Keynote: Towards Modular Open Science (Auditorium)

featuring Rowan Cockett (Curvenote, Continuous Science Fdn) and Matt Akamatsu (Asst. Prof, Discourse Graphs)

Keynote 9:15-10:00 AM

The traditional scientific record—anchored in static, monolithic PDFs and siloed journals—is increasingly ill-equipped to handle the speed and complexity of modern discovery. This keynote explores a transition toward Modular Open Science: a future where research is a continuous, federated, and computable graph of knowledge.

We outline a vision to move beyond isolated papers toward a world of interoperable research objects and introduce how the Open Exchange Architecture (OXA) and Discourse Graphs provide structural standards for this shift and can leverage the AT Protocol as a decentralized backbone. Additionally, we will discuss how tools like Curvenote and Discourse Graphs have enabled researchers to capture the computational origins of research and the granular logic of scientific inquiry in real-time, supporting networked research collaborations. Join us as we outline a roadmap for a modular ecosystem where data, code, and discourse are seamlessly integrated, verifiable, and interoperable.

Speaker Bios

Rowan Cockett

Rowan Cockett is the CEO and a founder of Curvenote (https://curvenote.com), where he leads the development of tools designed to free scientific communication from static PDF documents. Curvenote enables researchers, societies, and research institutes to publish interactive, reproducible, and richly linked scientific content, with a particular focus on computational research. By integrating narrative, data, code, and figures into cohesive, reusable research objects, Curvenote reflects how modern science is conducted.

Rowan is also a founder of the Continuous Science Foundation (https://continuousfoundation.org), a nonprofit organization for the next generation of scientific communication. Through this work, he helps lead the development of shared, open standards, including the Open Exchange Architecture (OXA, https://oxa.dev), which support modular, interoperable, and machine-actionable scientific content. These standards aim to enable experimentation, reuse, and long-term preservation across tools, publishers, and research communities, supporting a more continuous and composable model of science.

In addition, Rowan serves on the steering council for JupyterBook and MyST Markdown (https://mystmd.org), part of the Project Jupyter ecosystem. These widely adopted open-source tools support authoring and publishing of computational and scientific content, and Rowan has played a key role in shaping their technical direction and integration with emerging content standards.

Rowan holds a Ph.D. in computational geophysics from the University of British Columbia (UBC). While at UBC, he helped found SimPEG (https://simpeg.xyz), an open-source simulation and parameter-estimation framework for geophysical applications including electromagnetics, fluid flow, and gravity. SimPEG is now used across academia, national laboratories, and industry worldwide.

Rowan has received multiple awards for innovative research dissemination and open educational resources, including Visible Geology, an interactive geoscience modeling application used by over one million students globally. Prior to founding Curvenote, Rowan was Vice President of Cloud Architecture at Seequent, where he led large teams building computational platforms, visualization tools, and version-control systems for geoscientists.

Matt Akamatsu

Matt Akamatsu is an Assistant Professor of Biology at the University of Washington. He is also the cofounder of the Discourse Graphs Project, an organization supported by the Chan Zuckerberg Initiative and Navigation Fund creating systems and software tools for modular research collaboration in the age of AI.  He is a recipient of the 2020 Porter Prize for Research Excellence from the American Society for Cell Biology, K99 Pathway to Independence Award, and The Experiment Foundation's Beyond The Journal award.

Matt Akamatsu received his PhD in the department of Molecular Biophysics and Biochemistry at Yale University as the first student in Yale’s Integrated Graduate Program in Physics, Engineering and Biology. His postdoctoral work at UC Berkeley (...WIP!)

Building AT Science: Infrastructure (Auditorium)

featuring talks from Ronen Tamari, Maria Antoniak, and Aaron White

Presentations 10-10:45 AM

10:00 AM Presentation

10:15 AM Presentation

10:30 AM Presentation

AI/Data on ATProto (Auditorium)

featuring talks from Martin Karlsson, Dr. Maxine Levesque, and Dr. Sean Jungbluth

Presentations 11:00-11:45 AM

11:00 AM Presentation

11:15 AM Presentation

11:30 AM Lightning

Sensemaking Systems (Auditorium)

featuring lightning talks from Travis Simpson, Alex Garcia-Joyner, and Anish Lakhwara

Presentations 11:45-12:15 PM

11:45 Lightning

11:55 Lightning

12:05 Lightning

Can decentralists cooperate? Rethinking commons and collective action in the age of platforms and AI (Lounge)

a conversation with Laure Haak, Ellie DeSota, and Nick Vincent (tbc)

Discussion 11-12:15 PM

Building AT Science: Community (Auditorium)

featuring presentations from Dr. Emily Hunt, Dr. Teon Brooks, and Dr. Scott McGrath

Presentations 13:15-13:50 PM

13:15 PM Presentation

13:30 PM Lightning Talk

13:40 PM Lightning Talk

Future of Science Social Media (Auditorium)

panel featuring Dr. Scott McGrath, Maria Antoniak, Ariel Lighty, and Ronen Tamari (more details soon)

Panel 13:50-14:30 PM

Sensemaking Systems + AI for Science (Lounge)

demos from Travis Simpson, Alex Garcia-Joyner, Anish Lakhwara, Semble, Martin Karlsson, and Sean Jungbluth

Workshop 13:15-14:30 PM

Social Media Research (Auditorium)

featuring presentations from Jay Patel, Vikas Reddy, Sophie Greenwood, Francisco Carvalho, and Billy Pierce

Presentations 14:45-15:50 PM

14:45 PM Lightning Talk

14:55 PM Lightning Talk

15:05 PM Presentation

15:20 PM Presentation

15:35 PM Presentation

Your research institution in the Atmosphere

Research institutions face a structural gap between institutional knowledge (formal, slow, siloed) and the personal knowledge networks (informal, fast, distributed) of their faculty and students. The Atmosphere is the first infrastructure that can bridge this gap — not by centralising personal knowledge, but by making both layers speak the same protocol.

