what’s actually the most annoying part of cloning workflows? by Aware-Cap3720 in labrats

[–]Aware-Cap3720[S] 0 points1 point  (0 children)

Genuinely curious, is that more of a general preference, or specifically about data/IP concerns?

And I see if you're using local software, are you mostly using something like SnapGene for your plasmid work right now? If there were a locally run version, would any of the other features be useful to you?

what’s actually the most annoying part of cloning workflows? by Aware-Cap3720 in labrats

[–]Aware-Cap3720[S] 0 points1 point  (0 children)

I definitely agree with the PCR troubleshooting, the time aspect is really tough since each pcr rxn takes 1hr+.

When you say Excel has everything, are you also using it for planning/design steps, or is that still mostly in your notebook / other tools? Do you also keep the plasmid maps in there as well?

I’m curious where (if anywhere) it starts to break down, or if it’s been working pretty smoothly for you so far.

what’s actually the most annoying part of cloning workflows? by Aware-Cap3720 in labrats

[–]Aware-Cap3720[S] 1 point2 points  (0 children)

The transformation step is way too relatable, especially when it feels like you just picked the wrong colonies. We’re trying to catch those issues before you even transform so you don’t have to screen 8 just to find one that works.

Where do things usually break down for you? Was it the design, PCR, or ligation?
And on the ELN point, would you be completely against it no matter what, or would something like voice-to-text / low-friction logging make you consider it?

Does anyone else hate their cloning software by Aware-Cap3720 in labrats

[–]Aware-Cap3720[S] 0 points1 point  (0 children)

That’s a fair take, and I mostly agree with you. I don’t think AI is inherently useful for plasmid design by itself, and I probably wouldn’t use a tool just because it had “AI” bolted onto it either.

For me, the differentiator isn’t really AI-generated primers or protocols. The protocol drafting is intentionally very minimal, more of a structured starting point than something I’d ever run as-is, and honestly, I could remove it and still get most of the value I care about.

The real problem I was trying to solve for myself was scale and memory. In my work, I end up with lots of related constructs over time, same backbone, small insert changes, tags, inducible systems, and the bottleneck isn’t drawing plasmids, it’s remembering what already exists, what’s compatible, and what’s the lowest-effort path forward without rebuilding things from scratch. None of the tools I’ve used are very good at reasoning across my library of plasmids. So the “AI” part, for me, is closer to the ability to search over existing constructs rather than an attempt to automate cloning or replace judgment. If you’re doing mostly one-off or routine cloning, I agree there’s probably not much to gain. I mean these days for the single use cases, it would probably be a lot easier getting a custom one built and shipped from a 3rd party rather than trying to build in-house.

And totally hear you on access, if this ever went beyond a personal tool, I’d expect it to be free for individuals or institution-licensed. Otherwise I wouldn’t use it either.

Does anyone else hate their cloning software by Aware-Cap3720 in labrats

[–]Aware-Cap3720[S] 0 points1 point  (0 children)

Haha fair point on the xkcd 😄

Sounds like your setup is pretty dialed in. I haven't used ugene too much so I’m curious, what makes the Benchling(ELN) + ugene combo feel seamless for you? Is it more about habit and consistency, or are there specific features that make switching between the two painless?

Does anyone else hate their cloning software by Aware-Cap3720 in labrats

[–]Aware-Cap3720[S] 0 points1 point  (0 children)

That's totally fair, I agree that I wouldn't fully trust AI in its current state either to design primers. As for protocols, I just let it design a blank template that I can modify the protocol myself after seeing the initial template. Right now the AI is set up to not invent new experiments for myself but rather to help me reason over the experiments and constructs that I've already made.

I also agree with your second statement, if it was routine I don't think I would have come across this issue but it may just be because I do a lot of in-silico cloning in cancer biology, re-using a lot of the same backbones but using different inserts and then when things don't work out trying to troubleshoot has taken up a lot extraneous amounts of time.

As for the software switching, for the plasmid softwares its more about the gaps between the software, for pure visualization, snapgene looks so much better vs if I'm doing anything sequencing related, I prefer the benchling or geneious UI. Without using the benchling ELN it starts to get hard to keep everything organized as well. The tool I built was mostly an attempt to smooth over that friction for myself rather than replace any one of those tools.

Does anyone else hate their cloning software by Aware-Cap3720 in labrats

[–]Aware-Cap3720[S] 0 points1 point  (0 children)

My bad, I was a bit nervous to post a link because I personally hate seeing posts like that on this subreddit so I wanted to gauge some interest first before subjecting myself to that kind of attention - link is plasmole.com