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