If your collaborators don't want to learn Git/GitHub but you don't want to silo paper writing away from your code and data, calkit.io now has a LaTeX editor and WASM compiler :) #opensource #openscience #reproducibility

If you're building a writing tool for scientists, it's pretty important to make it easy to connect to visualization/analysis tools. That is, if you make users manually upload their data or figures, that's bad.

New blog post: "Conviviality in computational science" blog.khinsen.net/posts/2026/0... "Conviviality matters for science ... if you want to derive knowledge from your work, you need to know exactly what you are doing, and that includes a detailed understanding of your tools." 🧪 #metascience

Instead of compiling a replication package or repro pack at journal article submission time, imagine if you worked inside of a repro pack the whole project... #reproducibility #openscience

@plos.org's concept of the "knowledge stack" in science is interesting from an architectural perspective. Is any layer truly valuable on its own? I'd argue the full stack is the most valuable unit, which means you should be shipping the whole thing with every study. #openscience #opensource

If you know what individual to ask for help in a separate team, you are probably tightly-coupled, and maybe should be part of the same team

The Calkit VS Code extension now allows viewing interactive @plotly.com figures, and includes a gallery view.

If a human is supposed to read it, it shouldn't be written by AI

For those who manage research groups: Do you tend to be more individual-focused, with each member getting their own independent project, or team-focused, where individuals need to find their niche to contribute to a larger collective goal?

Been spending some time on the Calkit VS Code extension. Here's a screenshot using it with Claude to profile CUDA kernels in SLURM jobs and keep track of Nsight reports for each code change: #aiagents #cuda #gpu #claude

AI agents will happily create figures for you. They'll even export some source code. But can you trust that they did what they said they did? Here's a tutorial on how to get your AI agents to work reproducibly: docs.calkit.org/tutorials/ai...

I'm not a fan of splitting up code into a bunch of tiny functions as a default practice. It's like creating a bunch of minor characters in a story. It should only be done if those characters really add something, because each one will take away some attention. #swe #softwareengineering #dev

Made a little poster to "sell" my free software #opensource #openscience #reproducibility

The golden rule of architecture: Avoid moving horizontal slices away from each other, either into different repos or different teams

Maybe we can build more human interfaces for our computing tools without making them nondeterministic and extremely computationally expensive

On one side, you have literate programming, which views code and prose as belonging to a monolithic artifact. On the other, you have total fragmentation with code in one silo, data in another, writing in another, and no real interface between them. I think we need modularity with real interfaces.

Tightly coupled code should not be split across multiple repos #softwareengineering #swe #softwaredesign

IMO, the most important rule for using AI agents to do scientific research: Don't allow them to create artifacts like figures or numerical results on their own. Have them create, save, and run pipelines that create artifacts so provenance is preserved and traceable. #openscience #agentic

Success boils down to properly defining how to measure it then doing as many iterations as possible.

New feature on calkit.io: Comment on publication PDFs and create GitHub issues from them. This was inspired by the process I used to get my PhD thesis done on time. Every comment from my advisor became a GitHub issue and I calculated the necessary daily "velocity" working backward from the deadline.

Super helpful, Google. Thanks. #nodejs

This may be extremely niche, but if you need to run a Jupyter kernel in a SLURM job, e.g., to reserve a GPU, and connect it to a notebook in VS Code, here's a solution: docs.calkit.org/tutorials/vs... #opensource #jupyter #hpc #cuda

The best time to automate your project is 10 months ago when you started. The second best time is now.

One of the limitations of DVC is that it's relatively slow/inefficient working with large folders consisting of many small files. Here's a solution: docs.calkit.org/version-cont... #dataversioncontrol #datascience #python

Is there a parallel to Conway's Law for cognitive load, i.e., that software complexity will increase to hit the cognitive load limit of the team that owns it regardless of the inherent complexity of the problem? #softwareengineering

In support of #OpenScience, we routinely ask authors to openly share their #research #code before publication. We are now formalizing this practice with a mandatory #CodeSharing policy and clarifying what we mean by code sharing.

