Cell Engineering Repository Addresses Research Bottleneck

An international team led by Newcastle University has launched a species and strain database that uses cell barcodes to monitor and track engineered organisms.  Dubbed CellRepo, the database keeps track and organizes digital data produced during cell engineering and molecularly links that data to the associated living samples.

“CellRepo, at its core, is a collaboration platform in which cell engineers can document their work and share it with others (within their own lab or more widely),” says lead author Natalio Krasnogor, Professor of Computer Science and Synthetic Biology at Newcastle University’s School of Computing. “By enabling more collaboration and the seamless sharing of engineered strains we hope to accelerate and improve synthetic biology processes and reporting for everybody.”

The community resource enables traceability by providing the exact documentation for a strain and properly crediting laboratory work. It also emphasizes responsibility by making it easier to track and assign ownership.  

Dr. Jonathan Tellechea says he faces misidentification issues frequently in his own work. “Fortunately I was able to find them early on and solve them but I can’t imagine how many good projects have failed or stalled because of this. Some other chunk of my time as a biologist goes into retroactively building the history of the plasmids and strains I use. I may get the genetic material from someone, but who was the original author? Sometimes I am lucky and it is just one paper away, sometimes it’s down a rabbit hole that may end up in the 80s. CellRepo fixes these and other important problems for experimentalists. "

Available globally, CellRepo also has significant safety advantages, such as limiting the impact of deliberately or accidentally released genetically modified microorganisms by enabling faster tracing of the organisms’ lab of origin and design details.  CellRepo is built on version control, a concept from software engineering that records and tracks changes to software code. The scientists believe that version control for cell engineering will make engineering biology more open, reproducible, easier to trace and share, and more trustworthy. The tool will also help researchers reproduce results and collaborate more easily and reduce costs associated with data and source code losses. 

The work was published in a recent issue of Nature Communications.