software

The Synthetic Biology Open Language – SBOL

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...

Design of expression vectors for Chlamydomonas reinhardtii using domain-specific language

Design of expression vectors for Chlamydomonas reinhardtii using domain-specific language

The design of expression vectors often requires to follow specific rules dictated by the requirements of a project. In this paper, we introduced the GenoCAD grammar editor. We demonstrated how it could be used to capture set of design rules...

Next-generation DNA sequencing

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...

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

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....

CloneQC: Lightweight Sequence Verification For Synthetic Biology

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...

Writing DNA with GenoCAD

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...

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

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...

Möbius: an integrated discrete-event modeling environment

Möbius: an integrated discrete-event modeling environment

Möbius has found numerous applications in computational biology to build and solve stochastic models of biological processes. It provides the user with a modeling workflow and several sophisticated features that are not available in the simulation tools commonly used by...