Gitter Lab Graduate student Milica Cvetkovic is speaking at a Gitter Lab team meeting.

Chronicling pandemic science in real time

In the span of six months, thousands of the world’s trained scientists have pivoted their focus to the COVID-19 pandemic, making it one of the largest and fastest-moving research efforts ever assembled. In this avalanche of new knowledge, how will we determine the right path?

A Morgridge Institute for Research investigator developed a tool that is getting dozens of COVID-19 researchers on the same page, literally and figuratively.

Anthony Gitter

Morgridge virology investigator Anthony Gitter, an assistant professor of biostatistics and medical informatics at UW–Madison, has co-developed a software tool called Manubot to help orchestrate a rapid expert assessment of COVID-19 diagnostics and therapeutics. The tool is contributing to an international effort to organize and consolidate the rapidly emerging scientific literature related to COVID-19. Today, more than 40 scientists around the world are participating.

Manubot was launched a couple years ago by Gitter and colleagues Casey Greene and Daniel Himmelstein at the University of Pennsylvania as a way to invite dozens of voices into a manuscript looking at deep learning techniques in biology and healthcare. The tool allows people both to contribute and critically assess information in an automated and continuously updated manuscript.

Research manuscripts are the ubiquitous communication tool in science, but they are prepared in a closed manner, usually by a handful of people who represent a small sample of knowledge on the topic. It’s almost the opposite direction of where science is moving, Gitter says.

Now two years since the launch, Greene and Halie Rando recognized that Manubot seems almost tailor made to help share and manage information for COVID-19 research, which is rapidly emerging and being tackled across many fields. The program gives scientists access to the latest information, both published and from preprint servers, across a very disjointed group of experts. It gets the immunologists talking to the epidemiologists, the virologists talking to the data scientists, and every combination in between, Gitter says.

“People can decide to spend time contributing to this one big group effort instead of spinning off their own thing, because the group efforts are going to be better for society.”

Anthony Gitter

Gitter says the goal behind the COVID-19 project is simple: “How can we crowdsource expert knowledge about a topic that’s too big and growing too rapidly for any one lab, or any one small team of collaborators, to really know everything? We bring in people who have the expertise to be peer reviewers of these manuscripts, form a collective opinion about them and try to summarize the different approaches that might advance treatment.”

For example, one new Manubot feature pulls in preprint reviews written by the Immunology Institute of the Icahn School of Medicine at Mount Sinai. Members of the institute have been reviewing new COVID-19 preprints — new manuscripts that have not yet been reviewed by scientific peers — giving their expert interpretation on the limitations and relevance of those studies. There are dozens of rapid assessments of different treatments listed in the manuscript.

One of the valuable features about Manubot is it meticulously tracks contributions across all participants, allowing for ways to assign appropriate credit for ideas across such a large group. This helps incentivize participation while also keeping things moving fast and the process transparent. Says Gitter: “People can decide to spend time contributing to this one big group effort instead of spinning off their own thing, because the group efforts are going to be better for society.”

The results of the shared project are likely to result in a traditional research paper in a refereed journal, but Gitter says the deliberative process of getting there is more important. “Certainly putting everything out there in public from day one, when you first have an idea, and then letting anybody see it and contribute and run with it, is an extremely open and transparent way of doing science.”