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Open source tools for multi-source and cross-format academic publishing

I’m working with Sasha Engelmann and Sophie Dyer on the Open Weather platform, an archive and learning resource related to NOAA satellite 🛰 imagery. Sasha just shared a few open source publication tools that were brought to her attention by a friend and fellow artist at her Akademie Schloss Solitude residency, wanted to add them here for further research and future reference.

Manifold: A platform for publishing academic texts online

Manifold is a free “intuitive, collaborative, open-source platform for scholarly publishing”. See their repo on GitHub.

Manifold powers the Fembot Collective including Ada, Fembot’s journal on gender, new media, and technology. Looks like Fembot has been working with Manifold since about a year ago when the platform launched their pilot. Read Ada 16: Emerging Gender, Media and Technology Scholarship in Africa.

It looks pretty cool (and so does Fembot + Ada!). Manifold can bring together a whole lot of different methods of writing such as Epub, Markdown, HTML, and Google Docs. Hence the name Manifold, I guess. This is incredibly useful when bringing the work of different researchers together. Also makes it clear to me that good markup in writing is so worth it.

Manifold wants to make a digital book much more than just a screen version of a physical book, something that can easily fold in explorations, supplements, and other resources that augment the main text. It also incorporates annotation and discussion settings to keep the conversation going.

I’d love to see a book that really heavily uses the platform’s unusual features. Metagaming: Playing, Competing, Spectating, Cheating, Trading, Making, and Breaking Videogames is a featured project that’s worth a look. The chapters are punctuated with metagames they’ve created that you can download and install.

As a reader, I feel that the typography lets it down a bit. I found it hard to read, particularly on larger screens. A slightly narrower maximum width to the main text column would help a lot. Losing the justification and greater paragraph indentations would help too. Manifold does have some theme options, but it doesn’t involve control over the typography.

If your priorities are bringing together content from a wide arrange of sources, incorporating the work of disparate researchers with varying levels of technical abilities, and relative ease of setup (the documentation seems comprehensive), then Manifold seems like an incredible tool. If you need to retain any control over the design though or if you also want print publishing tools, it might not be the right fit for the job.

And probably worth mentioning: I think you’d need at least a bit of technical know-how to get this set up safely and securely. Probably worth getting in touch with Manifold directly if you’re an org since they’re still in beta.

B-ber: A tool for single-source, cross-format, design-conscious publishing

Triple Canopy is a magazine that “resists the atomization of culture”. They’re responsible for b-ber, a tool for single-source, cross-format, design-conscious publishing. Here’s how they describe it in the b-ber GitHub repo:

b-ber is both a method and an application for producing publications in a variety of formats—EPUB 3, Mobi/KF8, static website, PDF, and XML file, which can be imported into InDesign for print layouts—from a single source that consists of plain-text files and other assets. b-ber also functions as a browser-based EPUB reader, which explains the name.

Their text introducing b-ber “Working on our thoughts”—title from the Nietzche quote “Our writing tools are also working on our thoughts” according to the footnotes—is a good read, explains the impetus and a bit about the ups and downs of how it evolved.

B-ber can only consume one input, an extended form of Markdown. This makes it more limited than Manifold in that regard, but the output options are substantial. It’s particularly strong for the design-conscious, the fact that you can import to InDesign and easily theme the browser-based EPUB reader is pretty fantastic. This is exactly the sort of thing I was looking for back when I was working at Occasional Papers!

The reading experience of the default b-ber theme (or whichever they use on their post) is nicer than Manifold in my opinion, it’s just a lot easier to read. There are some snags, but I imagine you could resolve these in a custom theme. Related to that, see their repository of b-ber demos and b-ber theme starter.

It’s definitely worth following the development of this project if you’re in to digital publishing. Their announcement post was published back in December, not very long ago! Excited to see how it develops.

As with Manifold, I think you’d need a reasonable amount of technical knowledge to get this set up. Since it seems to be more of an internal Triple Canopy tool that they’ve kindly made open source for wider use, they probably wouldn’t be able to provide as much support as Manifold might be able to. (This is just a guess though!)

My experience

Though I’ve been tempted, I’ve never built something that was meant to have a digital bookish-ness, everything I’ve developed has had online-first layouts and components in mind. Some sites have had fairly extensive print styles, but that’s usually as far as it goes.

The most common related problem I’ve run in to on sites with long-format academic writing is footnotes. I’ve never come across a CMS that handles footnotes well. Heck, even HTML doesn’t handle them all that well, there aren’t any appropriate semantic elements as far as I’m aware (though there were in HTML3?).

The only easily accessible markup system that works with footnotes AFAIK is extended Markdown syntax. To use extended Markdown on a client site though, A) I have to be sure that the client is on board with learning quite a bit of Markdown (they often are once they understand the benefit, but some are stubborn!), and B) it needs to be compatible with whatever layout system the designer has devised.

I used this approach a while ago on the Jock Kinneir Library site, as of right now they’re using footnotes on the Biography page.

