Emerging Standards in Synthetic Biology Herbert M Sauro Michal Galdzicki and Deepak Chandran University of Washington, Seattle 1

SBML in a Nutshell Bottom-Up Effort A machine-readable format for representing computational models in systems biology Domain: systems of biochemical reactions Specified using XML Components in SBML reflect the natural conceptual constructs of the domain Now over 200 tools use SBML 2 Funding

SBML Ecosystem SBML Databases Unambiguous Model Exchange Semantic Annotations Simulator Comparison and Compliance Journals Diagrams SEDML: Simulation Experiment Description Language SBGN : Systems Biology Graphical Notation 3

What is Synthetic Biology Synthetic Biology is the “design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems.” (Royal Society) 4

10 years of Synthetic Biology Gardner TS, et al. Construction of a genetic toggle switch in Escherichia coli. Nature 2000; 403: Elowitz and Leibler; A Synthetic Oscillatory Network of Transcriptional Regulators Nature. 2000; 403:

Synthetic Biology Workflow “Creating cells that are able to excrete insulin at a specified rate during their optimal growth.” 6

Overall Aim of the Standardization Effort To support the synthetic biology workflow: 1.Laboratory parts management 2.Simulation/Analysis 3.Design 4.Assembly 5.Repositories - preferably distributed 7

The Immediate Need Take any current publication on a synthetic circuit and try to reproduce it, let me know how you get on. 8

Long-term Aim of the Standardization Effort Specifically: To allow researches to electronically exchange designs with round-tripping. To sent designs to bio-fabrication centers for assembly. To allow storage of designs in repositories and for publication purposes. 9

Synthetic Biology Open Language: SBOL 1.SBOL Semantic* 2.SBOL Visual* 3.SBOL Script First meeting in 2008, Seattle, funded by Microsoft 10

Synthetic Biology Data Exchange Group Synthetic Biology Open Language (SBOL) 11 SBOL-visual SBOL-semantic iBioSim UK, Imperial College EU 7th Framework Programme

SBOL Visual (SBOLv) Developed at the Berkeley BIOFAB (Endy and Arkin) Current about 40 symbols Used to visually annotate ‘features’ on a DNA Three symbol groups at present: 1. Central Dogma 2. Genetic Engineering 3. Devices 12

SBOL Visual (Implemented in Spectacles and TinkerCell) 13

SBOL: Reuse of biological parts semantic Sequence Annotation 1-80 Terminator BioBrick Scar Terminator B0010 B0012 Part B0015 Create a common language for engineers to describe and send parts Synthetic Biologist A Synthetic Biologist B Fabricate Synthetic Biology Open Language (SBOL) visual DNA Components Engineer New genetic device Michal Galdzicki describe and send 14

Figure 1. Diagram of the SBOL Semantic structure, illustrated with a set of information about a synthetic biology construct. a. A simplified Class (black rectangles) hierarchy (black open faced arrows) describes types (colored open faced arrows )of Individual data elements (yellow rounded rectangles) and the composition relationships between them (closed faced arrows). The example can be read as: Sample (pink) SS002 contains UW002 cells (dark green) of the MG1655 E. coli strain, which contain a plasmid (purple) pUW4510, which is composed of an parts (dark blue) an insert B0015 and vector backbone pSB1A2. The pSB1A2 vector backbone complies with the Assembly Standard (light blue) BBF RFC 10. The B0015 sequence annotations (green) specify three features (orange), the BioBrick Scar, and the parts (blue and orange indicating multiple inheritance), B0010 and B0012, which serve as transcriptional termination signals. b. Data type Properties used to hold information for each SBOL class follow the colon. Sequence Annotation Vector Backbone Sample Cell Physical DNA Assembly Standard pSB1A2 BBF RFC 10 SS002 pUW4510 MG1655 type cell dna insertvector format UW002 strain Sequence Feature B0015 type annotation 1-80 feature Terminator BioBrick Scar feature BioBrick Scar feature Terminator annotation type subClassOf B0010B0012 Part type Plasmid subClassOf type 15

Parts Registry at MIT Database of parts, basically a wiki, object model not documented and was generally not available to the public until this year. 16

SBOLr is a web front for a knowledge base of standard biological parts 17 JBEIr Software by Timothy Ham & Zinovii Dmytriv

Software support: libSBOL 18 Michal Galdzicki CAD Tool TinkerCell Sequence Editor Parts KB libSBOL SBOL-semantic Repository Allow for ease of access to information by software tools, using Semantic Web standards.

