larger circle indicates qualitatively an RNA molecule with a long half-life.</span></td>
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<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
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<td>
+
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<ul>
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<li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
<li>[[User:Endy | Endy]]</li>
+
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</ul>
+
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</td>
+
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</tr>
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<tr>
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<td>[[Image:rna_stability_element_intermediate.sbolv.png]]</td>
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<td><span style=" font-weight: normal"><b>RNA Stability Element, "Intermediate"<br>
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</b>Represents a location on a DNA sequence that codes for an RNA secondary structure that effects the stability of the RNA. &nbsp;The dashed line indicates a functional element located on the RNA. &nbsp;The diameter of the circle SHOULD indicate the half life of the RNA. &nbsp;A log scale is RECOMMENDED. &nbsp;The smaller circle indicates qualitatively an RNA molecule with an intermediate half-life.</span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
<td>
+
-
<ul>
+
-
<li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
<li>[[User:Endy | Endy]]</li>
+
-
</ul>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:rna_stability_element_unstable.sbolv.png]]</td>
+
-
<td><span style="font-weight: normal"><b>RNA Stability Element, "Unstable"<br>
+
-
</b>Represents the location on a DNA sequence that codes for an RNA secondary structure that effects the stability of the RNA. &nbsp;The dashed line indicates a functional element located on the RNA. &nbsp;The diameter of the circle SHOULD indicate the half-life of the RNA. &nbsp;A log scale is RECOMMENDED. &nbsp;The smallest circle indicates qualitatively an RNA molecule with a short life span.</span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
<td>
+
-
<ul>
+
-
<li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
<li>[[User:Endy | Endy]]</li>
+
-
</ul>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:protease_site.sbolv.png]]</td>
+
-
<td><span style=" font-weight: normal;"><b>Protease Site<br>
+
-
</b>Represents the location on a DNA sequence that codes for a protease cleavage site. &nbsp;The solid line indicates a functional element located on a peptide/protein. &nbsp;The "x" symbol indicates cleavage of a peptide or protein.</span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
<td>
+
-
<ul>
+
-
<li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
<li>[[User:Endy | Endy]]</li>
+
-
</ul>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:degradation_element_stable.sbolv.png]]</td>
+
-
<td><span style=" font-weight: normal"><b>Protein&nbsp;</b><b>Degradation Element "Stable"&nbsp;<br>
+
-
<span style="font-weight: normal">Represents a location on a DNA sequence that codes for a degradation-related structure in a peptide/protein . &nbsp;The solid line indicates a functional element located on the peptide/protein. &nbsp;The diameter of the circle SHOULD indicate the half-life of the peptide/protein. &nbsp;A log scale is RECOMMENDED. &nbsp;The larger circle indicates qualitatively a peptide/protein with a long half-life.</span></b></span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
<td>
+
-
<ul>
+
-
<li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
<li>[[User:Endy | Endy]]</li>
+
-
</ul>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:degradation_element_intermediate.sbolv.png]]</td>
+
-
<td><span style="font-weight: normal"><b>Protein&nbsp;</b><b>Degradation Element "Intermediate"</b><br>
+
-
Represents a location on a DNA sequence that codes for a degradation-related structure in a peptide/protein . &nbsp;The solid line indicates a functional element located on the peptide/protein. &nbsp;The diameter of the circle SHOULD indicate the half-life of the peptide/protein. &nbsp;A log scale is RECOMMENDED. &nbsp;The smaller circle indicates qualitatively a peptide/protein with an intermediate half-life.</span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
<td>
+
-
<ul>
+
-
<li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
<li>[[User:Endy | Endy]]</li>
+
-
</ul>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:degradation_element_unstable.sbolv.png]]</td>
+
-
<td><span style=" font-weight: normal"><b>Protein&nbsp;</b><b>Degradation Element "Unstable"<br>
+
-
<span style="font-weight: normal">Represents a location on a DNA sequence that codes for a degradation-related structure in a peptide/protein . &nbsp;The solid line indicates a functional element located on the peptide/protein. &nbsp;The diameter of the circle SHOULD indicate the half-life of the peptide/protein. &nbsp;A log scale is RECOMMENDED. &nbsp;The smallest circle indicates qualitatively a peptide/protein with a short half-life.</span></b></span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
<td>
+
-
<ul>
+
-
<li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
<li>[[User:Endy | Endy]]</li>
+
-
</ul>
+
-
</td>
+
-
</tr>
+
-
</table>
+
-
 
