A New Kind of Core Lab: An Interview with the DAMP Lab at Boston University

Core labs are essential in academic life science research settings. They provide centralized facilities equipped with advanced technologies and expertise. These labs offer services, including high-throughput sequencing, microscopy, proteomics, and bioinformatics support, which are often too costly or complex for individual labs to manage independently.

However, specific core labs, such as the DAMP Lab at Boston University, can go well beyond this model, acting as their own innovation ecosystems and driving research initiatives to new heights. These unique few operate like incubators, a unique position within the academic space. 

eLabNext got acquainted with the DAMP Lab – which stands for Design, Automation, Manufacturing, and Processes – during the COVID-19 pandemic as they transformed their operations to manage over 10,000 samples a day, with multi-million API calls on an hourly basis, integration with three databases, and several Hamilton liquid handling robots. 

And that only scratches the surface of what the DAMP lab does. The lab aims to develop novel biological systems using formal representations of protocols and experiments for the specify-design-build-test cycle. This will allow for faster, more scalable, and reproducible research results that can be transitioned from academia to society.

In this interview, we sit down with PI Douglas Densmore, PhD, to learn more about DAMP Lab and their work! Enjoy! 

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Q: Please tell us a little bit about DAMP Lab and the kind of services that you provide.

A: The mission of the DAMP lab is to develop novel biological systems using formal representations of protocols and experiments for the specify-design-build-test cycle. This will allow for faster, more scalable, and reproducible research results that can be transitioned from academia to society. The DAMP lab uses its expertise to deliver consistent, reproducible, and high-throughput results that researchers can share. These characteristics are vital to address synthetic biology-related research efforts where time, cost, scalability, and result quality are paramount. We offer over 45 molecular biology protocols, including DNA assembly, PCR, DNA/RNA purification, cloning (e.g., transformation, plating, colony picking, and DNA quantification), preparation of libraries for next-generation sequencing (NGS), gene reporter assays, flow cytometry sample preparation, among others. We also offer automation development, consulting, and clinical testing services.

Our operations are staffed by myself, Professor Cathie Klapperich, Lab Operations Manager Courtney Tretheway, and several talented staff members of research associates, technologists, automation engineers, and software engineers.

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Q: How do you differentiate yourself from other core labs?

A: A key differentiation point is that our goal is to be completely “virtual” in that you only interface with software. That interaction can be manual (via a website) or programmatic via a connection to another software tool (e.g., “click to checkout” in a DNA sequence editor). In the same way fast food restaurants are moving to “kiosks,” we would like all “orders” to be done via a parameterized set of services and requested formally, which reduces ambiguity and enforces standardization. Not only does this force customers to select things we know how to do well, but it also reduces errors, allows for easier order tracking and updates, and paves the way for computers (and AI) to, ultimately, play a bigger role in the future. 

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Q: Can you expand on your DNA Assembly and Cloning Services? 

A: Generally speaking, we offer molecular cloning and Gibson assembly. DAMP is a member of the IGSC (International Gene Synthesis Consortium), an organization formed to execute a common protocol to screen the sequences of synthetic gene orders to ensure that synthesized genes are safe. We are unique in this as our goal is to make this a completely automated process that begins when a DNA assembly job is submitted. 

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Q: For your Automation Development and Consulting Services, what are the most common challenges you see from your clients? 

A: The key challenge is translating customer needs to our fixed “menu” of services. We either have to map those needs 1:1 to our services or transform either the needs or the services so that we can meet the customer requirements. When these transformations happen, we must carefully weigh the costs and benefits. We must prevent creating one-off services or efforts that other customers won’t want. Simultaneously, we must engage with as many customers as possible to meet our financial obligations to our staff and the University. 

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Q: What are the most common motivations for researchers to leverage a facility such as the DAMP Lab for NGS and library prep services?

A: Setting up and maintaining NGS capabilities in-house can be prohibitively expensive for many research groups, especially in academia. By outsourcing to the DAMP lab, researchers can access these resources without the upfront costs or technical expertise needed for these instruments. With DAMP’s modular and high-throughput workflows utilizing liquid handlers, scientists can easily streamline their experimental timelines for large-scale and small-scale projects without constraints. One of the main challenges with library prep is the need for sample normalization to ensure a balanced flow cell output. DAMP’s ability to address these obstacles by precisely controlling sample inputs and outputs through every stage ensures a uniform and robust library preparation with even the most difficult or diverse sample types. 

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Q: For your Clinical Testing Services, can you discuss some of the regulations you and others must comply with, especially regarding the digital management of those samples? 

A: Some of the most relevant regulations our customers must comply with are HIPAA and CLIA regulations. HIPAA regulations enforce the protection of patient data. We did ~2.5 million COVID-19 tests from 2020-2023. In our case, we put systems in place to de-identify all patient data before it even entered our system. We were able to utilize eLabNext for sample management and storage as well as storage of SOPs. SOPs must be reviewed regularly, and having them all in a central and version-controlled environment was incredibly useful for us. Additionally, sample data needs to be kept and maintained for several years after processing, which is much easier to do with a LIMS. Combining our LIMS and some integration software allowed us to create a completely paper-free lab from process start to data delivery and comply with relevant HIPAA and CLIA regulations. 

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Q: From what I understand, you have both internal and external clients. Can you tell us more about the external clients and what kind of companies use your services? 

A: Our external clients, including Mitre, Align to Innovate, and Draper Labs, are interested in long-term projects highlighting specific initiatives in the larger synthetic biology community. They are also interested in proof-of-concept activities that combine multiple services, material transfers, and data analysis. 

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Q: What AI tools is DAMP Lab considering, and how do you predict AI will impact your services?

A: There are two broad ways that AI can help at a cloud lab, such as DAMP. First, it can help you learn about what you have done and suggest that you bias your processes toward or away from what you have done in the past. In the former, it might be moving you toward past successes, processes that save you money since you can “combine” past results/artifacts/etc., and helping you create new things that help you cover the “design space” intelligently. Hence, you have more data that covers more examples to help you further learn. The latter might move you away from duplicate efforts, past failures, or what might be an incremental design.

The second way AI can be used is to examine what users request from the lab. This allows us to preemptively order materials, expand our service offerings and bundles, monitor activity for biosecurity threats, and propose alternative workflows to users based on other successful customer experiences. 

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The Future of the DAMP Lab

The DAMP Lab at Boston University exemplifies a new breed of core labs that transcend traditional boundaries to become innovation hubs within academia. By leveraging cutting-edge automation, extensive molecular biology protocols, and an unwavering commitment to reproducibility and scalability, the DAMP Lab supports high-throughput research and drives it forward. Their unique approach to virtual interfacing and AI integration positions them at the forefront of synthetic biology, offering a blueprint for the future of research facilities. The insights shared by Dr. Douglas Densmore illuminate the lab's pivotal role in advancing scientific discovery and translating academic research into societal applications. As the landscape of life science research continues to evolve, the DAMP Lab’s innovative methodologies and services will undoubtedly play a crucial role in shaping the future of this field.

The DAMP Lab is hosting the 3^rd International Workshop on BioManufacturing Automation (IWBMA) from November 16^th to 19^th at Boston University. For more information about the IWBMA, please visit https://www.damplab.org/iwbma. 

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To learn more about the DAMP Lab, visit www.damplab.org/

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