Like Berkeley Lab’s other cutting edge user facilities, the Joint Genome Institute (JGI) is helping to transform science. When it was established 26 years ago, it focused on sequencing for the Human Genome Project. Since then, it has evolved to advance genomics in support of the DOE missions related to clean energy and the environment.
Research News spoke with Nigel Mouncey, who joined the Lab in 2017 as the Institute’s director (Nigel came from industry, holding R&D lead positions at Dow Agrosciences, DSM Nutritional Products, and Roche), about the JGI’s plans and what makes the institute special.
What differentiates JGI from other genome institutes?
JGI is the only genomics user facility in the world that focuses on energy and environment. We work in three sectors of the bioeconomy: energy, climate, and bioproducts. Other genome institutes are focused primarily on health. To achieve our revised vision of leading genomic innovation for a sustainable bioeconomy, we are sequencing and data mining a vast range of biological functions, for example, in plants, fungi, algae, bacteria, and viruses to better understand the carbon cycle and other biogeochemical cycles, and to provide approaches to engineer applications for the bioeconomy. Together, this knowledge is critical for mitigating climate change. And we are leveraging the ever-increasing amounts and types of sequence and sequence-related data we are collecting – developing systems for the analysis, storage, and dissemination of this data to the scientific community.
How we work with our users, for whom we generate and provide data and products, is also special. In order to maximize efficiency of our platforms, most of our users are remote. Our scientists help them make sense of all the data, which is often more than they thought they would get, and this means that we often end up being collaborators who provide consultation and expertise.
What are you looking forward to in the near future?
The DNA/RNA blueprint to life is how information is recorded in organisms. There is so much potential for this area of scientific research, and JGI is helping to lead the way.
For example, we are looking not just to understand the sequencing data we collect, but to create models for predictions using machine learning and other tools. With a better understanding of which bioenergy feedstock plants will grow better and which will have a tougher time, we will be able to predict what the ecosystem will look like in 15 years, and use that information to build optimal ecosystems as our climate changes. We will be doing this adaptation work in partnership with other user facilities across the Office of Science, such as the Environmental Molecular Sciences Laboratory (EMSL).
On the synthetic biology front, we are hoping users will be able to engineer most organisms to do all sorts of things. They will be able to produce new molecules and materials for new aviation fuels, building materials such as self-repairing bioconcrete, biopolymers to be used in electronic devices, and of course health applications. It’s such an exciting time; the genomics community is at the cusp of being able to uncover new science and JGI will be helping to lead the charge.
What will JGI look like in ten years?
These huge advancements that I described will require new technologies and new ways in which we can make data usable. JGI will be collaborating with others at the Lab and elsewhere on multiple fronts to make these happen.
Capturing data in real time, from the field, is one aspect. Not having to bring samples back to the lab will be a huge step forward for the scientific community. JGI is discussing new approaches to miniaturize sequencing of environmental samples, as well as thinking about field- deployable cell-free technologies that will allow us to, for example, rapidly detect metabolic states of plants or soil microbes using nucleic acid or enzymatic processes
Equally important is the seamless integration of many different data types (integrating plant data with field images captured by drones, for example). Of course, computational capabilities, including machine learning, will play a critical role in making sense of this data, such as through the development of predictive models.
Having these capabilities will take our understanding of biological systems to a new level. We will better understand not just what they do, but how they are responding or adapting to change.
I would also like to broaden our user base. Today we are working with more than 2,000 primary users with active proposals, and more than 15,000 people are using our data. We’re working hard to attract industry users and new communities, such as the agricultural sector. I also hope that we will be reaching members of the scientific community whom we are not reaching today, those who don’t have substantial funding for research, or those who are just starting out in their academic careers, for example.
What else do you want the Lab community to know about JGI?
JGI has a strong culture of collaboration and inclusivity, and we have wonderful, talented, and supportive people doing extraordinary work. We moved to the Hill site in 2019 after 20 years in Walnut Creek, hoping to encourage stronger collaboration with the rest of the Lab. The COVID lockdown slowed this effort a bit, but now our doors are fully open. For example, we are working with the Molecular Foundry on building a biomolecular materials science area to better understand the synthesis of biomaterials in nature. We also have strong partnerships across the Lab’s computation community, especially with Lab IT with whom we’ve partnered to site JGI’s new midrange compute cluster, Dori, and with NERSC where we’ve been fortunate to take advantage of their high-performance computing capabilities to power large scale analyses. We look forward to ideas and partnerships from across the Lab. Just reach out to me or any member of the JGI team.