1. Copyright OpenHelix. No use or reproduction without express written consent1

2. GenoCAD Introduction Computer-Assisted Design Software for Synthetic Biology Materials prepared by: Mary E. Mangan PhD www.openhelix.com/genocad Version 1

3. Copyright OpenHelix. No use or reproduction without express written consent3 GenoCAD Introduction Agenda Introduction and Credits Register and Log In Step 1: Parts Parts Grammar Import the Training Set Step 2: Design Step 3: Simulate Summary Exercises GenoCAD: http://www.genocad.org/http://www.genocad.org/

4. Introduction to GenoCAD Computer-assisted design software for synthetic biology Visit GenoCAD.org Copyright OpenHelix. No use or reproduction without express written consent4 genocad.org

5. Support for GenoCAD Peccoud team NSF support Copyright OpenHelix. No use or reproduction without express written consent5 peccoud.org nsf.gov click

6. Process Flow Parts and grammars, public or custom collections Design constructs Simulate processes Copyright OpenHelix. No use or reproduction without express written consent6

7. Conceptual Framework for GenoCAD Aspects of DNA function explained with language metaphors: transcription, translation, code GenoCAD lets you develop language for programming cells Copyright OpenHelix. No use or reproduction without express written consent7

8. Data Model, Concepts Parts form the foundation, stored in project libraries Grammar rules specify the way the parts work in series Parts + Grammars give you synthetic construct designs Copyright OpenHelix. No use or reproduction without express written consent8 Promoter A Coding Seq B Coding Seq A Promoter B Promoters Coding Seqs Terminators Your constructs peccoud.vbi.vt.edu/publications 2007: 10.1093/bioinformatics/btm446 2009: 10.1371/journal.pcbi.1000529

9. Further Reading Publications: theoretical, software, ongoing development Cite GenoCAD if you use the tools Copyright OpenHelix. No use or reproduction without express written consent9 doi: 10.1093/bioinformatics/btm446 doi: 10.1371/journal.pcbi.1000529 doi: 10.1093/nar/gkp361 doi: 10.1016/j.tibtech.2011.09.001

10. Getting Assistance Help: context-sensitive help from ? Button Support link for asking questions or offering feedback Social media Copyright OpenHelix. No use or reproduction without express written consent10 support

11. Copyright OpenHelix. No use or reproduction without express written consent11 GenoCAD Introduction Agenda Introduction and Credits Register and Log In Step 1: Parts Step 2: Design Step 3: Simulate Summary Exercises GenoCAD: http://www.genocad.org/http://www.genocad.org/

12. Register at GenoCAD Not required, but very handy Your preferences, parts and creations will be saved Copyright OpenHelix. No use or reproduction without express written consent12

13. Password Recovery or Reset If needed in the future, you can reset password easily Copyright OpenHelix. No use or reproduction without express written consent13

14. Copyright OpenHelix. No use or reproduction without express written consent14 GenoCAD Introduction Agenda Introduction and Credits Register and Log In Step 1: Parts Parts Grammars Import the Training Set Step 2: Design Constructs Step 3: Simulate Summary Exercises GenoCAD: http://www.genocad.org/http://www.genocad.org/

15. Step 1: Parts Step 1: Exploring parts libraries and grammars Public parts and libraries samples are pre-loaded You will add other sources and your own project libraries Access to the pieces you need for subsequent steps Copyright OpenHelix. No use or reproduction without express written consent15 click Logged in

16. Parts and Parts Libraries Libraries will store the parts Public libraries are not editable by users Later we’ll create and edit custom project libraries Copyright OpenHelix. No use or reproduction without express written consent16 library

17. Libraries contain Categories with Parts Folder contains parts associated with a grammar Copyright OpenHelix. No use or reproduction without express written consent17 library Selected items will be displayed with relevant details Choose: Promoter (PRO) category

18. Examine a Part Category: Promoter A category may have multiple part items Copyright OpenHelix. No use or reproduction without express written consent18 click filter select all Parts list PartID is unique sort select one

19. Part Detail Features Part Detail includes important features and sequence Copyright OpenHelix. No use or reproduction without express written consent19 sequence Unique PartID Name Only A T G C (limit: ~16 million bases) Description Parts can be shared across libraries These are the features that can be located with the “search” tool later.