+
-
====Genetic Engineering====
+
-
<table width="100%" cellpadding="3" cellspacing="0" border="1" class="zeroBorder" bordercolor="#000000">
+
-
<tr>
+
-
<th>Symbol</th>
+
-
<th>Name & Description</th>
+
-
<th>Status</th>
+
-
<th>Proposed By</th>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:forward_primer_site.sbolv.png]]</td>
+
-
<td><span style="font-weight: normal"><b>Forward Primer Site<br>
+
-
</b>Represents a site for primer binding in the forward strand.</span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
      <li>Common Use</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:reverse_primer_site.sbolv.png]]</td>
+
-
<td><span style="font-weight: normal"><b>Reverse Primer Site<br>
+
-
</b>Represents a site for primer binding in the reverse strand.</span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
      <li>Common Use</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:forward_barcode.sbolv.png]]</td>
+
-
<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>
+
-
</span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
        <li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
        <li>[[User:Endy | Endy]]</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:reverse_barcode.sbolv.png]]</td>
+
-
<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>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
      <li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
      <li>[[User:Endy | Endy]]</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:prefix.sbolv.png]]</td>
+
-
<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>
+
-
</span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
        <li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
        <li>[[User:Endy | Endy]]</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:shorthand_prefix.sbolv.png]]</td>
+
-
<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>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
        <li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
        <li>[[User:Endy | Endy]]</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:suffix.sbolv.png]]</td>
+
-
<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>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
        <li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
        <li>[[User:Endy | Endy]]</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:shorthand_suffix.sbolv.png]]</td>
+
-
<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>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
        <li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
        <li>[[User:Endy | Endy]]</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:scar.sbolv.png]]</td>
+
-
<td><span style=" font-weight: normal"><b>Scar</b>&nbsp;<br>
+
-
Represents where a suffix and prefix sequence were ligated.</span></td>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
        <li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
        <li>[[User:Endy | Endy]]</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:3_prime_overhang_restriction_site.sbolv.png]]</td>
+
-
<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>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
        <li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
        <li>[[User:Endy | Endy]]</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:5_prime_overhang_restriction_site.sbolv.png]]</td>
+
-
<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>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
        <li>[[User:Suzanne_Bartram | Bartram]]</li>
+
-
        <li>[[User:Endy | Endy]]</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td>[[Image:blunt_restriction_site.sbolv.png]]</td>
+
-
<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>
+
-
<td><span style="font-weight: normal">Included in v. 1.0</span></td>
+
-
    <td>
+
-
      <ul>
+
-
      <li>[[User:Raik | Gruenberg]]</li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
</table>
+
-
 
+
-
====[[Endy:Notebook/Synthetic_Biology_Open_Language/Prior_Table | Prior Table]]====
+
-
 
+
-
===Devices===
+
-
<table width="100%" cellpadding="3" cellspacing="0" border="1" class="zeroBorder" bordercolor="#000000">
+
-
<tr>
+
-
<th>Symbol</th>
+
-
<th>Name & Description</th>
+
-
<th>Status</th>
+
-
<th>Proposed By</th>
+
-
</tr>
+
-
<tr>
+
-
<td></td>
+
-
<td><span style="font-weight: normal"><b>Reporter<br>
+
-
</b>Description...</span></td>
+
-
<td><span style="font-weight: normal">Request for Proposals</span></td>
+
-
    <td>
+
-
      <ul>
+
-
      <li></li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td></td>
+
-
<td><span style="font-weight: normal"><b>AND Gate<br>
+
-
</b>Description...</span></td>
+
-
<td><span style="font-weight: normal">Request for Proposals</span></td>
+
-
    <td>
+
-
      <ul>
+
-
      <li></li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td></td>
+
-
<td><span style="font-weight: normal"><b>OR Gate<br>
+
-
</b>Description...</span></td>
+
-
<td><span style="font-weight: normal">Request for Proposals</span></td>
+
-
    <td>
+
-
      <ul>
+
-
      <li></li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td></td>
+
-
<td><span style="font-weight: normal"><b>XOR Gate<br>
+
-
</b>Description...</span></td>
+
-
<td><span style="font-weight: normal">Request for Proposals</span></td>
+
-
    <td>
+
-
      <ul>
+
-
      <li></li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td></td>
+
-
<td><span style="font-weight: normal"><b>NOR Gate<br>
+
-
</b>Description...</span></td>
+
-
<td><span style="font-weight: normal">Request for Proposals</span></td>
+
-
    <td>
+
-
      <ul>
+
-
      <li></li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
<tr>
+
-
<td></td>
+
-
<td><span style="font-weight: normal"><b>NOT Gate<br>
+
-
</b>Description...</span></td>
+
-
<td><span style="font-weight: normal">Request for Proposals</span></td>
+
-
    <td>
+
-
      <ul>
+
-
      <li></li>
+
-
      </ul>
+
-
    </td>
+
-
</tr>
+
-
</table>
+
-
 
