Solid project management helped a lab rapidly learn about COVID-19 spread

Project managers can enable scientists to tackle big challenges.

The Sabeti lab and project managers met regularly on Zoom to keep the COVID-19 sequencing project moving.
The Sabeti lab and project managers met regularly on Zoom to keep the COVID-19 sequencing project moving.

On the morning of March 11th, as COVID-19 was taking hold in the Boston area and Broad Institute employees were advised to work from home, if they could, starting the next day, I bumped into an old friend in the elevator at Broad. I first met Bronwyn MacInnis when I was a program manager in the Genomic Center for Infectious Diseases (GCID) at Broad, before I moved to the Stanley Center for Psychiatric Research to lead the center’s project management team. 

Bronwyn is director of pathogen genomic surveillance working closely with Pardis Sabeti, a Broad institute member and a professor at Harvard University and the Harvard T.H. Chan School of Public Health — together they study the genomics of pathogens and how they spread. The Sabeti lab is best known for its genomic surveillance work during the 2014 Ebola outbreak in West Africa, the 2016 Zika epidemic, and a mumps outbreak in Massachusetts. Now it was gearing up to respond to COVID-19. 

As the elevator sped up to the sixth floor, Bronwyn quickly relayed that the lab was supporting colleagues at hospitals and public health labs in Boston and West Africa to set up diagnostic testing and sequencing-based virus tracking to understand how the virus was spreading. Bronwyn said things were ramping up at a furious pace. Then the doors of the elevator opened and she dashed to a meeting. 

Over the next few days, I transitioned to working from home and saw a slight slow down in my usual day-to-day work with the global human psychiatric genomics projects that I and others manage at the Stanley Center. I remembered my brief conversation with Bronwyn and so I emailed her, offering help in the form of operations and project management. With the pandemic quickly taking a grip in Boston, it was apparent that the Sabeti lab would need certain processes and structures to effectively and efficiently manage the complexity of rapidly sequencing and analyzing hundreds of viral genomes. This was something my team and I, most of whom are certified as Project Management Professionals (PMPs), knew how to do. 

Ambitious and complex scientific endeavors, like the one the Sabeti lab was embarking on, require a solid fusion of science and management to make sure every step in the work is well choreographed and executed, with efficient use of resources. 

Recognizing the value of project management in research, the Broad Institute, over the past five years, has been investing in career development, including the PMP certification, of its project managers: scientifically astute staff who are equipped with a formal project management toolkit learned from industry. The Broad has built up a cohort of more than 60 scientific project managers supporting a variety of research labs across the institute.

Bronwyn enthusiastically accepted my offer to help, and she, Pardis and I quickly got to work, mapping out their plans, each of us knowing we were only beginning to appreciate the magnitude of what laid ahead. We were beginning to lay the foundation for work that has led to new insight into the spread of the COVID-19 virus in the Boston area. 

Team science in action

Every big scientific challenge can be tackled by breaking it down into a number of small pieces of work. In project management terms, we call these pieces work breakdown structures. Each work breakdown structure related to SARS-CoV-2 diagnostics and surveillance was going to need an owner to champion it and achieve specific goals while synergizing with the rest of the team. I knew more project managers could help. 

When I asked my fellow Stanley Center project managers — a cohesive team with complementary skills — if they would be willing to dive into the viral world, many agreed with a heightened eagerness and were thrilled to be able to bring their technical skill sets to work on pandemic response, and help the Broad community. 

The business at hand in the Sabeti Lab — establishing partnerships and obtaining SARS-CoV-2 samples for research from partnering hospitals or public health agencies, amending or creating institutional review board (IRB) protocols; developing and testing new diagnostics and sequencing protocols; procuring funds and reagents; analyzing and sharing data — was no small feat. It involved a great deal of coordination of people and processes, without the luxury of a lengthy initiation phase or face-to-face meetings. All personnel, including research associates, had to rapidly shift gears and quickly adapt to an agile work life, and with the blessing of our managers at the Stanley Center, the project managers jumped in with both feet.

