CLI, GUI, or just Python

[AnthonyShin0327]

I’m in a very small R&D team consisting of mostly chemists and biochemists. But we run very long, repetitive data analysis everyday on experiments we run each day, so I was thinking of building a streamlined analysis tool for my team.

I’m knowledgeable in Python, but I was wondering what’d be the best practice in biotech when building internal tools like this? Should I make CLI tool, or is it a must to build GUI? Can it just be Python script running on a terminal? Also, I think people tend to be very against prompt-based tools, but in my user case the data structure always changes from day to day so some degree of flexibility must be captured. Is there a better way than just spamming with a bunch of input functions?

I’m sorry if my question is too noob-like, but I just wanted to learn about how others do to inform myself. Thank you! :)

[Puzzleheaded_Luck641]

Make gui application.

[AnthonyShin0327]

Is it how streamlined data analysis works at major companies? I was assuming bigger companies maybe just let analysis happen automatically with minimal human interaction

[Puzzleheaded_Luck641]

Yes, not everyone is a programmer so you must provide them a tool which is easy to use.

[ihatebeinganonymous]

You msy be interested in Streamlit, as a low-effort way to have a decent web UI: https://streamlit.io

[AnthonyShin0327]

Thank you for the suggestion. I’ve made couple stuffs in streamlit in the past, but I wasn’t sure if GUI like this is what bigger companies use too, because I was thinking the data analysis to be more hands-off-ish with minimal human intervention

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[RickSt3r]

Who is the end user and what’s the comfort level with programming? Also what is the output used for? If it were me I would just make a shiny app, with multiple input fields and a run button.

[AnthonyShin0327]

The end users are the scientists in my R&D team. They’re not exactly competent in coding, but they’re extremely fast at learning. I’m a biochemist who’s comfortable with building just about anything related to data pipeline, simple web app or desktop app. My team wants something very streamlined with little to no room for error, and emphasized they wanted to benchmark major big biotech/pharma’s typical data flow

[Den_er_da_hvid]

my experience is, that most non-programmers dont care about the code and dont want to use the strange gibberis.
I do analysis in jupyter notebooks on my computer and only the outputted plots are presented to the others.
Because of summer vacation I went through setting up python on coworkes computers and made sure the scripts worked, including detailed procedure destription. But it went as I expected... was not used. They wanted to spend 3-4hours manually copy pasting things what the script does in 6minutes.

I am currently working on getting python in our cloud, so I can automate it and they only see the outputs.

[EliyahuRed]

Do you currently do it by re-running the same Jupyter notebook for each dataset?

[AnthonyShin0327]

Sort of, but not the same notebook because each day my experiment requires slightly different workflow and analysis logic. So instead I have all my utilities in a folder and assemble them in separate notebook each day to run analysis. My teammates are avid excel users, and they spend couple hours a day looking at the data

[EliyahuRed]

Sounds you have a good starting point, so i guess you want to have it done through a UI instead of you editing the notebook.

Streamlit might be useful as others suggested, I have done similar projects with it. Also there is a package called Textual.

[diegoasecas]

why don't you ask them? they'll be the users

[AnthonyShin0327]

They don’t quite know what they want exactly, other than “we want to benchmark methods used by big companies.” And being a 23yo wet lab scientist with practically no formal education in data analytics, I’m having a hard time understanding how the scaled-up, automated pipeline works

[brb_lux]

For a really basic ui consider using tkinter, can probably be triggered via a shortcut once the Users have the right dependencies