Should I buy a new apple M1-max with 64Gb Ram for single cell RNA seq analysis?
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6 weeks ago
tg02081300 ▴ 10

Hi everyone,

Apple has released the new generation of apple sillicon macbook pros, and honestly I'm impressed. Do you think it's reasonable to purchase a MBP equipped with M1-max chip, 64G Ram, and 2T storage for single cell RNA seq data analysis? I really wish any professional bioinformatist from this forum can share their idea, or even post some testing videos when they get this new model.

thank you

Best

cell single seq M1 apple scRNA-seq max RNA • 972 views
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Genomax made an in-depth review of apple M1: Apple M1 processor for bioinformactics . My impression is that it is a great all-around computer, but the heavy stuff should still be done on remote server.

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Thank you all for sharing your opinions. I basically have calmed down, and in deed, i do agree that remote server can be more efficient and future proof.

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5 weeks ago
GenoMax 110k

Sometimes we purchase things because we like the idea of having them rather than considering their actual utility. In this case the purchase would fall somewhere in the middle.

It would be a fine overall computer that will give you years of service as long as you take care of it but don't buy it for specifically doing scRNAseq analysis. As others have noted, depending on the size of the datasets there may be parts of the workflow that you can certainly run on the laptop you describe. Once you have various count matrices those should be amenable to analysis with R on the laptop locally.

If you need a laptop at present and can afford to spend the extra money then you will not be disappointed.

Anandtech has a technical review of M1Max. It is a beast of a chip. A Mac Pro whenever it appears should have a chip better then this.

Note: Apple is not building these for bioinformatics. MBP's are being targeted to creative professionals (video/audio etc). Which is why M1Max gets double the GPU/encoding/decoding/memory, while its CPU core count stays the same.

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6 weeks ago
5heikki 10k

It's way more cost effective to carry out heavy stuff on headless servers. They're also far more future-proof as things can be added/upgraded later on. With laptops you're generally stuck with the soldered components you initially chose.

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5 weeks ago
lethalfang ▴ 80

I generally don't like to use laptops for serious bioinformatic work. scRNAseq analyses that involve a large number of samples will require days or weeks of continuous heavy load on a single computer. A laptop isn't really designed for sustained heavy load. The CPU heats up and a laptop doesn't have good ventilation, and the CPU will throttle its own speed to cool itself down. The kind of sustained high temperature and heavy IO load can really shorten the laptop's lifespan.

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5 weeks ago
4galaxy77 ★ 1.2k

Short answer if all you are concerned about is bang for your buck: absolutely not. Save the money and use a HPC instead, it will make your life much easier for the reasons others have mentioned.

That said, there's nothing wrong with getting the MBP, particularly if you need to use it for other things (presentations etc), it's just not the most cost efficient way to get your work done.

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It's presumably a good if not excellent machine for prototyping. Two days ago, someone approached me with a similar question. I was convinced the MBP hhas to be completely overpriced and looked for machines with comparable specs from other vendors but realised that the 64 GB mobile workstations I found lie in a very similar price range.

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27 days ago
Igor ▴ 40

I have another take on this: it's absolutely worth it. Running on HPC most often means non-interactive workflow where you run a script and can't see the result immediately (unless there's a high-mem Jupyter instance available). At the moment, I'm running Seurat with Jupyter on a virtual machine in the cloud. Integrating 30-40k cells requires about 25-30G of RAM. So with 64G you can process even more than that. Scanpy is much more modest, so you'll be able to analyse larger datasets.

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it's absolutely worth it.

We are not disputing that part. If past is any indication, Apple supports their hardware for a long while and the computer is likely to provide years of service (as long as it is properly cared for). If it is financially feasible then by all means one can buy a MBP (my understanding is that mainly US institutions buy computers for employees, where as elsewhere people may be using their own funds) . All we were saying is don't buy a MBP as your sole machine for the explicit purpose of scRNAseq analysis.

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