These project managers were keen to help the Sabeti lab scale up its work.

Caroline Cusick, who had also worked in the GCID and Broad’s Genomics Platform prior to moving to the Stanley Center, brought expertise to the new sample-tracking needs to manage incoming sample plates. She created a new system that connected to an electronic notebook system so that lab members could easily monitor batches of samples moving through analysis pipelines. Katelyn Flowers, also a former Genomics Platform employee, facilitated sample tracking and walk-up sequencing needs. Felecia Cerrato immersed herself in the management of CARMEN, a diagnostic technology for pathogen detection, to prepare the lab for a rapid scale-up of sample processing for surveillance. Anna Neumann took ownership of the many compliance pieces, including amending key legal and IRB documents, to allow viral sequencing and surveillance work to forge ahead in a safe and ethical manner. I established and ran dynamic meeting structures for the whole team to check in daily on administrative and scientific strategies using tools like Trello and Smartsheet to continually track and monitor progress. Working alongside members from Broad’s Data Sciences Platform, the Genomics Platform, the Office of Research Subjects Protection, and the Office of Strategic Partnerships and Alliances, we collectively navigated the evolving landscape. 

It became apparent from the very beginning that morning check-in meetings were crucial during the initiation and planning phases to parse out the availability, strengths, and interests of each team member, and how they could be deployed to a particular function. Lab members and project managers worked from a virtual project Trello board to break down all of the components into subtasks. Each subtask had one or more owners who were called upon to provide updates in the check-in meetings to track progress. Lab personnel were coordinated into two shift teams to adhere to COVID-19 safety guidelines and maximize their ability to accomplish the work at hand.  

As the team quickly progressed into the execution phases, and batches of samples started moving through the pipelines, the management team supported the emergence of smaller meeting groups that were dedicated to particular functions. Each process had an owner who monitored and managed the quality and time taken for the work, and kept stakeholders informed. We put in place and shared longer term recommendations, optimization protocols, and tracking systems. Lab members quickly realized the benefits of having scientifically minded project managers facilitate all activities. 

These systems and pipelines led to the rapid generation and analysis of data from more than 300 SARS-CoV-2 genomes in June, a preprint in August that builds on this data with even more viral sequences and deeper insight into the spread of the virus in Massachusetts, as well as enhancements in our diagnostics pipeline.  

“The project management team was invaluable in helping us set up a production-style viral sequencing and analysis pipeline, under the most challenging of circumstances,” Bronwyn said. “With a true commitment to their community, they worked tirelessly to establish project and process management solutions that gave us the framework we needed to scale our work and that we continue to rely on today.”

A synergy of science and management

Traditionally, academic labs do not have dedicated project management personnel on staff. The need for this expertise is becoming even greater as many scientific projects are increasingly collaborative and complex. The central dogma of project management teaches us five key processes: initiate, plan, execute, control & monitor, and close. Following this framework requires project managers to be on board from the beginning to map the project out and see the work through to completion, all the while anticipating what will come next. Project managers play a critical role in keeping large projects moving, establishing systems to track progress, solving problems, and communicating with and clearing away roadblocks for all stakeholders.

After Broad general onsite scientific operations began to ramp back up in June, welcoming many researchers back to the bench to work on disease areas other than COVID-19, the Stanley Center project management team returned to our regular roles. I’m happy that we were able to demonstrate the value of technical project management in an academic lab, not only to optimize and manage scientific operations, but also to instill in researchers that agile practices can open up a lab’s ability to rapidly respond to complex challenges. 

“We are so grateful to Sinéad and the team for demonstrating the enormous impact of project management to our COVID efforts,” Pardis said. “We are excited to now have the opportunity to build on this experience and incorporate project management as we launch our new initiative Sentinel at the Broad. Sinéad and the team set a high standard.” 

The Sabeti lab recently hired a dedicated project manager who has taken over many of the systems we helped establish, and continues working on existing and new partnerships. So while future elevator rides will require us to stand six feet apart, let’s bring academic science and project management closer together in our ‘New Normal’.