software

The Synthetic Biology Open Language – SBOL

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange […]

Next-generation DNA sequencing

This article is an interesting review of how Next-Generation sequencing differs from traditional Sanger sequencing, along with the pros and cons of each approach.  Overall, the advantage of NextGen sequencing seems to be that it bypasses some of the traditional bottlenecks of Sanger sequencing, such E. Coli transformation and colony selection, and can be done […]

A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD.

GenoCAD is an open source web-based system that provides a streamlined, rule-driven process for designing genetic sequences. GenoCAD provides a graphical interface that allows users to design sequences consistent with formalized design strategies specific to a domain, organization, or project. Design strategies include limited sets of user-defined parts and rules indicating how these parts are […]

CloneQC: Lightweight Sequence Verification For Synthetic Biology

Article Summary Sequence verification is an important step in the Gene Synthesis process.  Creating a plasmid or chromosome from a series of smaller building blocks introduces many opportunities for error, so sequence verification as a quality control has relevance throughout the process, including after development of the building blocks, and after they have been combined […]

Writing DNA with GenoCAD

This paper is a little dated now but I still like to look at these screenshots. They are good memories of a time when GenoCAD was blazing a new trail in synthetic biology. Several years later, we are still living the vision. It just takes longer than expected to make it a reality.

A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts

Motivation: The sequence of artificial genetic constructs is composed of multiple functional fragments, or genetic parts, involved in different molecular steps of gene expression mechanisms. Biologists have deciphered structural rules that the design of genetic constructs needs to follow in order to ensure a successful completion of the gene expression process, but these rules have […]