Quick demo of something I've been working on: Execute some Python, R, Julia, MATLAB, and LaTeX scripts/notebooks/docs and they automatically become a DVC pipeline (DAG). #opensource #reproducibility #datascience

A demo of the new calkit xr ("execute-and-record") feature that will automatically turn a sequence of Python, R, Julia, or MATLAB scripts, notebooks, or LaTeX docs into a pipeline by simply running them. No need to learn Make, Snakemake, DVC, et al. Environment management included!

Why #openscience? Whether or not the input data and processes are described accurately in prose/mathematics doesn't matter if the code and data are included--those become the actual source of truth. A paper is almost never sufficient to describe what actually happened in the research.

If you're stuck with Conda (can't switch to uv or Pixi for whatever reason), here's a way to get a similar experience (no need to create/activate/update environments): github.com/calkit/calki...

What do you do if you're reviewing a paper and the journal policy clearly states all code and data must be supplied, but the authors only share the source code--no input data, no configs, no run scripts, no plotting scripts? #openscience #opendata #reproducibility

This article focuses more on the positive potential of doing open science, but I find it very frustrating how common it is to see openness done in a half-baked, almost performative way. doi.org/10.1073/pnas... #openscience #opensource

Being able to reproduce a computational environment is not the same thing as being able to reproduce the science, but it is an important step

Stop numbering your Jupyter Notebooks and running them one-by-one to deliver "final" results. Turn them into a reproducible pipeline instead: youtu.be/8q-nFxqfP-k #openscience #reproducibility #datascience #jupyter

New JupyterLab extension just dropped! Manage environments and assemble your notebooks into a pipeline all in the UI. Give it a try with: uv tool install --upgrade calkit-python or pip install --upgrade calkit-python docs.calkit.org/jupyterlab/ #openscience #reproducibility #jupyter

What if we had an open-source, decentralized "GitHub for science?" Instead of all the code needed to build the binary of an app or library, researchers would share all of the code, data, etc., necessary to build their papers. #openscience #opensource

Should you put your front end and back end in separate repos? Probably not. You should have at lease one product per repo, and if the front end can't provide value on its own, it's not a product.

Before moving code away from other code, e.g., into a different module, package, repo, etc., make sure it's loosely coupled. If you can't loosely couple it, keep it close together. #swe #softwareengineering #softwaredesign

Check out this cool CFD simulation I did with my "in house code." Just kidding. I faked this in 5 seconds using AI. Are journals requiring source code and reproducibility checks for all submissions yet? #openscience #cfd #aislop

True or false: If your paper can't be reproduced by everyone on your team it's an indication that it could have been done much more quickly. #openscience #reproducibility

NASA's free course "Open Science 101" recently reopened for registration: science.nasa.gov/open-science... #openscience

When I was in grad school and started learning software engineering, I got midway between these. I had multiple instead of one pipeline to run to build each paper but there was no environment management or "staleness detection" for intermediate outputs. Working on making those easy/obvious.

I'm still angry they renamed NREL. Stupid political nonsense.

Has "open science" even been attempted yet? About 10% of articles share code, and of those, maybe 10% share code and data in a way that actually runs. Virtually none are single-button reproducible. We have a long way to go. #openscience #reproducibility

Next year, instead of filing a tax return, I will file a "tax return availability statement": Available upon reasonable request. #openscience #opendata

Couldn't find any extensions for research/analytics project management in JupyterLab, so I started building one. Here's the PR if you want to chime in with your wish list: github.com/calkit/calki... Happy holidays! ⛄ 🎅 #opensource #jupyter #openscience

TIL about ipyflow, which adds a reactive IPython kernel for Jupyter (basically the marimo value prop): github.com/ipyflow/ipyf...

When is closed-source commercial software okay to use for science? As long as it's interoperable with an open file format/protocol? GitHub, for example. #openscience #opensource

Thanks @insidehighered.com for publishing our OpEd w Annie K. Lamar #publicvoices of The Oped Project @ucsantabarbara.bsky.social ! 🤖Open source software & infra accelerates scientific discoveries by removing financial & technical barriers. It's about time we start treating it as a public good👇

For those who think we can solve the reproducibility crisis with policy and education alone, consider the pedestrian and cyclist injury/fatality rate from drivers in the US versus somewhere like the Netherlands. Infrastructure matters. #openscience #reproducibility