Reply to Open Science notebooks | Ryan Barrett

Replied to a post by Ryan BarrettRyan Barrett (
Notebooks like Jupyter and Observable are great for research, data science, and really any interactive computing or documentation. I want to start using them for ops/SRE projects too. Thomas Kluyver‘s bash_kernel works, but has lots of rough edges. Anyone have any other ideas?

I’ve been watching that space for a few years. Apparently you saw the same article push them into the broader mainstream consciousness. I would mention Mathematica, but you’re certainly aware of it. There are a few other math-related platforms I’ve used, but I suspect they’re not within the realm you’re looking for.

I’ve seen one or two much smaller projects along the lines of bash_kernel, but they’re either in incredibly rough shape or have very limited scopes or very niche uses. There’s a reasonably interesting list of open science related resources on GitHub, but it’s a tad old and some of the projects on it have merged or changed drastically since it was started. Foster has some interesting material and resources on open science if you care to dig through it. One day I’ll delve into the Open Science Framework to see if they’ve got anything I haven’t seen before too.

I keep meaning to document people who are using their own websites for pieces of this type of thing , but most are doing it in a hybrid fashion. Carl Boettiger is certainly a good example[1][2] and may be aware of some additional resources including one he helps manage.

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reply to tkasasagi tweet

Replied to a tweet by tkasasagitkasasagi (Twitter)

I hope you do blog about it, I’m sure many would find it useful. I’ve been using my own website as a commonplace book for a while now, not only for blogging as you’ve considered, but also to bookmark interesting things, to highlight and make notes of what I read, and generally use it as my online notebook/research/study space. I do post some personal tidbits, but a large amount of what I post (both research and personal) is actually private and only viewable by me. Perhaps worth considering as you continue your studies which others have interest in as well?

Syndicated copies to: and the IndieWeb

A new plugin helps to improve annotations on the internet

Last night I saw two great little articles about, a web-based annotation engine, written by a proponent of the IndieWeb: as a public research notebook Aggregator ― a WordPress plugin

As a researcher, I fully appreciate the pro-commonplace book conceptualization of the first post, and the second takes things amazingly further with a plugin that allows one to easily display one’s annotations on one’s own WordPress-based site in a dead-simple fashion.

This functionality is a great first step, though honestly, in keeping with IndieWeb principles of owning one’s own data, I think it would be easier/better if both accepted and sent webmentions. This would potentially allow me to physically own the data on my own site while still participating in the larger annotation community as well as give me notifications when someone either comments or augments on one of my annotations or even annotates one of my own pages (bits of which I’ve written about before.)

Either way, kudos to Kris Shaffer for moving the ball forward!


My Notebook

The plugin mentioned in the second article allows me to keep a running online “notebook” of all of my annotations on my own site.

My IndieWeb annotations

I can also easily embed my recent annotations about the IndieWeb below:

[ hypothesis user = 'chrisaldrich' tags = 'indieweb']

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