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Use Cases



Scenario

Sean, a synthetic biologist, sets out to improve evolutionary stability of BBa_T9002. He sketches a design using TinkerCell (example drawn from Sleight 2010). The new circuit design (Figure 1) calls for the use of DnaComponents in the following order: R0040 (pTetR), B0034, C0062(luxR), B0010, B0012, R0062 (pLuxR), B0032, E0040 (gfp), and J61048 (replacing  B0015).

After completing the design, Sean would like Bryan, the student working on the project with him, to fill in the sequence information and then send it to get additional annotations needed for the assembly process.   Sean does not specify which software tool Bryan should use. The choice of tools is Bryan’s responsibility so he should be able to take one file type and choose an appropriate tool for his task. Currently, Clotho apps (Eugene, MatchMaker) and GenoCAD offer automated or semi-automated solutions, but both are capable of assisting the process. Also a sequence editor such as ApE, VectorNTI, etc can be used to manually do so.  Alternatively, Sean could perform this sequence annotation himself, but for the purpose of this case, he would not pre-plan which tool to use, therefore would like to save his design in a generic file before choosing the downstream tool.

This case lists the specific IDs for components, but it does not specify the sequence, nor position coordinates. Technically unspecified sequences could be inserted between the components, without invalidating the design. ie the components are specified to be in relative order (using partial order). BBa_ IDs imply and mean BioBrick Parts from the PartsRegistry are to be used, but the assembly choices, such as choices of scar sequence, are left to the user in use case #02.

A generalization of this use case is to not specify IDs and instead to specify “other” required parameters for the design specification.

SBOL Structure to be used:
Generic Composite DNA Design Template

DCØ → (SArp1 (DCt1), SArp2 (DCt2), …, SArpØ (DCt))


Send DNA Design Template

Actors: Sean as the sender; Bryan as the recipient.

Goal: Sean wants to send a design template to Bryan so he may fill in the DNA sequence.

Overview and scope: Representation of a composite DNA design, independent of sequence. The design is the specification of an ordered set of required template DNA components. For this use case, the identifiers for the constituent DNA components and types are specified, but their DNA sequence and coordinate-based positions are not.  Diagrams representing this type of structural information are published as genetic level design layouts in most synthetic biology primary literature.

Successful Scenario: Main
Actor Action System Action
Sean: Save As SBOL from TinkerCell Create a file containing Composite DNA Component Design for T9002_J61048 design from TinkerCell.
Sean: Send T9002_J61048 SBOL file by email to Bryan Outside scope of system.
Bryan: Open SBOL file in Eugene/Clotho or GenoCAD. Read file containing the Composite DNA Component Design
Bryan: Fill in the sequence annotation information Actually filling in the sequence information is outside the scope of system, see next use case


Precondition: Diagram as in Figure 1 drawn in TinkerCell.

Post condition:  A Eugene input script file (String)  as specified below.
Device T9002_J61048 (Promoter BBa_ R0040, BBa_B0034, ORF BBa_C0062, Terminator BBa_B0010, Terminator BBa_B0012, Promoter BBa_R0062, BBa_B0032, ORF BBa_E0040, Terminator BBa_ J61048);
*
Figure 1. The T9002_J61048 design from TinkerCell. This design specifies a linear layout of the circuit along a single strand of DNA. The design includes the specification of types of DNA components with names and simplified partsregistry.org IDs, as well as component names where appropriate. The example shown contains no additional information in “hidden” form (eg DNA sequence, model parameters). However, some implied information such as order and type will be interpreted from the TinkerCell API.  We have chosen this limited case as a simple example of a design template; it does not take advantage of the many other functions TinkerCell can perform.  


Send Annotated DNA Sequence

Actors: Bryan as the sender; Jane as the recipient.

Goal: To send the annotated DNA sequence for assembly planning.

Description of Scenario:
Bryan, a synthetic biology PhD student, sets out to build T9002_J61048. He will fill in the sequence of the design using Eugene. His result will be a compilation of the DNA components fulfilling the design that Sean specified. To do this, Eugene will need a collection of DNA components retrieved from partsregistry.org . Therefore, Bryan will retrieve this collection and translate it into Eugene Part files (see Use Case #03).  Once Bryan is finished running Eugene, he will export the results and send them to Jane, an undergraduate student in the lab, who will plan, assemble, and sequence-verify the new circuit.

