Endy:Notebook/BioBrick Open Language Specification/Doug Approach

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Response to Emma's Requirements

//Sample "Eugene" (BOL) file which illustrates the requests from SynBioSS Group
//Doug Densmore
//Date - 7/10/09


   * BioBrick ID: To allow for the design of custom BioBricks, I think this property should be defined by default but not mandatory.
   * BioBrick nickname: Mandatory. For naming custom bricks, and convenience; "pTet" is more descriptive than "BBa_R0040".
   * BioBrick type: Promoter, RBS, Coding DNA, Terminator, etc. SynBioSS only cares about these four types, but obviously BOL should support every type in the Parts Registry.
   * BioBrick order: For devices and whatnot. 

Property BioBrickID(txt);
Property Nickname(txt);
//Type and order will not be properties ; order can be determined by other things 

Type-Specific Characteristics

   * Constitutively ON/OFF: That is, whether a promoter is "ON" or "OFF" when no protein is bound to it.
   * Operator Site Name(s): Such as tetO, lacO, etc....
   * Operator Site Location(s): A start/end is all we need.
   * Location of -10/-35 sites: Start/end. We are interested in this because the leakiness of a system is affected by the location of any operator site(s) relative to these sites. 

Property OnOff(boolean); //we added a boolean type, "true" or "false" are possible values (without quotes)
Property OperatorSiteName(txt[]); //changed to reflex Emma's comments
Property OperatorSiteLocation(num[]); //changed to reflex Emma's comments
Property Negative10Negative35(num[]); //changed to reflex Emma's comments

Coding DNA

   * Corresponding protein: For example, BBa_E0040 codes for GFP. 

Property Protein(txt);

Regulatory/System Information

I do not know if the scope of BOL will eventually include entire systems, instead of just BioBrick devices. If so, the following information would be helpful to us:
Protein Properties

   * Constitutive or Non-Constitutive: Self-explanatory.
   * Protein "type": The general behavior of the protein. Currently, SynBioSS can handle activators, repressors, and reporters.
   * Binding Sites: A list of operator sites that the protein can bind do.
   * Complex: This is just an integer representing the number of protein monomers that are in an active complex. For example, TetR and LacI bind DNA as dimers(2) and tetramers(4), respectively. 

Property Constitutive(boolean); //Changed to boolean
Property ProteinType(txt);
Property BindingSites(txt[]);
Property Complex(num);

Effector Properties

Such as aTc, IPTG, etc....

   * Binding behavior: Protein(s) that the effector binds to.
   * Act in Concert: For every protein/effector pair, this is a yes-no question. Some proteins (e.g. LuxR) will not bind to DNA until a small molecule (e.g. HSL) first binds to them. 

Property BindingBehavior(txt);
Property ActInConcert(num);

All properties about can be kept in a header file called SynBioSSProperties.h

//Examples of part
Part Promoter(BioBrickID, Nickname, OnOff, OperatorSiteName, OperatorSiteLocation, Negative10Negative35);
Part RBS(BioBrickID, Nickname);
Part CodingDNA(BioBrickID, Nickname, Protein);
Part Terminator(BioBrickID, Nickname);

All components definintions can be in a headerfile called SynBioSSComponents.h

Promoter p("BBa_R0040", "ptet", true, ["TetR1", "TetR2"] , [1, 19, 26, 44], [19,44]); //reflects Emma's comments
RBS r("BBa_R0040", "rbs");
CodingDNA c("BBa_R0040", "CDS", "lasR");
Terminator t("BBa_B0010", "term");

All instantiations can be in a headerfile called <x>instantiations.h
This will be created by parsing information from a database, xml file, etc

//Now once all this has been captured in header files, devices can be defined

Device d(p, r, c, t);
Device d2(p, d);

//sample print statements