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Computer-Assisted Design software for synthetic biology

Tutorial and training materials by OpenHelix

Learn to use advanced features of GenoCAD, a Computer-Assisted Design application for synthetic biology projects, with this free tutorial provided by the Peccoud Lab at Virginia Tech. As described in the Introductory tutorial, the GenoCAD website allows researchers to assemble libraries of parts that can be used and re-used to develop an unlimited number of designs supporting bench biologists in molecular biology construction efforts. This advanced topics tutorial expands on the concepts presented in that first tutorial by demonstrating how new project libraries can be created using the Advanced Search and Cart tools; creation and modification of grammars and their underlying rules; and additional design features, such as cloning and exporting designs to GenBank format. To reinforce these concepts, advanced functions of the software are demonstrated with hands-on tasks.

Note: The training set data required for this tutorial can be accessed at FigShare: GenoCAD Tutorials. Download the "Training_Set_EColi_With_Parts.genocad" file.


You'll learn:

  • the key features of advanced searches
  • advanced design strategies for quickly creating and modifying new constructs
  • exporting designs as GenBank-compatible files that can be used by third-party tools
  • managing grammars to support new projects
  • creating and modifying grammars to suit customized design needs

Related tutorials

This tutorial is a part of the tutorial group GenoCAD. You might find the other tutorials in the group interesting:

  • GenoCAD: Computer-Assisted Design software for synthetic biology


View additional tutorials for resources in

Recent BioMed Central research articles citing this resource

Kahl J Linda et al., A survey of enabling technologies in synthetic biology. Journal of Biological Engineering (2013) doi:10.1186/1754-1611-7-13

Leguia Mariana et al., 2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts. Journal of Biological Engineering (2013) doi:10.1186/1754-1611-7-2

Marchisio Andrea Mario et al., Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits Synthetic biology. BMC Systems Biology (2013) doi:10.1186/1752-0509-7-42

Chen Joanna et al., DeviceEditor visual biological CAD canvas. Journal of Biological Engineering (2012) doi:10.1186/1754-1611-6-1

More about the resource:

GenoCAD is developed and maintained by the Peccoud Lab team at the Virginia Bioinformatics Institute at Virginia Tech. Support for this research and outreach has been provided by the National Science Foundation under grant EF-0850100

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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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