Overview and scope: Representation of an annotated DNA sequence as a DNA component with sequence annotations. The DNA sequence is annotated by position with sub-components and other features. The position is specified using the base pair coordinates along the 5’ to 3’ direction. For this use case, the constituent DNA components and their types are specified, but their relative position (order) on the DNA sequence is not specified explicitly.  Annotated DNA sequences such as this is are often found in the familiar GenBank flatfile format.

Precondition: SBOL structure Design Template: DCØ (SArp1 (DCt1), SArp2 (DCt2), …, SAØ (DCt)). and Collection of DNA Components Col(DCst1, DCst2, … DCstN

Post condition: Annotated DNA sequence

DCst → SArp1 (DCst1)
        →  SApos2 (DCst2), …
        →  SAposN (DCst)

Output  containing information as specified below:
T9002_J61048 1929bp of DNA sequence
1..54 = R0040
63..74 = B0034
81..836 = C0062
870..949 = B0010
958..998 = B0012
1007..1061 = R0062
1070..1082 = B0032
1089..1808 = E0040
1817..1929 = J61048

Successful Scenario: Main
Actor Action System Action
Bryan: Run Eugene and Export As SBOL Create a file containing Annotated DNA sequence
Sean: Send T9002_J61048 SBOL file by email to Jane Outside of this scope
Jane: Open SBOL file in J5. Read file containing the Annotated DNA sequence
Jane: Generates the optimal assembly strategy using J5 Outside this scope, see use case #03

SBOL Structure:
Generic Annotated DNA Sequence
DCs → (SApos1 (DCts1), SApos2 (DCts2), …, SAposN (DCtsN))



Publish Collection of DNA Components

Actors: Mike as the publisher; Bryan as the consumer.

Goal: To publish a collection of DNA components to be re-used for design of novel DNA circuits.

Description of Scenario:
Mike, a bioinformatics PhD student, wants to make the Parts Registry available in SBOL format for others to re-use. He transforms the PartsRegistry XML format (ie rsbpml) into SBOL and publishes them on the web as a service to the community. 

Overview and scope: Representation of a collection of DNA components annotated and typed. The collection is an unordered set of DNA components. For the first iteration of this use case the set of DNA components are basic, meaning they do not have sub-components specified, other DNA component structures can be used to extend this case as a set of alternatives.

Precondition: Sequence information for BBa_R0040, BBa_B0034, BBa_C0062, BBa_B0010, BBa_B0012, BBa_R0062, BBa_B0032, BBa_E0040, BBa_J61048.

Post condition:  Eugene Part files as specified below.
Promoter BBa_ J61048 (.ID("BBa_ J61048"), .Sequence("GATCTttgacagctagctcagtcctagggactatgctagcG"), .Orientation("Forward"));
etc.

Successful Scenario: Main
Actor Action System Action
Mike: Transform the PartsRegistry Basic BioBricks into SBOL Create a file a Collection of basic DNA Components
Mike: publish the SBOL Collection on the web Outside of this scope, see SBPkb
Bryan: Open SBOL Collection in Clotho Read file containing the Collection of basic DNA Components
Bryan: export to Eugene Part files. See use case #02

Implementation Note: The PartsRegistry in SBOL format can both be retrieved directly as a file and queried using a RESTful API query format, whichever suits the user best.  

SBOL Structure to be used:
Generic basic DNA Component Collection
Col(DCst1, DCst2, … DCstN)


Multi-Step Exchange of Annotated Plasmid DNA Sequence


Goal: To retrieve and send annotated plasmid DNA sequence information between multiple software packages.

Overview and scope:
Information exchange mediated by the Clotho platform between web-based  resources GD-ICE, PartRegistry via SBPkb, BIOFAB to TinkerCell, Gene Designer, VectorNTI , back to Clotho.

Description of Scenario:
A Clotho user imports a plasmid from GD-ICE, a part from SPBkb, and a part from BIOFAB Emeryville.  She includes the parts and plasmid in an emerging design.  She exports the design in a SBOL formatted file.  She emails the SBOL file to a TinkerCell, Gene Designer, and VectorNTI user.  The TinkerCell, Gene Designer, and VectorNTI users view the design, make changes, and email the modified design back to the Clotho user.  She views the modifications with Clotho.
--Cesar Rodriguez