bonito VS httm

There is a technology called Nanopore. I’ve never used it myself but the concept was to be able to sequence samples of nucleic acid out in the field. A quick pubmed search indicated that it can detect miRNA, but maybe with some modifications. https://nanoporetech.com Best of luck with it!

> An unpopular opinion: there are too many other logos that look like the original logo

There are also too many logos that look like the new logo. The first blue circle logos that spring to mind are Blue Circle Cement/Tarmac/Lafarge [1] and Oxford Nanopore [2].

[1]: https://en.wikipedia.org/wiki/Tarmac_(company)

[2]: https://nanoporetech.com/

Oxford Nanopore Technologies (https://nanoporetech.com/) | Front end developer | Full-time | Oxford | Remote (UK)

Oxford Nanopore Technologies is headquartered at the Oxford Science Park outside Oxford, UK, with satellite offices and commercial presence in many global locations across the US, APAC and Europe. Our DNA/RNA sequencing platform is the only technology that offers real-time analysis (for rapid insights), in fully scalable formats from pocket to population scale. Our goal is to enable the analysis of any living thing, by anyone, anywhere.

Tech stack: Electron, Stencil, React, Typescript, RxJS, GRPC

For more details, please email: [email protected]

Ok this isn't really my area but I know that there are labs/companies performing these types of electrical current disturbance measurements of membrane-type proteins for both DNA sequencing (https://nanoporetech.com/) and protein sequencing (https://www.nature.com/articles/s41587-019-0401-y).

Now nanopore sequencing is solid state and gets much longer reads. https://nanoporetech.com/ and https://en.wikipedia.org/wiki/Nanopore_sequencing

Also best of luck with the basecaller, I will say that the latest guppy versions are very good, both in terms of accuracy and speed, as they are GPU accelerated and the best I've seen in accuracy. You may also be interested in Bonito, a tool to generate your own GPU basecalling model or tweak existing models to your data. https://github.com/nanoporetech/bonito.

My projects and many projects include a THIRD-PARTY-LICENSES.html file when I distribute binaries. See: https://github.com/kimono-koans/httm/blob/master/third_party/LICENSES_THIRD_PARTY.html

The only real advantage I can think of with nested ZFS is that the files in the KVM would obviously be individual inodes in the nested ZFS filesystem and datasets, in addition to the one inode per virtual volume on the hypervisor (or zvol). This would allow for granular file management on the kvm and the use of tools like https://github.com/kimono-koans/httm which is like a command line time machine for ZFS.

> It's worth noting that copy_file_range is used by a lot of things.

Yes, but the trigger feature, block cloning, only landed in the latest 2.2 release. If you immediately hopped on 2.2, and used a system with lots copy_file_range and FICLONE use, yes, you may have a problem (like, as you note, on Gentoo, where this problem surfaced).

Most people were just hopping on the bandwagon. My distro ships 2.1.5, so I have a 6 month wait until this feature lands, so I was just building copy_file_range support into my ZFS apps, right before news of this bug hit.[0]

> There are other things required to trigger the bug that are a lot less common though.

Exactly. My guess is the incidence of this will exceedingly rare for the common user/small NAS user/etc. I've run a corruption detector[0], and what I've found mostly indicates false positives. Some are build artifact fingerprints, which I don't care about, and which were deleted with the next build. The ones with an extant file on another system, I confirmed were a diff match with the origin using `rsync -rincv` and whats on snapshots with `httm --map-aliases`. So far no positive matches.

[0]: https://github.com/kimono-koans/httm

cargo install --git https://github.com/kimono-koans/httm --branch clones strace -f -o stderr.txt -e ioctl -- httm -r -R ~/.zshenv

httm prints the size, date and corresponding locations of available unique versions (deduplicated by modify time and size) of files residing on snapshots, but can also be used interactively to select and restore files, even snapshot mounts by file! httm might change the way you use snapshots (because ZFS/BTRFS/NILFS2 aren't designed for finding for unique file versions) or the Time Machine concept (because httm is very fast!).

All btrfs snapshot tools can have different layouts. It's mostly a nightmare for any one tool to support. Although its not the tool you're looking for, FYI AFAIK httm supports all/most btrfs layouts, but it took more work than necessary to get there.

ZFS only option which requires super user privileges.

[0]: https://github.com/kimono-koans/httm/blob/master/httm.1

httm - Interactive, file-level Time Machine-like tool for ZFS/btrfs/nilfs2