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 will 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


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

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

Complete Microbial Genomes: An extensive collection of data, resources and tools for prokaryotic genomic analysis

Viral Genomes at NCBI: Viral genome resources including single-stranded or double-stranded RNA or DNA viruses

CMR: Comprehensive Microbial Resource

Integrated Microbial Genomes (IMG): IMG is a powerful community resource for the comparative analysis and annotation of microbial genome data.

Integrated Microbial Genomes with Microbiome samples (IMG/M): IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome sequence

VBRC: The Viral Bioinformatics Resource Center

UCSC Archaeal Genome Browser: Provides you with many research and analysis tools that can be used to examine the genomes of more than 50 microbial species from the domain archaea.

GenoCAD: Computer-Assisted Design software for synthetic biology


Nucleotides : Tools that are primarily used in the storage, retrieval, or exploration of nucleotide-based data. Some tools may also involve protein sequence information.


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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