Outbreak, a micropublishing journal for collaborative COVID-19 research

How flashpub.io crowdsources science for all researchers.
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Nate Jacobs, CEO of flashpub.io

Science is a crowdsourced endeavor. Publishing research allows the world to see, review, use, and build off of each other's work. Yet the speed of scientific discovery, and the flurry of communications and collaborative interactions that fuel it, has completely outpaced the time it takes to formally publish a manuscript.

That can mean that the bulk of research outputs is left unpublished. It means that the scientific record is a years-long delayed history of past work. To contribute to rapidly evolving lines of inquiry that result in a preprint or journal article, researchers often have to rely on informal and private communications, which means that up-to-the-minute science can be crowdsourced for a privileged few, but largely inaccessible for many others.

The flashpub.io team is building micropublishing journals that crowdsource science for all researchers, are open-sourced, and are free to read and free to publish in. Their focus on smaller, faster articles capture iterative contributions that can be organized into visually compelling, collaborative research stories. The flashpub.io platform is currently being piloted with Outbreak, the micropublishing journal for infectious disease informatics.

Smaller, faster scientific reports

Micropublications are narrowly scoped research articles focused on a single claim. Roughly the size of a single figure, they communicate a single result regardless of its scope, potential impact, or ability to "tell a story."

Our micropublication format includes a single structured claim, a title, a single figure (broken down into panels), a short description written as a results section, labeled references (support, contradict, or extend), and links to detailed code, methods, and data.

We use an open, post-publication peer-review process in which micropublications are immediately visible in an "under review" state, similar to a preprint, and then undergo crowdsourced review. The current criteria for passing peer review is at least three endorsements, no editorial holds (i.e. desk rejection), has been posted for at least seven days, and no valid retraction requests were received. These criteria will evolve and change depending on community behavior to ensure scientific rigor and integrity.

Micropublications are designed to be small, well-structured nuggets of knowledge that prove a single, narrowly scoped result with a high degree of confidence, regardless of relevance or broader impact. This simplicity and lack of narrative is the key feature that allows micropublications to be easily integrated into broader community driven narratives.

Spark a movement with research campaigns

By itself, a micropublication doesn't tell much of a story. If a traditional journal article is a house, a micropublication is a brick. You don't know how or where that brick will be used, but with enough people and the right coordination you may end up with a castle that will stand the test of time.

Research campaigns connect micropublications to bring emerging research stories to life. Like a cross between a GitHub repository and a special issue in a journal, a campaign focuses on a specific research aim and provides the motivation and framework to coordinate the community contributions needed to achieve it.

Dashboard for our first campaign hosted on Outbreak, the micropublishing journal for infectious disease informatics. The campaign focused on county-level COVID-19 forecasts.

The arc of a campaign starts with a research question, builds into a coordinated movement of loosely collaborating independent research groups, and results in a dataset that can be used for meta-analyses, final reports, or maintained as a resource for downstream research.

A roadmap for launching a campaign for a research project with flashpub.io would look something like this:

  1. Discuss and design. Articulate research aims, define data standards, identify points of collaboration vs independent research. Mock-ups for dashboard. (1–2 months)
  2. Finalize leadership team. Decide who the principal investigator is (analogous to ‘first author’) and form a steering committee.
  3. Build community. Slack team, monthly calls, participation guidelines, community feedback on design and structure of campaign. Build and test dashboard. (1–2 months)
  4. Launch. Publish initial micropublications. A live dashboard is generated. Promotion, outreach, press, social media campaigns follow.
  5. Growth. Iterate and improve workflow, submission system, and data visualizations. Build and deploy relevant APIs. Publish major milestones. (6–12 months)
  6. Impact and sunsetting. Provide any materials or resources for grants, journal articles, and other research outputs. Preserve and archive web assets. Promote outcomes and impact analyses. (2–3 months)

The beating heart of a campaign is a simple, compelling dashboard featured on the micropublishing journal for your field (e.g. Outbreak, discussed in more detail below). It serves as a hub to visualize new findings, gather resources, and inspire contributions. The dashboard is automatically populated with micropublications using structured claims, and interwoven with any external data needed for context. The principal investigator and steering committee of the campaign design how the data in context is presented to track progress, highlight trends, and ensure appropriate and rigorous communication of scientific data.

Critical to this architecture is the structured claim expressed in each micropublication. The structured claim, which expresses a single finding and its contextual parameters, allows micropublications to be automatically pulled into a research campaign. In the same way that using a certain hashtag ensures that your tweet will be aggregated for that topic, using a certain claim in your micropublication ensures it will be aggregated for that campaign.