Part of Building ATScience (Lounge, 14:45-15:50).

(A repost of v4 of workshop proposal published on my wiki, where the latest version can always be found.).

At the top of my mind is the recognition that the Atmosphere's killer app is not Bluesky - it's interoperability. But it's not enough to have some of your staff using interoperable Atmosphere apps - it requires coordination and knowledge management techniques to get the most out of it.

So in this session we'll try to pick up ideas from all the sessions preceding it, and weave together some ideas and practical steps for research organisations seeking to get the most out of the Atmosphere.

I'd really love your ideas before the event so I can give you the floor on the day, so please post a comment here and/or select some text, click "Share via Bluesky" and post your comment or question to Bluesky, adding @mathewlowry.eurosky.social to ensure I spot it ;)

Opportunities

The Atmosphere provides new opportunities for all organisations to better integrate institutional communications, knowledge management and sensemaking with the personal communications, knowledge management and sensemaking of their staff (past, present and future). For educational institutions, moreover, their students may offer another layer of opportunity.

Getting this right could allow your institution to better tap the knowledge and networks of your staff and students, reinforcing research communities and knowledge transfers. There have been several technological solutions to exploiting this opportunity, from centralised knowledgebases to linked data. I want to explore whether the Atmosphere provides better answers.

The key differences are:

• The institution doesn't have to own knowledge to benefit from it

• Staff/students don't have to donate anything, or even make extra effort to contribute knowledge - it flows frictionlessly from their personal data servers (PDSs) if they choose

• When someone leaves your organisation, connections don't have to break.

Challenges & Solutions

Exploiting this opportunity fully, however, means interlinking infrastructure (HR systems, website content management and other IT infrastructure) and encouraging/training staff in the use of a variety of Atmosphere apps, from Bluesky to Semble, Margin to standard.site.

I think, however, that this makes it sound harder than it is. Moreover, you don't have to do everything at once - like any programme, one should start small and build over time, learning as you go.

Custom feeds & Starter packs

Last November in Berlin for example, I explored what I now see as many organisations' first real step into the Atmosphere: using Bluesky starter packs and custom feeds, an organisation can both create a powerful Bluesky presence and benefit from the trust in their faculty's personal networks to convene highly valuable conversations arounds topics of importance to the institution.

Building on the personal networks of faculty, this can amplify the work and reputation of the institution and its faculty, and help the institution discover new knowledge and build better networks.

More: How newsrooms, scientific institutions & governments can best use Bluesky (November 2025)

Website as community scaffolding

The above strategy, however, is building entirely within Bluesky. Benefiting from other apps requires using your institutional website as scaffolding to integrate your community of staff and students, the apps they use, and the knowledge and networks flowing through them.

Your website, in other words, should be much more than just an online brochure - it should become a node in the Atmosphere, and a "homebase" for your institution's community and the knowledge they're sharing and discussing.

When I first started exploring this, I discovered that farming out your website's interactivity to the Atmosphere brings you greater reach and engagement, while radically simplifying your website publishing technology (Simple sites, powerful communities). I suspect this is just the tip of an iceberg.

Collective knowledge discovery

Note that that pattern only involved standard.site and Bluesky, and there's much more to the Atmosphere than that.

I'm wondering, for example, how an organisation could aggregate its community's use of Semble, Margin, Skysquare and Seams (all being presented in Vancouver) to tap into the community's collective sensemaking and knowledge discovery, and then add value to it somehow.

Similarly, tools like Sill allow individual users to discover knowledge popular with each user's social graph. What would happen if you aggregated this knowledge together in a form of collective listening?

Knowledge publishing

Unsurprisingly there's a lot going on in the Atmosphere for scientific publishing.

An early workshop, for example, will include a presentation of Chive: "a decentralized preprint service featuring threaded review, formal endorsements, and a community-curated field taxonomy - all as portable ATProto records users own".

With Chive, each researcher's record travels with them as they move between institutions, rather than being locked into a single journal or repository. But I think it's fair to say that the institution which hosted that research would like it to appear on their website as well.

Moreover, from the sounds of it a "community-curated field taxonomy" sounds like distributed sensemaking, echoing the collective listening made possible by Sill, but applied to scholarly categorisation rather than news and links.

Similarly, Morning Session 2 will see:

• "Automated science coordination with ATProto", which will present ATProto as "a core component of the coordination.network stack... [enabling] direct nano-publishing from the lab bench" -

• "atdata: Distributed datasets over atproto", which will explore "how atproto enables a step-change for the use of large-scale, distributed, open, interoperable scientific datasets"

What I love about all of these apps is that while the data on them is owned by the researchers who put it there, it can not only be used on the app itself. The content's on the users' PDSs, and so can also pulled into other apps, where it can be combined with other knowledge from other apps to add further value.

This is where the idea of University website as scaffolding might become useful: with a University's various researchers creating content on a variety of different apps, it might be helpful to bring it all together in a single website, while respecting the researcher's ownership of the data.

Suggestions, Questions?

As mentioned before, please help me flesh this out before the event - I would be very happy to give you a slot in this workshop.

Either post a comment here and/or select some text, click "Share via Bluesky" and post your comment or question to Bluesky, adding @mathewlowry.eurosky.social to ensure I spot it.