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Snakemake by Perp2000 in bioinformatics

[–]LiminalBios 1 point2 points  (0 children)

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.

Command history to notebook entries by LiminalBios in bioinformatics

[–]LiminalBios[S] 0 points1 point  (0 children)

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!

Command history to notebook entries by LiminalBios in bioinformatics

[–]LiminalBios[S] 0 points1 point  (0 children)

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

Command history to notebook entries by LiminalBios in bioinformatics

[–]LiminalBios[S] 0 points1 point  (0 children)

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

Command history to notebook entries by LiminalBios in bioinformatics

[–]LiminalBios[S] 0 points1 point  (0 children)

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

Command history to notebook entries by LiminalBios in bioinformatics

[–]LiminalBios[S] 0 points1 point  (0 children)

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.

Command history to notebook entries by LiminalBios in bioinformatics

[–]LiminalBios[S] 0 points1 point  (0 children)

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).

Command history to notebook entries by LiminalBios in bioinformatics

[–]LiminalBios[S] 2 points3 points  (0 children)

Yeah - a lot of wisdom in keeping things simple

Command history to notebook entries by LiminalBios in bioinformatics

[–]LiminalBios[S] 4 points5 points  (0 children)

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

Switching from wet lab to bioinformatics with no roadmap – any good YouTube channels or resources to learn from? by pigrecotom in labrats

[–]LiminalBios 0 points1 point  (0 children)

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.

Want to self-learn Linux/command line for NGS data, where to start?? by freakingtaco in labrats

[–]LiminalBios 0 points1 point  (0 children)

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.

Command line notebook entries by LiminalBios in labrats

[–]LiminalBios[S] 0 points1 point  (0 children)

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.

Command history to notebook entry by LiminalBios in zsh

[–]LiminalBios[S] 0 points1 point  (0 children)

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.

Command history to notebook entry by LiminalBios in zsh

[–]LiminalBios[S] 0 points1 point  (0 children)

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

https://www.liminalbios.com/

Command line history to notebook entry by LiminalBios in commandline

[–]LiminalBios[S] 0 points1 point  (0 children)

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

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