Learn to use GenoCAD, a Computer-Assisted Design application for synthetic biology projects, with this free tutorial provided by the Peccoud Lab at Virginia Tech. The GenoCAD website enables researchers to generate libraries of parts that can be used and re-used to generate unlimited designs supporting bench biologists in molecular biology construction efforts. Grammars that specify the order of elements provide a consistent yet flexible framework for creating construct designs. In this introductory tutorial, the foundations of the GenoCAD system are explored, and basic functionality of the software is 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 basic aspects of the site usage with an orientation and overview
  • the organizational features of libraries and their component parts
  • to use a grammar to create customized designs of expression constructs
  • to run a simple simulation to investigate the behavior of synthetic systems
TUTORIAL RELATED CONTENT

TUTORIALS

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

GenoCAD Advanced Topics: 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:

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.

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

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 Advanced Topics: Computer-Assisted Design software for synthetic biology

CATEGORIES

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

BLOG POSTS

Video Tip of the Week: canEvolve: Frequently when we go to a site to do workshops, we get requests about other workshops that they might host at their site. Last week at the workshop we did (UCSC Genome Browser, GenoCAD), I was asked a...

GenoCAD webinar this Thursday, March 27: Although it's already posted in our news feed, I just wanted to add a reminder about our upcoming webinar on GenoCAD: open-source computer-assisted design software for synthetic biology. You can see th...

Free “Introduction to GenoCAD” Webinar presented March 27th.: The Peccoud Lab, based at Virginia Bioinformatics Institute at Virginia Tech, is sponsoring a free webinar on GenoCAD, presented by OpenHelix on Thursday, March 27th, at 18:00 p.m. UTC/2:00 p.m. ET/11:...

Video Tip of the Week: Advanced Topics in GenoCAD: Recently we announced our newest training materials on GenoCAD. The introductory tutorial provides a great foundation for understanding the features that are available and how it could help you in the ...

Video Tip of the Week: GenoCAD, computer-assisted design for synthetic biology: For this week's video tip of the week, we've got a real treat. This time it's a whole tutorial. Freely available to everyone because it is sponsored by the Peccoud Lab team, you have access to the full...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

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

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

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