List of Software in the Working Group Clotho (BU,Berkeley), Java Connects users to repositories of biological parts. Plugin tools then define the various functions that can be performed, mainly related to lab and parts managements. Douglas Densmore GenoCAD (VT) Web based tool for the design of biological devices using an attribute grammar which defines the legal composition of parts. Jean Peccoud iBioSim (Utah), Java Advanced s imulation and analysis tool for synthetic and systems biology. Chris Myers JBEI Repository (Java), DOE support infrastructure Timothy Ham & Zinovii Dmytriv SBOLr (Currently Python but moving to Java) Test parts repository, ~5000 parts Michal Galdzicki TinkerCell (UW), C++/Qt Extensible visual design tool with support for modules, eg simulation, annotation. Deepak Chandran 19

Current Status of Standard First official release will be at Synthetic Biology 5.0 at Stanford, June, 2011 libSBOL 1.0 available at: Import/Export: GenBank, RDF, JSON 20

TinkerCell: Project to explore the potential of computer aided design in synthetic biology First prototype called Athena Developed by Bergmann and Chandran funded by Microsoft 21

Layered Architecture: Based on C++/Qt Octave, 22

All Parts can be Semantically Annotated. This allow plug-ins to interpret a given design. Enzyme Transcription Factor Enzyme catalysis Binding Translation Reporter Elongation CodingPromoter Terminator Transcription mRNA Currently there is no formal ontology for synthetic biology but one will need to be developed. 23

A TinkerCell model can be composed of sub-models 24

A TinkerCell model can be composed of sub-models ? ? ? ? ? ? 25

Users can add new plugins using C++, C, Octave, or Python languages 26

Availability (Windows, Mac and Linux, released under BSD) Contact author for details 27

SciPy optimization matrix operations statistics numerical methods frequency analysis NetworkX (lanl.gov) graph analysis graph layout structural analysis sensitivity analysis bifurcation analysis parameter scan simulation lp_solve flux balance analysis Many C and Python packages are included with TinkerCell Sundials Time-course simulation Steady state plot Custom programs Gillespie algorithm Hill equation derivation 2^N automatic binding events Loops in Jacobian Antimony SBML and CellML support 28

DemoDemo: Repressilator 29

Acknowledgements: Collaborators and Funding UW Deepak Chandran, Michal Galdziki, Sean Sleight, Bryan Bartley, Alex Neilson BioFAB (Berkeley, Stanford) Cesar Rodriguez, Drew Endy, Chris Anderson Virginia TechJBEI (DOE) Jean Peccoud Timothy Ham & Zinovii Dmytriv Boston University CRG, Spain Douglas Densmore Raik Grunberg Funding National Library of Medicine (Galdziki) Other funding from NIH (JSim/SBW), NIH (SBW) and NSF (FIBR,Tinkercell), Microsoft Strategic Research, BioFAB (NSF), JBEI (DOE) 30

Textbook: Enzyme Kinetics for Systems Biology Available as e-book or paperback on & 318 pages, 94 illustrations and 75 exercises E-book - $9.95 Paperback - $

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Sequence Refinement Examples include avoiding specific restriction sites or optimizing the codon usage. The sequence might also be optimized to avoid repeated regions that may be prone to recombination or secondary structures. 33

The SBOL semantic structure 34 Sequence Annotation type annotation 1-80 feature Terminator BioBrick Scar feature BioBrick Scar feature Terminator annotation type B0010 B0012 Part type B0015 type = instance-of

Each component in the TinkerCell diagram is associated with one or more tables 35