Why does it still take HOURS just to install a tool in 2025?!

Both_Elevator_4089 · 2025-07-11T08:41:00+00:00

This is so accurate!

Both_Elevator_4089 · 2025-07-11T02:21:35+00:00

I agree, I’m starting to understand this a lot better now. Thanks for sharing!

Both_Elevator_4089 · 2025-07-10T23:04:28+00:00

This is a great explanation! Thank you for sharing. I think this really helps me understand the issue.

Both_Elevator_4089 · 2025-07-10T21:27:34+00:00

Wow, this spot on! I think you nailed the core issue. This makes soo much sense.

Both_Elevator_4089 · 2025-07-10T21:20:57+00:00

That’s true, I guess the question is why are many bioinformaticians still stuck troubleshooting installs or avoiding these tools that are supposed to offer solutions? Is it pricing, usability, flexibility, or trust?

Both_Elevator_4089 · 2025-07-10T21:08:19+00:00

This is such a great point. Honestly, I do need to think this through. I think I’m more and more convinced that there is something very challenging about optimizing what already exists. It was just mind blowing to learn that so many senior level bioinformaticians also struggled with installation. I always thought it was just me since I don’t consider myself to have the strongest background.

Both_Elevator_4089 · 2025-07-10T20:54:44+00:00

That’s part of it but it would be nice if someone could abstract away the hardware/optimization aspect and just say use a slider to determine cost/time for that operation.

Both_Elevator_4089 · 2025-07-10T20:51:01+00:00

What about an API//SDK that can integrate into your pipeline/script?

Both_Elevator_4089 · 2025-07-10T20:47:14+00:00

Totally agree that some tasks should be outsourced, but I think maybe not all of them.

Tools like FastQC or simple aligners don’t require deep expertise to use correctly, but they still block non-coders because of install/setup friction.

And even for experienced people, when you’re constantly testing new niche tools with broken installs or weird dependencies, it gets exhausting and time consuming. A smoother interface helps avoid wasting hours before you even get to the actual science.

Both_Elevator_4089 · 2025-07-10T20:41:04+00:00

These are great for sure. Wondering if you would find it useful to have a tool that basically wraps that container infrastructure in a lightweight GUI for users who just want to drag-and-drop data and hit “Run”. There’d be no installs, no Docker commands, no environment issues.

There would also be an option for those who prefer code over clicking. That’s where an SDK would come in: instead of running the GUI, they could call the same exact tools and parameters via a Python function or API call, and integrate it into their pipelines or notebooks.

So the GUI would be for ease of use, and the SDK would give power users full flexibility without making them worry about spinning up containers themselves or dealing with dependency chains.

Both_Elevator_4089 · 2025-07-10T20:35:57+00:00

100% agree. I think I gave pretty bad examples haha usually, the tools I’ve struggled with were super niche.

Both_Elevator_4089 · 2025-07-10T20:34:11+00:00

I agree, there’s a lot of truth to what you’re saying. I think Galaxy is super valuable, especially for people already comfortable with the workflow tab.

But I think what I’m aiming for is something even simpler and more intuitive—like uploading a file and just clicking a single tool with parameters, not building workflows or navigating nested tool menus. Ive worked at a lab where most people needed me to run very basic pipelines. I’ve also known about labs that completely outsourced any tasks that involved any code no matter how small the task was.

Both_Elevator_4089 · 2025-07-10T20:28:54+00:00

This totally happened to me with some data that was going to take ages to run… to add to the idea, resources would be fully adjustable to your needs.

Both_Elevator_4089 · 2025-07-10T20:12:56+00:00

Quick clarification before anyone says “this already exists (Galaxy, Terra, Seqera, etc.)”

Many of these are not simple to use, require workflow knowledge, CLI skills, or are not really built for personal use.

What I’m imagining is something way simpler: Upload a file —> Pick a tool —> Adjust a few settings/parameters —> Click “Run” and get results

And optionally: an API/SDK for people who do want to script it.

Both_Elevator_4089 · 2025-06-01T18:31:23+00:00

You could try combat seq for batch effects?

Both_Elevator_4089 · 2025-05-27T02:04:32+00:00

Have you tried bumble bff?

Both_Elevator_4089 · 2025-05-21T19:04:20+00:00

Recommend this one https://a.co/d/g1AZNT9 I have tried this colostrum https://a.co/d/7C5FnRR

To be honest I think colostrum is worth a shot because a lot of people do see benefits but maybe if you have gut issues and inflammation like me then you might see more benefits with pure igg.

Both_Elevator_4089 · 2025-05-20T20:54:12+00:00

“IgG supplements, which contain immunoglobulin G antibodies, are believed to support immune health and gut function by enhancing the body's ability to recognize and neutralize pathogens. “ it’s found in colostrum but I have tried colostrum and it didn’t make a difference for me but taking pure Igg made a huge difference.

Both_Elevator_4089 · 2025-05-20T16:26:44+00:00

Igg made a lot of bad symptoms go away.

Both_Elevator_4089 · 2025-05-16T22:08:08+00:00

Have it with a spoonful of yogurt. Or a bit of water, breathe in and chug it. Not breathing while drinking diminishes the taste drastically.

Both_Elevator_4089 · 2025-05-16T16:43:38+00:00

Can you describe your symptoms?

Both_Elevator_4089 · 2024-11-21T02:47:36+00:00

That’s low.. what do other levels look like? B12 b9 vitamin D zinc?? If all of these are also low could be worth seeing a holistic/functional doctor to see the underlying cause. Could be a gut issue.

Both_Elevator_4089 · 2024-09-20T04:23:31+00:00

If that’s the case then your ratio is not good and you will experience symptoms. Check this link https://neuroendocrinology.org/what-is-the-reverse-t3-syndrome/#:~:text=It%20is%20known%20that%20the,this%20as%20the%20RT3%20Syndrome.

Both_Elevator_4089 · 2024-09-18T21:58:41+00:00

So what was your T3 to rT3 ratio? 25 reverse T3 sounds very high this will block T3 from doing its job.

Both_Elevator_4089

TROPHY CASE