GenoCAM: Managing Synthetic Biology Workflows

genocam: managing synthetic biology workflows

Managing Synthetic Biology Workflows

GenoCAM is integrated information system to manage synthetic biology workflows. GenoCAM includes a suite of bioinformatics applications that can communicate with a Laboratory Information Management System and an Electronic Laboratory Notebook systems. GenoCAM is still under development but let us know if you want to join the beta test program.

The Challenge

One of the distinctive features of synthetic biology is the complexity of the underlying workflows. Many projects require the development of large libraries of related genetic constructs. As a matter of fact, assembling these plasmid libraries can require a team of several scientists to generate hundreds or thousands of intermediates.  Unless the team is able to properly keep track of all these samples, the project success is unlikely.

Many projects include a number of bioinformatics steps that are an integral part of the research project. Scientists use various bioinformatics tools. However, they struggle to properly document this important aspect of their project. As a result, they keep track of their experimental work independently of the computational effort that supports their experiment.  For example, many scientists who are working with synthetic genes have lost track of the codon optimization algorithm used to design the gene.

Bioinformatics features

GenoCAM includes a collection of bioinformatics tools used in synthetic biology projects. This collection includes:

  • Primer design algorithms for amplification, Gibson assembly, or sequencing.
  • Design of building blocks, gBlocks, and other synthetic DNA parts
  • Pipelines to analyze sequencing data

These bioinformatics tools rely on a database of DNA sequences to document the computational work.

Laboratory Information Management System

GenoCAM can communicate with Laboratory Information Management Systems (LIMS). It captures the relation between DNA sequences and other types of records associated with DNA fabrication workflows.