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Construct design, gene synthesis, and personal foundry, all in a single platform: an interview with Doulix

PLOS Blogs Interview

 

As synthetic biology advances, researchers should spend less time in the lab and more time on designing and evaluating constructs. Doulix, a synbio company from Italy offers a virtual platform that can help achieve this goal. I had the chance to chat with Davide de Lucrezia, Doulix’s founder, and learn more about the integrated synbio solution they are offering.

 

Kostas Vavitsas: How did Doulix start?

Davide de Lucrezia: As a PhD and later postdoc, I felt empowered by the synthetic biology approach. So many new tools and resources I could leverage to work better and faster toward my objectives. I soon realized that most of those resources fell short to meet the promise of synthetic biology: rationale framework for the forward engineering of biological systems.

Back then, the routine synthetic biology workflow was highly fragmented, jumping from one database to another, from one software to the next, striving to combine different tools and resources to make the magic happen in the lab. Basically, I spent most of my time fixing and integrating the very tools that should have helped me to work better.

From this realization sprouted DOULIX in 2015, a cloud-based platform designed for synthetic biologists to streamline the entire synbio workflow, from design to synthesis.

 

Kostas: Why should someone prefer your platform from the competition?

Davide: Doulix integrates a curated DNA database with an advanced sequence editor that allows you to directly compute synthesis fragments for most common cloning methods. With Doulix you can seamlessly move from design to synthesis placing an order for synthesis from within your sequence editor. No more missing bp or frameshifts as you copy and paste your sequences between your editor and your gene synthesis provider. This dramatically reduces clerical errors and design time. In addition, Doulix leverages on smart algorithms to compute the optimal synthesis fragments for the cloning method of your choice, thus turning a time-consuming task into a software-driven automated process. Doulix frees up your time so that you can spend it on what you are best at: designing DNA.

 

Kostas: Synbio is moving towards automation and computerization. Where does Doulix fit in this consideration?

Davide: Doulix is designed around the very concept of standardization; we fully support multiple exchange data standards in order to ensure full interoperability between labs and among different equipment. As far as automation is concerned, we are deeply involved with the SBOL community to push the adoption of this standard for data exchange including automation specifications. We also act as foundry-for-a-fee leveraging on highly standardized assembly protocols to reduce turn-around time and manufacturing costs of complex constructs. Recently, we established a DNA physical repository for public sequences to leverage on part modularity and reusability to further decrease manufacturing costs.

 

Kostas: Can you tell us more about your participation in BioRoboost and the SBOL industrial consortium?

Davide: We are glad to be among the founding members of the SBOL industrial consortium coordinated by Jacob Beal, Raytheon BBN Technologies (US), to further develop the SBOL standard to include metadata and manufacturing specifications. This will allow embedding tech specifications of all stages of the engineering cycle: from design to testing and debugging. Together with Amyris, IDT, TeselaGen, and Zymergen, we aim to promote SBOL standard adoption for practical applications in industrial environments. The EU-funded BIOROBOOST project is the other side of the coin; it brings together world leading universities to develop the standards of the future for synthetic biology. One of the most daunting tasks of BIOROBOOST is to develop and promote a reduced set of host chassis for specific applications. The participation in these two complementary projects are part of our wider commitment toward a true forward engineering approach of biological systems.

 

Kostas: How was the experience of founding a company in Italy?

Davide: Admittedly, Italy is not renowned for its vibrant biotech scene let alone synthetic biology. Italy’s strongest assets are more traditional segments like pharma R&D and chemical manufacturing. We struggled to find financial partners willing to invest in what was little more than a whiteboard sketch. Even finding the right place for a company living just in between the analogical world of living things and the digital world was a daunting task. The biggest challenge we faced was the lack of a synbio community we could relate to. We were basically the only one talking of synthetic biology and we missed the fruitful engagement you may enjoy in more established synbio hubs such as London or Mission Bay. Yet, we managed to gather a truly interdisciplinary team of people with a passion for working at the interface between disciplines and who feel comfortable to step into adjacent fields. To this regard, the EU Framework Programs and H2020 were instrumental to reach beyond Italy. Indeed, the EU R&D fund was game changer for us. By participating to several EU-funded projects we were able to link to the best and brightest minds in Europe. That’s why we pride ourselves with the Made in EU logo.

 

Kostas:  Where do you see Doulix in 5 or 10 years?

Davide: I believe synbio can deliver greener chemicals, safer drugs and greater knowledge but I like to quote Confucius who said: “the mechanic that would perfect his work must first sharpen his tools”. I hope Doulix becomes the tool for synthetic biology, the premier suite for biology computer-aided design. We want to empower researchers to confidently design, simulate and manufacture their synthetic biology constructs. It would be nice to see the next phthalate-remediating engineered P. putida powered by Doulix.

 

Dr. Davide De Lucrezia is the managing director and co-founder of Doulix.com. His work in synthetic biology includes development of methods for protein and RNA degenerated libraries design and construction, modular protein-based nanomaterials for tissue regeneration and cell-free systems for information processing. Dr. De Lucrezia is a member of  the Industrial SBOL Steering Committee and co-chairman of the Portabolomics External Advisory Board.

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