A research campaign articulates an ambitious but focused research goal, designs a framework for harmonizing independent contributions towards that goal, and inspires a movement to make it happen.

Can I still publish a regular article?

Yes! Research campaigns are simply a way to accelerate and build traction for your big ideas. As a campaign takes off, the visibility it generates will improve the quality of your grant proposals and create opportunities to publish in traditional journals for milestones and final reports. Micropublications of methods or other foundational work can be used as references in grants or traditional journal articles.

Outbreak — a new home for COVID-19 informatics research

As the pandemic unfolded on a global stage in 2020, the urgent need to quickly understand SARS-CoV-2, COVID-19, and how it was spreading prompted one of the largest crowdsourced scientific efforts in history. As part of this global effort, the flashpub.io team dove in and launched Outbreak, its first micropublishing journal focused on dissemination of COVID-19 informatics, modeling, and computational research.

The initial community of researchers quickly gravitated towards a missing gap in the COVID-19 forecasts being produced - the lack of local, county level estimates. The emergence of a specific research focal point prompted the Outbreak team to organize a campaign and simple dashboard to support the effort.

After an initial burst of micropublications and a wealth of feedback about our platform and workflow, we temporarily paused new submissions to regroup and calibrate our approach. The most important lesson we learned from that early experience was that campaigns come before micropublications. Micropublications have a relatively high incentive threshold, despite their low research burden. Campaigns help lower that incentive threshold by providing community, purpose, and clear structure for collaborative interactions.

Upcoming Campaigns on Outbreak

We're excited to be working towards an informal "relaunch" of Outbreak that will feature a whole new suite of researcher-led campaigns and calls for micropublications.

The pilots below are in various stages of discussion and development, and represent the breadth of what we hope can be accomplished with research campaigns on Outbreak.

Launching in the coming months, the SARS-CoV-2 Population Immunity campaign aims to track local population immunity (vaccinations + natural immunity) in individual counties. The campaign is being led by Jeff Morgan (principal investigator) and Dr. Prahlad Menon (steering committee lead). The first county estimates are expected to be published in April for three counties in California (San Diego, LA, and SF) and will expand to other counties in the US and abroad. The project is planning to incorporate variant-specific immunity estimates as that data becomes more widely available.

Mockups of SARS-CoV-2 Population Immunity campaign dashboard with placeholder values. A map shows the most recent ensemble output for each target county; clicking on a county opens up time series data of all point estimates for that county.

Almost all published COVID-19 research to date has excluded pregnant women from sample populations. A potential Perinatal COVID-19 campaign under discussion with Dr. Emily Smith would amplify and augment her ongoing prospective meta-analysis that is capturing basic COVID-19 data and vaccine effectiveness for perinatal populations across dozens of sites.

Mockup of Perinatal COVID-19 campaign dashboard main view with placeholder values. Clicking into each panel would display point estimates and other aggregated micropublication results.

The COVID-19 Characteristics campaign, which is still forming a leadership team, will be designed as a consensus seeking workflow for key parameters of COVID-19 and SARS-CoV-2 used for modeling spread and outcomes. The campaign was inspired by and would continue an early effort led by the MIDAS team (https://midasnetwork.us/) to aggregate and form consensus for infection fatality rate. Existing point estimates would be individually structured as "micro-reviews" and new point estimates would be solicited to resolve key knowledge gaps.

Mockup for COVID-19 Characteristics campaign of detail panel displaying placeholder infection fatality rate point estimates, that can be explored by changing which dimension is plotted on the x-axis (e.g. date, region, age distribution).

Code with us

The flashpub.io team is currently refactoring their codebase and would love to work with anyone interested in contributing to our web app. It is a front-end heavy web app built in React (next.js) and uses Firebase for back-end services. The front end has a modular architecture and uses modern web tools.

Get involved

Join the Outbreak community

Friends of flashpub newsletter

Research with us. We'd love to discuss how to build a movement for the research questions you're passionate about. Outbreak is also recruiting members for its editorial board, interested postdocs and faculty. Please check out our application for associate editor of Outbreak.

Partner with us. We'd love to launch a micropublishing journal in the community you support. Whether you're a funder, society, or existing journal there are many opportunities to work together to accelerate research.

Chat with us. Everything else, just ping us on twitter @flashpub_io or @OutbreakScience.


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