This implementation wasn’t super straightforward since the site couldn’t use a single Markdown field for content, we needed more of a page builder to accomplish the layout. Because of that, I had to do some trickery to recompile the footnotes at the base of the page content as opposed to after each text section. Honestly I can’t 100% remember how I accomplished it… It’s on Craft so uses Twig templates, and I don’t think we had the time to make a custom module that would take advantage of server-side logic. I do remember that it was a bit hackier than I wanted, but it safely accomplished what needed to be done.

If I need to include footnotes or something similar in the future, I’ll probably refer to this comprehensive article on footnotes, endnotes, and sidenotes (via @s3ththompson).


Would be curious if others have come across similar free, open source tools, or if anyone knows of work being done on the HTML spec to get some progress with footnotes.

At any rate, all of the above just reinforces my opinion that anyone who writes, regardless of how tech-savvy, should learn how to write in Markdown at minimum, ideally the extended syntax. If your archive of writing is in a machine-readable format, you’re miles ahead should you ever wish to publish it somewhere remotely digital or want to convert it to an IDML file or something similar.

Edit 24 September 2020: Added link to article about sidenotes.

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First swim in the Pacific in… 10? 15 years?

A distant woman standing in the surf at Baker Beach

My first swim in the Pacific in probably 10–15 years, photo by Sam.

On the Fourth of July, we walked 10 miles from the Sutro Heights Stairs on Balboa Street through Land’s End, past the enormous houses near China Beach, paused at Baker Beach, dipped down to Marshall’s Beach, walked under the Golden Gate, along Crissy Field and through the park at Fort Mason, then took a rest at the Maritime Museum ampitheater before heading back.

I thought I did so well with sunscreen but oh my, the backs of my knees…

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Command to delete all `node_modules` directories

How to delete all node_modules directories from your computer

Sam just pointed out this article, so useful! I ran the command to check how much space my node_modules folders are taking up, it’s 6.2G in total. Probably more on my external drives. Not necessary for sites I haven’t touched in quite a while (particularly since I’m still trying to keep my old laptop kicking…).

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“I propose to take our countrymen’s claims of American exceptionalism seriously”

America believes itself exceptional, the greatest and noblest nation ever to exist, a lone champion standing between the white city of democracy and the terrorists, despots, barbarians, and other enemies of civilization. One cannot, at once, claim to be superhuman and then plead mortal error. I propose to take our countrymen’s claims of American exceptionalism seriously, which is to say I propose subjecting our country to an exceptional moral standard.

Ta-Nehisi Coates, Between the World and Me

Many passages in Between the World and Me are worth quoting, but this one really hit home. Coates also brands this “patriotism à la carte” in his Atlantic article “The Case for Reparations” (see below).

This blind national pride has been particularly painful to many people recently with the wildly inadequate pandemic response, the killing of George Floyd, unmarked federal officers’ violence in Portland, and so many more recent events.

I’d forgotten about how very pervasive it is until I got back to the US in early June. It’s insidious, sad and borderline delusional. And it’s not just a right / conservative thing.

It’s all well and good to be proud of your accomplishments, but if you can’t identify and work to rectify your failings then what the hell is the point?


I’ve been speaking with some friends about this book, they mentioned a few resources I’d like to follow up on.

And I’m still working through my previous list.


I just finished “The Case for Reparations” and learned so much.

Coates weaves together individual and collective experiences, history, and data to connect the dots between the Jim Crow South, the Great Migration, redlining by the Federal Housing Association following the New Deal, the efforts of the Contract Buyers League, Belinda Royall’s early and successful petition for reparations in 1783, John Conyers’s HR 40 bill, the early history of slavery in the US, the failure of Reconstruction, the levelling of Tulsa’s “Black Wall Street” and its subsequent suppression in law and the media, the myth of fatherhood as the antidote to Black poverty, the fuzziness of affirmative action, the “gulag of the Mississippi” Parchman Farm, the impact of Germany’s post-WWII reparations on Israel and the evolution of contemporary Germany, the prevalence of subprime lenders preying on Black home buyers in the run up to the 2008 crisis, and so much more.

He argues for the cooperation of every aspect of society in a real discussion and debate about reparations to “reject the intoxication of hubris” and bring about “a revolution of the American consciousness, a reconciling of our self-image as the great democratizer with the facts of our history”.

HR 40, the Commission to Study and Develop Reparation Proposals for African-Americans “to examine slavery and discrimination in the colonies and the United States from 1619 to the present and recommend appropriate remedies”, has progressed since Coates wrote “The Case for Reparations” in 2014. Texas Representative Sheila Jackson Lee is now first sponsor of HR 40 having taken over from John Conyers in 2018. There has been some progress with the bill, but a vote has not been set.

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“You are a nesting doll. All the people you have been before are still inside you.”

You are a nesting doll. All the people you have been before are still inside you. Some yelling, still needing to be understood about the big shit that happened to them.

– – –

The Quaker clearness committee is a small group of people you take a personal issue to. They are prohibited from offering “fixes” or advice. For 3 hours they pose honest, open questions to help you discover you truth.