+
-
=== Grammar ===
+
-
 
+
-
== Implementation ==
+
-
*'''Symbols'''
+
-
**Version 1.0
+
-
***'''[[Media:SBOLv_v1.zip | Download]]'''
+
-
***Released on 11-18-2009
+
-
***PDF Vector Images
+
-
***72 & 300 dpi PNGs
+
-
**[[Endy:Notebook/Synthetic_Biology_Open_Language/Prior_Releases | Prior Versions]]
+
-
*'''OmniGraffle Files'''
+
-
**'''[http://dl.dropbox.com/u/3564908/SBOLv.zip Download]'''
+
-
*'''Software Tools'''
+
-
**[http://sourceforge.net/projects/clothocad/ Clotho-Spectacles]
+
-
**[http://www.omnigroup.com/applications/OmniGraffle/ OmniGraffle]
+
-
*'''Tutorials'''
+
-
**[[Media:MACvBOL.pdf | Incorporating Symbols into PowerPoint 2004 for Macs]]
+
-
**[[Media:SBOLvWin.pdf | Incorporating Symbols into PowerPoint 2007 for Windows]]
+
-
 
+
-
== Maintenance ==
+
-
====Symbol Status====
+
-
<table width="100%" cellpadding="3" cellspacing="0" border="1" class="zeroBorder" bordercolor="#000000">
+
-
  <tr>
+
-
    <th>Status</th>
+
-
    <th>Definition</th>
+
-
  </tr>
+
-
  <tr>
+
-
    <td><b>Request for Proposals</b></td>
+
-
    <td>A symbol is needed but their isn't consensus on the appearance of the symbol.
+
-
    </td>
+
-
  </tr>
+
-
  <tr>
+
-
    <td><b>Under Development</b></td>
+
-
    <td>A rough draft of a symbol was submitted.
+
-
    </td>
+
-
  </tr>
+
-
  <tr>
+
-
    <td><b>Proposed</b></td>
+
-
    <td>The final version of a symbol was submitted and the author is seeking comments.
+
-
    </td>
+
-
  </tr>
+
-
  <tr>
+
-
    <td><b>Consensus</b></td>
+
-
    <td>A rough consensus has been reached that the symbol is a candidate for inclusion in an official release of SBOLv.
+
-
    </td>
+
-
  </tr>
+
-
  <tr>
+
-
    <td><b>Included in v. #</b></td>
+
-
    <td>The version of SBOLv where the symbol was included.
+
-
    </td>
+
-
  </tr>
+
-
  <tr>
+
-
    <td><b>Deprecated</b></td>
+
-
    <td>A symbol is not being considered for inclusion in SBOLv.
+
-
    </td>
+
-
  </tr>
+
-
</table>
+
-
 
+
-
====Deprecated Symbols====
+
-
*[[Endy:Notebook/Synthetic_Biology_Open_Language/Deprecated_Symbols | Link]]
+
-
 
+
-
==Notes==
+
-
* Request for Comments
+
-
**[[The_BioBricks_Foundation:RFC#BBF_RFC_16:_Synthetic_Biology_Open_Language_Visual_.28SBOLv.29_Specification|RFC 16]]
+
-
**[[The_BioBricks_Foundation:RFC|RFC 18]]
+
-
* Tiny URL
+
-
**http://tinyurl.com/sbolv
+
-
 
+
-
 
+
-
|-
+
-
|colspan="2" style="background-color: #F2F2F2;"|
+
-
{{LnNotebookRecentChanges2}}
+
-
|}
+
-
 
+
-
__NOTOC__
+

Current revision

It has been requested that this page be removed with restriction endonucleases.
Other articles for deletion are listed here.
Retrieved from "http://openwetware.org/wiki/Endy:Notebook/Synthetic_Biology_Open_Language"
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