Genocad Introduction

GenoCAD Introduction Computer-Assisted Design Software for Synthetic Biology Materials prepared by: Mary E. Mangan PhD www.openhelix.com/genocad Version 1 GenoCAD Introduction Agenda Introduction to GenoCAD genocad.org 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/ Computer-assisted design software for synthetic biology Visit GenoCAD.org 1 Support for GenoCAD Process Flow click peccoud.org nsf.gov Parts and grammars, public or custom collections Peccoud team Design constructs NSF support Simulate processes Conceptual Framework for GenoCAD Data Model, Concepts Promoters Coding Seqs Terminators peccoud.vbi.vt.edu/publications 2007: 10.1093/bioinformatics/btm446 2009: 10.1371/journal.pcbi.1000529 Promoter A Coding Seq A Promoter B Coding Seq B Your constructs Parts form the foundation, stored in project libraries Aspects of DNA function explained with language metaphors: transcription, translation, code Grammar rules specify the way the parts work in series GenoCAD lets you develop language for programming cells Parts + Grammars give you synthetic construct designs 2 Further Reading Getting Assistance doi: 10.1093/bioinformatics/btm446 doi: 10.1371/journal.pcbi.1000529 doi: 10.1093/nar/gkp361 doi: 10.1016/j.tibtech.2011.09.001 support Help: context-sensitive help from ? Button Publications: theoretical, software, ongoing development Support link for asking questions or offering feedback Cite GenoCAD if you use the tools Social media GenoCAD Introduction Agenda Register at GenoCAD Introduction and Credits Register and Log In Step 1: Parts Step 2: Design Step 3: Simulate Summary Exercises GenoCAD: http://www.genocad.org/ Not required, but very handy Your preferences, parts and creations will be saved 3 Password Recovery or Reset 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/ If needed in the future, you can reset password easily Step 1: Parts Parts and Parts Libraries Logged in library click Step 1: Exploring parts libraries and grammars Public parts and libraries samples are pre-loaded Libraries will store the parts You will add other sources and your own project libraries Public libraries are not editable by users Access to the pieces you need for subsequent steps Later we’ll create and edit custom project libraries 4 Libraries contain Categories with Parts Examine a Part Category: Promoter filter library select all sort click category Selected items will be displayed select one with relevant details Choose: Promoter (PRO) Parts list PartID is unique Folder contains parts associated with a grammar A category may have multiple part items Part Detail Features Search for Items Unique PartID search Name Only A T G C sequence (limit: ~16 million bases) Description Parts can be shared across libraries These are the features that can be located with the “search” tool later. Part Detail includes important features and sequence Locate specific parts quickly with a search 5 Basic Search and My Cart Parts need Grammars Advanced tet* click all_promoters save choose Search the parts fields to locate specific items quickly Parts form the foundation, the building blocks you need Use * as a wildcard Grammar rules specify the way the parts work in series Grammars for Parts Grammars choose Grammars establish the design strategy Parts form the foundation, the building blocks you need Subject-Verb-Object Grammar rules specify the way the parts work in series Promoter-Cistron-Terminator 6 Public Grammars Obtain the Training Set GenoCAD figshare.com Training_Set…Parts.genocad click save http://dx.doi.org/10.6084/m9.figshare.153827 Basic Grammar—No Simulation for this example www.figshare.com Characteristics of this grammar Download the GenoCAD Tutorial I “Training Set” “Manage Grammar” for more details (advanced tutorial) Click Add/Import Grammar Upload the Training Set Imported Training Set is available Click Parts click click Use existing An editable Grammar is now available Will be used for further work Upload the zipped file that came from FigShare 7 Training Set is Integrated Create a Custom Part Fake RBS Only aaggaattaa A T G C Fictitious Ribosome Binding Site for training Can only add parts to your own libraries The training set grammar, library, and parts are available Editable, so you can change or add new Good strategy: create a library for each project Let’s add a new part as an example Put relevant parts in that project library User Grammar, Library, Part Created GenoCAD Introduction Agenda Introduction and Credits Register and Log In Step 1: Parts Step 2: Design Constructs Your part Step 3: Simulate Summary Exercises Your custom items will be stored, now available to use GenoCAD: http://www.genocad.org/ Import parts to use and export parts for sharing or backups 8 Step 2: Design Constructs Design Constructs Choose grammar Choose library Begin to design click Choices are listed clickclick click click Build a simple cassette • Inducible promoter click • RBS A • Luciferase • T7 terminator Public and user parts, libraries, grammars in place Use them to create a construct with “Design” options Construct is Complete Browse for Constructs New options export Ready! check Download Save design check view clone “Load Design” or “Available Designs” folder to see the list Yours + public designs are shown 9 Data Model GenoCAD Agenda Introduction and Credits Register and Log In Step 1: Parts and Grammar Step 2: Design Constructs Step 3: Simulate Summary Exercises Parts and Libraries Grammar and Rules Design your constructs GenoCAD: http://www.genocad.org/ Step 3: Simulate Constructs Ready for Simulation COPASI doi: 10.1016/j.cell.2012.05.044 click www.copasi.org Click www.sbml.org Status If you generate with attributes for simulation, they will be listed Step 3: Simulate Public examples 10 Repressilator Example Simulation Sample doi: 10.1038/35002125 Click Lacl 100 5 clts TetR Click Design of the construct 3 cassettes in a network Duration and interval are set Parts + Grammar + Design carries key details Run Simulation to obtain the display GenoCAD Introduction Agenda GenoCAD Introduction Summary 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/ GenoCAD is a toolbox for synthetic biology Parts, grammars, designs, and simulations 11 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/ 12.

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