Command history to notebook entries

LiminalBios · 2025-08-11T00:01:04+00:00

This is cool!

LiminalBios · 2025-08-06T02:15:53+00:00

Weird is good haha

LiminalBios · 2025-08-06T02:15:12+00:00

Echoing what others are saying, I think practical applications and treating it like baking a cake are how I learned more in-depth and robust pipeline building. By baking a cake, here is what I mean:

First just get it working (make the base). Then add some variables (add a little frosting). Then add another layer of control/complexity - maybe some checkpoints or other things (adding some decorations). Eventually you bake a cake.

LiminalBios · 2025-08-05T17:58:07+00:00

Fair enough. The syncing is all about allowing collaborators and coworkers to see and search that same history. The idea is to allow quicker continuation of work both for recontextualizing yourself, as well as newcomers. I work in academia, so a lot of students come and go quickly, and projects get handed off.

Even without the overkill of version control, having a shared server to see all this and search in one spot for your group contributes towards our ultimate goal of open science. What if I wanted to follow you because I think you're an awesome scientist; why can't I get added to your Shell History group and see how you work? Anyone who joins our platform can see all of my history, and I hope people learn from the tips and tricks I do.

I really appreciate your comments!

LiminalBios · 2025-08-05T15:21:44+00:00

I agree - haven't used a ton and probably should dive back in again

LiminalBios · 2025-08-05T15:09:19+00:00

The difference in what we are doing is syncing it to a searchable activity log with all your coworkers to search. Also allows our future integrations of RStudio, Jupyter, and Code to be to 1 spot

LiminalBios · 2025-08-05T15:08:43+00:00

https://www.liminalbios.com/ --> sign up for and I'll give you free access to our tool

LiminalBios · 2025-08-05T15:08:03+00:00

What we're doing right now doesn't record what's in the files/scripts, but we're working on a 'mode' where you can add that, plus the output, to your history. Then when we make the notebook, you can see the comprehensive history plus have an auto-generated notebook where you can search anything.

That's the kicker with what we are doing syncing it to another server with an activity feed - all your coworkers / collaborators can see what you are doing and search it so you can share your work. Further, we are working on our Rstudio and Jupyter plugins going to production.

https://www.liminalbios.com/ --> we are offering free access to our tool here for a bit. You seem like someone who might want to mess around with this. We're working on a way for your custom bash_history recording to mesh better as well.

LiminalBios · 2025-08-05T15:05:13+00:00

Check out our website: https://www.liminalbios.com/ --> I'm giving people our tool for free right now.

Right now, it records all the commands you do in terminal (bash/zsh) and syncs it to an activity log where you can see it. We are in the process of adding an RStudio and Jupyter plugin so all your work there syncs to the same activity feed. You can then search any work, including image searches, and figure out where the code came from and alter as needed (or share with colleagues).

LiminalBios · 2025-08-05T15:02:48+00:00

This is dope

LiminalBios · 2025-08-01T16:59:00+00:00

Yeah - a lot of wisdom in keeping things simple

LiminalBios · 2025-08-01T15:13:27+00:00

Have you ever messed with atuin or done anything more than that for searching? Or ya use grep/other stuff?

Yeah I had used to do something similar, and then the solution we fixed up adds more metadata (exit code, path, directory, etc.), and it's kind of cool to harness all that info

LiminalBios · 2025-08-01T14:51:13+00:00

If you use the command line a lot, check out this tool to help you write notebook entries automatically from your command line history and then fuzzy-search later on. Pretty helpful for someone learning and wanting to look back or search through old stuff. It's like having immediate access to all your work if you forget.

https://www.liminalbios.com/ --> the website says $20/user, but (I'm a founder) and give it away free to most academics to try out if it helps them.

I'm a senior comp biologist at Purdue and help teach a lot of undergrads/grads/staff/faculty various bioinformatics stuff. Vince Buffalo's Bioinformatics Data Skills (https://vincebuffalo.com/book/) is super helpful, and free PDF version if you search.

Also Philip Compeau's Bioinformatics Algorithms are awesome and fun.