– – –

Mimetic theory is a concept developed and advocated for by René Girard, 20th-century French anthropologist. Mimetic theory’s key insight is that human desire is not an autonomous process, but a collective one. We want things because other people want them.

As more and more people want something and that object remains scarce, there is a conflict.

This began as a natural phenomenon: animals and humans learn by imitating other members of their groups, but neither humans nor animals are able to differentiate between good, non-acquisitive mimesis (learning skills from others in your group) from bad, acquisitive mimesis (desiring scarce objects – money, fame, power, someone else’s mate, etc.)

Girard believed that historically human societies managed mimetic conflict through the scapegoat mechanism. If the conflict over a scarce object became too intense, the community subconsciously choose a scapegoat which was sacrificed (literally or metaphorically).

– – –

I don’t believe believe the world is made of quarks or electromagnetic waves, or stars, or planets, or any of these things. I believe the world is made of language.

Terence McKenna

From a particularly good Kleroteria I received today. The writer decided not to include any personal identifiers so I’ll leave it unattributed.

More on mimetic theory here.

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Finding the rhythm

I’ve finally fallen in to a decent daily rhythm, it’s taken a while post-move.

My ideal routine seems to involve being at my desk around 8:30am, then calls and correspondence with UK+EU clients and collaborators until 10 or 11.30am (depends on the day). A bit of toast or something, then try to get my head down on a particular dev task for 1–2 hrs before lunch. Not a lot of time to finish any one thing, but can usually at least progress with something. This is a good window for writing, actually! After lunch, a bit more correspondence with folks in North America and then try to get my head down again until the end of the day. That’s usually when I get the most tricky stuff done.

Of course not every day looks like that, but I think that’s what I need to aim for. When it’s thrown off, particularly when I have to interrupt the head-down time for some reason, I tend to feel like I haven’t accomplished anything in the day. Which is garbage, b/c of course I have got some stuff done. Still, it’s not a nice feeling.

Also I was doing so well with exercise before we moved, now have fallen of the horse. Need to work that back in somewhere.

I also need to be careful about not working too long of hours… It seems easy to slip in to overworking during lockdown since there’s SO LITTLE TO DO. But inevitably I start to feel burnt out after a few days of carelessness, even if the overworking is on projects I’m super thrilled about. Just need to keep tabs on it.

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Commonplace WordPress theme

I’ve been gradually updating the WordPress theme that powers this site with the help of a very talented designer and thinker, my friend Bec Worth.

It began with conversations about overhauling her own site. She had a few disparate Tumblrs with a ton (and I really do mean a ton) of great references, photos, and more that had accumulated over the years. All of them had fallen in to disuse for one reason or another, but she still felt like some sort of outlet for collecting these sorts of snippets and longer-format writing would be really useful. She brought up the Commonplace book as a particular inspiration. I’d never come across it before but it really resonated.

We continued talking about her site, and I started to restructure my old color-heavy Notebook theme (view in Wayback Machine) to strip out the less necessary functionality, improve the accessibility, etc. I wanted to make it something that could be more widely useful to not just me and Bec, but others as well. The early version of this new theme used variable Work Sans (view in Wayback Machine)

She liked where it was going, so we got her set up on a WordPress instance and used the Tumblr importer to pull in all of that old content. Since then, we’ve been using her log and my site to test out ideas and continue pushing the idea of what a Commonplace Book could be on the web. For more along these lines, I recommend reading her post “What would a Commonplace Book feel like on the web?

What’s next

It’s far from finished. The type is nowhere near as tight as Bec’s designs, I need to spend a bit more time on that! Amongst other things, I need to clean up the table of posts, add a thumbnail view, and improve the gallery block styles. We’re also going to figure out a way of highlighting work and other projects, something that draws a bit more attention than normal posts.

And color! We’d like to make it possible for people to select preferred text colors, maybe on a post-by-post basis or per category. Color is tricky though, I’d like to preserve some baseline of legibility and I’m not sure how much I could do as the developer to enforce that. Also, how do we handle this if we introduce dark mode support? The HSL or LCH color spaces might be helpful.

I’m not planning to submit this to the WordPress theme directory. Right now, this means that installation and updates are pretty manual, the theme has to be uploaded via FTP before it can be installed. Because of that, I’ll eventually set up an update server so that anyone using the theme can perform one-click updates from the WordPress admin area. Note to self: see this article for more on how to do this.

Realistically, people using the theme might want to change up certain aspects of the theme to be more “them”. Instead of adding a ton of theme options like font pickers and that sort of thing, I’d like to encourage people to tinker with it themselves. This is going to require a bit of documentation to point people in the right direction. I’ll probably start with how someone with little-to-no CSS experience could go about changing the font (i.e. upload font files in the Media library then add the necessary CSS lines in the Customizer, or setting up a child theme).

Clearly, it’s a work in progress!

But anyone is welcome to give it a try for themselves. I recommend it if you’ve been looking for a place to keep important references or get thoughts out of your head. Head to the commonplace-wp-theme GitHub repository to download it and read a bit more.

If you do end up using it, we’d love to know.