I am deeply interested in problems of collective behavior and future models of open scientific collaboration.

My work since 2011 has focused on designing and building open source platforms which enable people to visualize and interactively explore high dimensional spaces.

I am @colinmegill on Twitter, and open DMs are the best way to get in touch with me.

My bluesky is https://staging.bsky.app/profile/colinmegill.com

My mastodon is https://mastodon.social/@colinmegill

I love backpacking, surfing and parenting 3 boys. I travel frequently and love seeing new places.

Work

Polis

Polis is a real-time system for gathering, analyzing and understanding what large groups of people think in their own words, enabled by advanced statistics and machine learning. Polis has been used all over the world by governments, academics, independent media and citizens, and is completely open source.

The development of novel methods for gathering voice, and the development of the platform were a response to communication challenges within large scale decentralized movements evidenced in Occupy Wall Street and the Arab Spring.

Our startup (also called Polis after the technology) open sourced the technology at the 2016 g0v summit in Taiwan, and the organization transitioned to a 501c3 between 2018 and 2020. I transitioned from CEO of the startup to the board of the nonprofit, called The Computational Democracy Project, which stewards the codebase, the main deployment hosted at pol.is, and the mission and vision.

The AGPLv3 licensed codebase can be accessed on GitHub.

There are now multiple deployments of the technology, including at national scale by Taiwan's government and at city scale by the municipality of Amsterdam in the Netherlands.

Case studies and outcomes have been featured in The Atlantic, NYT, Wired, The Guardian, MIT Tech Review and The Economist among others, and have been the subject of a short BBC documentary as well as featured in multiple books from major publishers.

The foundational paper for Polis (@UsePolis) as a method has been released in a special edition of the journal RECERCA

Huge thanks to@cesifotifor advancing visibility+formalization of the democracy innovation space + for invaluable feedback in the production of the manuscript.https://t.co/ysws1VSctZ

— Colin Megill (@colinmegill)October 4, 2021

Nextstrain

From nextstrain.org: "Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response."

: We are studying new viral mutations in my lab that would never be on our radar without @trvrb and @richardneher Nextstrain

— Hensley Lab (@SCOTTeHENSLEY) March 14, 2017

My personal involvement with Nextstrain began with a weekend evening hack night project in 2014 to pull together real time statistics on the Ebola epidemic. This was very similar, in retrospect, to many of the hack projects that resulted in real time dashboards for COVID.

https://t.co/wCgy8M0hLt is an auto-updating visualization of #Ebola case counts and mortality by @colinmegill et al. pic.twitter.com/sukqUZGIaS

— Trevor Bedford (@trvrb) October 13, 2014

Between 2015 and 2017, I worked with Bedford Lab to platformitize, generalize and expand the nextflu prototype to handle arbitrary viral phylogeny datasets.

Thanks to efforts from @colinmegill, @jh_viz and @richardneher, we're relaunching https://t.co/WjdKmtoIuV today with tons of new features. pic.twitter.com/0xKpjjH5s9

— Trevor Bedford (@trvrb) February 28, 2017

Thanks to @colinmegill, https://t.co/WjdKmtGjmt now better links map and tree. We can show, for example, spread of Ebola across West Africa. pic.twitter.com/ProTVjCwNH

— Trevor Bedford (@trvrb) March 21, 2017

Nextstrain went on to win the Open Science Prize, and contribute to the surveillance of viruses like COVID. I was interviewed by Shirley Wu about the tool and how it's used to monitor virus evolution in March 2020 at the outset of the coronavirus pandemic.

https://t.co/5iPXiYxiZC wins the OpenSciencePrize! https://t.co/T4bbmlgRIE great collab with @trvrb @colinmegill @jh_viz

— Richard Neher (@richardneher) February 28, 2017

Visualize the virus radiating out from China, mutating as it spreads.

Right: map with different strains color-coded
Left: phylogenetic tree, showing how individual strains mutate and diverge

Very impressive work by @trvrb and the group at Nextstrain. https://t.co/p3wkhvtDPL pic.twitter.com/BuoxBaW81A

— balajis.com (@balajis) February 28, 2020

The Nextstrain paper was published in Bioinformatics, Volume 34, Issue 23, 01 December 2018, Pages 4121–4123.

The AGPLv3 codebase is available on GitHub.

Nextstrain has been featured in NYT, MIT Tech Review, Scientific American, Vanity Fair, Bloomberg and won a Webby.

cellxgene

cellxgene is a highly general, MIT licensed tool for visualizing, exploring, and interactivley running computation on high dimensional data (that is, large, sparce matrices, their features, and their metadata).

cellxgene was built for the purpose of enabling pre-publication (benchtop) data annotation and post publication sharing of the many scRNAseq datasets emerging from The Human Cell Atlas, a project described at length in the 2018 MIT Tech Review article The Cartographer of Cells.

Additionally, cellxgene was used to facilate rapid dissemination of many single cell datasets related to COVID-19 illnesses.

The paper, which describes the purpose, features, system architecture in depth, is available on bioRxiv.

The MIT licensed codebase is available on GitHub.

Above screenshot: four million cells interactively visualized from the Survey of Human Fetal Development.

See also: Mapping Cells To Build a Complete Atlas of the Human Body from The Economist.

Talks

Quotes