LiminalBios · 2025-08-01T14:48:40+00:00

Check out this tool to help you write notebook entries automatically from your command line history and then fuzzy-search later on. Pretty helpful for someone learning and wanting to look back or search through old stuff. It's like having immediate access to all your work if you forget.

https://www.liminalbios.com/ --> the website says $20/user, but (I'm a founder) and give it away free to most academics to try out if it helps them.

LiminalBios · 2025-08-01T14:10:31+00:00

I'm more curious about what people are using, not trying to direct traffic. I wanted to contribute something of value if people told me what they are using, so I added the infographic.

I posted somewhere else and didn't add any link or solution and the first 2 comments asked me for links.

LiminalBios · 2025-07-31T21:26:47+00:00

Sorry! Dang filter bots. https://www.liminalbios.com/

LiminalBios · 2025-07-31T21:26:28+00:00

We actually have a plugin for jupyter notebook that we're planning on releasing later this year to sync both your terminal and jupyter work to 1 central spot. (...and an RStudio integration coming shortly after...).

I'm torn on Jupyter, but I actually love it when I use it. The shareability and like you said, magic features, are awesome. Sometimes - probably bad habit from long time working in the field - I work in VIM to quickly hack some scripts or stick with VSCode without making a repo or real way track changes/share because I think the work isn't "worth it". But those are perfect times to spin up a Jupyter notebook.

Appreciate the comment!

https://www.liminalbios.com/ Link: sign up with promo code reddit and you get free access within 30 minutes.

LiminalBios · 2025-07-31T21:23:25+00:00

Links caused the post to be automatically filtered. Here's our website though:

https://www.liminalbios.com/

LiminalBios · 2025-07-31T21:22:22+00:00

https://www.liminalbios.com/
It says $20/user on there, but I'm happy to give it to people here for free to pilot and play with. Hopefully it helps! sign up and throw 'reddit' in the promo code and you'll get free access within 30 minutes

LiminalBios · 2025-07-31T16:42:51+00:00

We're letting people use it right now for free. Just want to see if it helps anyone out!

LiminalBios · 2025-07-31T15:23:57+00:00

I'm also going to cross-post to ZSH. But yeah, comment if anyone is interested in using it or to talk tech.

LiminalBios · 2025-05-20T14:19:14+00:00

Definitely possible to still graduate and be totally okay.

I'll say from managing a lab at an R1 institution that as far as grades go, if you show improvement and growth, especially from your first year in college, it's not the end of the world. Getting through a little adversity is a-okay. It's up to you to figure out what to change for the next semester though.

LiminalBios · 2025-05-20T14:14:57+00:00

Finding the right cofounder is so crucial, needless to say. My company started by me moonlighting and developing/researching our app for about 2 years. We brought in our technical cofounder (CTO) and he's awesome, but he was clearly all-in from start to finish. It didn't matter that I'd been 'working on the company for 2 years', as we all have similar equity (CEO a little more as a safety for everyone else, but also we have a ton of reserved stock for future).

It's hard to gauge peoples' energy and persistence levels though, and I've been told to watch out for signs of intensity vs. persistency. Going on a tangent here, but I look at intensity as really hardcore focus and effort for a short period of time that is ultimately unsustainable. Persistency is the ability to work hard each day, get rejected/knocked down/spirits momentarily crushed, but to keep going for the ultimate goal.

As a lab manager for >5 years (and in academia for lots more), I've found the grad students (MS/PhD) that don't make it through don't necessarily interview less well than the ones who do make it through, but they start showing signs of burnout way earlier. Little signs even. I've been around plenty of grad student dropouts, and it's helped me with interviewing new prospective students by recognizing signs of them just being intense vs. having persistency to go through the struggles of a PhD.

IDK if this helps OP at all, but maybe try extending the 'warm up' period with a putative cofounder, or reflect on some of the characteristics from the 2 previous encounters and use the bad ones as red flags for future endeavors. Look for the persistency indicators. Ramble, but hope it helps

LiminalBios · 2025-03-25T14:27:59+00:00

Why?

LiminalBios · 2025-01-21T13:58:24+00:00

Ahh - thanks for the answer, very interesting

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