CellRepo, a species and strain database that employs cell barcodes to monitor and track created organisms, has been launched by an international collaboration. The database manages and organizes the digital data generated during cell engineering. It also molecularly connects that data to the corresponding biological samples. A cloud-based library that generates a digital fingerprint of modified microbes has been tested and shown to be effective.
CellRepo, a species and strain database that employs cell barcodes to monitor and track created organisms, has been released by an international team led by Newcastle University. The database, described in a new study published in the journal Nature Communications, keeps track of and organizes the digital data generated during cell engineering. It also molecularly connects that data to the corresponding biological samples.
This resource, which is available globally, promotes international collaboration and offers major safety benefits, such as reducing the impact of intentionally or accidently released genetically modified microbes by enabling faster tracing of the lab of origin and design information.
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 research team emphasizes other advantages of this community resource, such as traceability – providing precise documentation for a strain and correctly acknowledging laboratory effort. The database also emphasizes accountability by making it easy to track and transfer ownership.
CellRepo is a platform that represents an extraordinary advancement in this field and can save researchers all around the world a lot of time and unnecessary labor. Furthermore, the worldwide strain archives that will be shared through this platform might be a beneficial open-source of samples as well as a bridge for new collaborations between different labs.
Elena Velázquez
Researchers will be able to replicate studies and collaborate more easily if they have access to a worldwide database. The experts also claim that the repository will increase transparency and lower the expenses associated with data and source code loss.
Lead author, Natalio Krasnogor, Professor of Computer Science and Synthetic Biology at Newcastle University’s School of Computing, said: “Engineering biology is not rocket science. It is much, much harder. And because of that it is imperative that we do it more openly and more collaboratively. 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).
By enabling more collaboration and the seamlessly sharing of engineered strains we hope to accelerate and improve synthetic biology processes and reporting for everybody. CellRepo is a community resource and as such we invite engineering biologists, synthetic biologists, biotechnologists and life scientists more generally to try it and get in touch with us so we know what works and what needs to be improved!”
Dr. Jonathan Tellechea, a synthetic biologist in the project says:
“During my projects, I’ve always experienced some misidentification concerns. Fortunately, I was able to identify and resolve them early on, but I can’t think how many good initiatives have failed or delayed as a result of this. Another portion of my time as a scientist is spent developing the history of the plasmids and strains I employ. I might be able to obtain the genetic material from someone, but who was the original author? Sometimes I’m lucky and it’s just one document away, and other times it’s a rabbit hole that could lead to the 80s. CellRepo solves these and other critical issues for experimenters.”
Leanne Hobbs, the senior software engineer in the project reflects: “As a software engineer coming from industry to academia, it has been both a challenge and pleasure to work on a project where I can use my skills for the public good. Version control is a staple of software engineering and I am proud that we are now bringing these tools to engineering biology.”
Dr. Lenka Pelechova, a social scientist at The Interdisciplinary Computing and Complex Biosystems (ICOS) research group, added, “As a social scientist, I believe the Responsible Research and Innovation framework is critical in addressing societal expectations and opening up public discussions about new research and technology.” These discussions, in my opinion, should begin early on, and CellRepo helps this by making research transparent from the start.’
Professor Vctor de Lorenzo of the Systems and Synthetic Biology Program at the Centro Nacional de Biotecnologa in Madrid, Spain, and study co-author, stated: “Given engineered constructs’ inherent proclivity to mutate and overcome any type of genetic firewall, decades of efforts to contain recombinant bacteria have yielded few practical results. Instead, CellRepo provides consistent and unmistakable identification of given strains, which may be rigorously tracked and related to digital twins with all information available if necessary for countermeasures, ownership, or liability purposes.”
Elena Velázquez, PhD student in Víctor de Lorenzo’s lab, added:
“As a synthetic biologist who works all day with plasmids and strains from different origins, I am used to find that the plasmid or strain I was using in my experiments were not what I requested. This, of course, cannot be blamed on scientists who kindly donate their hard work altruistically and, moreover, since there was not an easy way to label and identify if the strain at stake was the intended one.
“CellRepo is a platform that represents an extraordinary advancement in this field and can save researchers all around the world a lot of time and unnecessary labor. Furthermore, the worldwide strain archives that will be shared through this platform might be a beneficial open-source of samples as well as a bridge for new collaborations between different labs. Scientists can now speed up their investigations and increase the dependability of their Science thanks to CellRepo.”
Co-author Simon Woods, Professor of Bioethics at Newcastle University’s Policy Ethics and Life Sciences Research Centre, added: “The widespread adoption of the CellRepo platform will significantly benefit science culture by providing a mechanism that ensures traceability and transparency while also enabling reproducibility. Furthermore, CellRepo is a revolutionary science governance device that promotes responsible yet innovative work.”