20. Search for Items Locate specific parts quickly with a search Copyright OpenHelix. No use or reproduction without express written consent20 search

21. Basic Search and My Cart Search the parts fields to locate specific items quickly Use * as a wildcard Copyright OpenHelix. No use or reproduction without express written consent21 tet* click choose Advanced all_promoters save

22. Parts need Grammars Copyright OpenHelix. No use or reproduction without express written consent22 Parts form the foundation, the building blocks you need Grammar rules specify the way the parts work in series

23. Grammars for Parts Copyright OpenHelix. No use or reproduction without express written consent23 Parts form the foundation, the building blocks you need Grammar rules specify the way the parts work in series

24. Grammars Grammars establish the design strategy Subject-Verb-Object Promoter-Cistron-Terminator Copyright OpenHelix. No use or reproduction without express written consent24 choose

25. Public Grammars Basic Grammar—No Simulation for this example Characteristics of this grammar “Manage Grammar” for more details (advanced tutorial) Copyright OpenHelix. No use or reproduction without express written consent25

26. Obtain the Training Set www.figshare.com Download the GenoCAD Tutorial I “Training Set” Click Add/Import Grammar Copyright OpenHelix. No use or reproduction without express written consent26 click http://dx.doi.org/10.6084/m9.figshare.153827 GenoCAD figshare.com Training_Set…Parts.genocad save

27. click Upload the Training Set Upload the zipped file that came from FigShare Copyright OpenHelix. No use or reproduction without express written consent27 click Use existing

28. Imported Training Set is available An editable Grammar is now available Will be used for further work Copyright OpenHelix. No use or reproduction without express written consent28 Click Parts

29. Training Set is Integrated The training set grammar, library, and parts are available Editable, so you can change or add new Let’s add a new part as an example Copyright OpenHelix. No use or reproduction without express written consent29

30. Create a Custom Part Good strategy: create a library for each project Put relevant parts in that project library Copyright OpenHelix. No use or reproduction without express written consent30 Fake RBS aaggaattaa Fictitious Ribosome Binding Site for training Only A T G C Can only add parts to your own libraries

31. User Grammar, Library, Part Created Your custom items will be stored, now available to use Import parts to use and export parts for sharing or backups Copyright OpenHelix. No use or reproduction without express written consent31 Your part

32. Copyright OpenHelix. No use or reproduction without express written consent32 GenoCAD Introduction Agenda Introduction and Credits Register and Log In Step 1: Parts Step 2: Design Constructs Step 3: Simulate Summary Exercises GenoCAD: http://www.genocad.org/http://www.genocad.org/

33. Step 2: Design Constructs Public and user parts, libraries, grammars in place Use them to create a construct with “Design” options Copyright OpenHelix. No use or reproduction without express written consent33 click

34. Design Constructs Choose grammar Choose library Begin to design Choices are listed Copyright OpenHelix. No use or reproduction without express written consent click Build a simple cassette Inducible promoter RBS A Luciferase T7 terminator 34

35. Construct is Complete New options Download Save design Copyright OpenHelix. No use or reproduction without express written consent35 Ready!

36. Browse for Constructs “Load Design” or “Available Designs” folder to see the list Yours + public designs are shown Copyright OpenHelix. No use or reproduction without express written consent36 export view clone check

37. Data Model Parts and Libraries Grammar and Rules Design your constructs Copyright OpenHelix. No use or reproduction without express written consent37

38. Copyright OpenHelix. No use or reproduction without express written consent38 GenoCAD Agenda Introduction and Credits Register and Log In Step 1: Parts and Grammar Step 2: Design Constructs Step 3: Simulate Summary Exercises GenoCAD: http://www.genocad.org/http://www.genocad.org/

39. Step 3: Simulate Copyright OpenHelix. No use or reproduction without express written consent39 click doi: 10.1016/j.cell.2012.05.044

40. Constructs Ready for Simulation If you generate with attributes for simulation, they will be listed Public examples Copyright OpenHelix. No use or reproduction without express written consent40 COPASI Status www.sbml.org Click www.copasi.org

41. Repressilator Example Design of the construct 3 cassettes in a network Parts + Grammar + Design carries key details Copyright OpenHelix. No use or reproduction without express written consent41 Click doi: 10.1038/35002125

42. Simulation Sample Copyright OpenHelix. No use or reproduction without express written consent42 Duration and interval are set Run Simulation to obtain the display 1005 Click TetR Lacl clts

43. Copyright OpenHelix. No use or reproduction without express written consent43 GenoCAD Introduction Agenda Introduction and Credits Register and Log In Step 1: Parts and Grammar Step 2: Design Constructs Step 3: Simulate Summary Exercises GenoCAD: http://www.genocad.org/http://www.genocad.org/

44. Copyright OpenHelix. No use or reproduction without express written consent44 GenoCAD Introduction Summary GenoCAD is a toolbox for synthetic biology Parts, grammars, designs, and simulations

45. Copyright OpenHelix. No use or reproduction without express written consent45 GenoCAD Introduction Agenda Introduction and Credits Register and Log In Step 1: Parts and Grammar Step 2: Design Constructs Step 3: Simulate Summary Exercises GenoCAD: http://www.genocad.org/http://www.genocad.org/

46. Copyright OpenHelix. No use or reproduction without express written consent46