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bede

499 karma · joined April 17, 2012

Computational biologist. Oxford, UK https://bede.im b@bede.im
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bede··on Uncensored and Offensive Security AI Models Benchmark
Please use a categorical colour palette when visualising data like these
bede··on Two-tier encryption in the UK
Some other comments are discussing this. I just tried it but could still not enable ADP. Perhaps subscriptions etc. additionally require cancellation, as rumoured.
bede··on I hate you Microsoft
I've been using university-licensed Office for a decade across several fresh MacOS Installs. Only in the last year have I started frequently receiving "sign-in to verify license" nags not unlike the OP's. These also cripple editing functionality until you sign in, forcing you to do the 2FA dance every time. The same rot afflicts mobile apps lately. It's such bad taste to perform license checks this aggressively.

Teams is also flaky on the Mac. About 1 in 4 times I join a call Teams gets stuck and I either must restart it or use the browser (which never fails). This has recurred across multiple physical Macs.

bede··on I advertise malicious software on Google Ads
Seems not to be blacklisted, but I see the domain is only 22 days old, so that'll be it I imagine.
bede··on How I advertise malicious software on Google Ads
FYI https://race-term.com is blocked by NCSC's Protective DNS service using my UK University's connection. Are you sure your domain is not blacklisted somewhere?
bede··on Higher social class predicts increased unethical behavior
Thanks for sharing data. I suspect this effect is heavily stratified across demographics.

After a point, how much someone chooses to spend on their car is about their values more than their wealth.

I once lived in a street with many parked cars worth almost as much the houses of their owners. They were clearly bought (well, financed) as status symbols. I now live in a more affluent, desirable area where the cars are much more modest despite higher wealth and social status of their owners (doctors, scientists etc).

bede··on Higher social class predicts increased unethical behavior
"As vehicles are reliable indicators of a person's social rank and wealth"

The wealthiest Europeans I know drive the cheapest vehicles. Modesty is wealth in many parts of the world, but perhaps not in California (the authors are affiliated with UC Berkeley).

bede··on An update on recent Claude Code quality reports
I too would far rather bear a token cost than have my sessions rot silently beneath my feet. I usually have ~5 running CC sessions, some of which I may leave for a week or two of inactivity at a time.
bede··on Backblaze has stopped backing up OneDrive and Dropbox folders and maybe others
Thanks for publicising. I recently decided not to renew my Backblaze in favour of 'self hosting' encrypted backups outside the US. But I was horrified to learn that my git repos may not have been backed up, nor my Dropbox, whose subscription I also recently cancelled. Good riddance.

My experience using restic has been excellent so far, snapshots take 5 mins rather than 30 mins with backblaze's Mac client. I just hope I can trust it…

bede··on I put my whole life into a single database
> Probably obvious for many, but I didn't realize ACs don't transport any air into the room, but just moves it around

I had the same epiphany as you days after acquiring a CO2 monitor. Most people notice poor indoor air quality from proxies such as humidity and temperature. AC (without ventilation) eliminates these and tricks our senses very effectively, giving us cool and fresh feeling indoor spaces full of CO2 and devoid of oxygen.

bede··on How London cracked mobile phone coverage on the Underground
> There’s another distance limit at work here, and that is the speed of light. It takes milliseconds for the signal in your phone to reach the hotel above ground and be handed over to the mobile network.

It takes roughly 100us for light to travel 30km – Can you explain how the speed of light is relevant here?

bede··on OpenZL: An open source format-aware compression framework
For BAM this could be a good place to start: https://www.htslib.org/benchmarks/CRAM.html

Happy to discuss further

bede··on OpenZL: An open source format-aware compression framework
Author of [0] here. Congratulations and well done for resisting. Eager to try it!

Edit: Have you any specific advice for training a fasta compressor beyond that given in e.g. "Using OpenZL" (https://openzl.org/getting-started/using-openzl/)

bede··on Removing newlines in FASTA file increases ZSTD compression ratio by 10x
A Zstd maintainer clarified this: https://news.ycombinator.com/item?id=45251544

> Ultimately, Zstd is a byte-oriented compressor that doesn't understand the semantics of the data it compresses

bede··on Removing newlines in FASTA file increases ZSTD compression ratio by 10x
Fascinating, thank you.
bede··on Removing newlines in FASTA file increases ZSTD compression ratio by 10x
Thanks for reminding me to benchmark this!
bede··on Removing newlines in FASTA file increases ZSTD compression ratio by 10x
Yes, when doing anything intensive with lots of sequences it generally makes sense to liberate them from FASTA as early as possible and index them somehow. But as an interchange format FASTA seems quite sticky. I find the pervasiveness of fastq.gz particularly unfortunate with Gzip being as slow as it is.

> Took me a while to realize that Grace Blackwell refers to a person and not an Nvidia chip :)

I even confused myself about this while writing :-)

bede··on Removing newlines in FASTA file increases ZSTD compression ratio by 10x
BAM format is widely used but assemblies still tend to be generated and exchanged in FASTA text. BAM is quite a big spec and I think it's fair to say that none of the simpler binary equivalents to FASTA and FASTQ have caught on yet (XKCD competing standards etc.)

e.g. https://github.com/ArcInstitute/binseq

bede··on Removing newlines in FASTA file increases ZSTD compression ratio by 10x
Thank you for clarifying this – yes the non-semantic nature of these particular line breaks is a key detail I omitted.
bede··on Removing newlines in FASTA file increases ZSTD compression ratio by 10x
Exactly. The line breaks break the runs of otherwise identical bits in identical sequences. Unless two identical subsequences are exactly in phase with respect to their line breaks, the hashes used for long range matching are different for otherwise identical subsequences.
bede··on Removing newlines in FASTA file increases ZSTD compression ratio by 10x
Yes I'd expect a dict-based approach to do better here. That's probably how it should be done. But --long is compelling for me because using it requires almost no effort, it's still very fast, and yet it can dramatically improve compression ratio.
bede··on Removing newlines in FASTA file increases ZSTD compression ratio by 10x
Yes, it sounds like 7-Zip/LZMA can do this using custom filters, among other more exotic (and slow) statistical compression approaches.
bede··on QuakeNotch: Quake Terminal on your MacBook's notch
Just watched my iPhone 15 battery drop 2% scrolling for <60s
bede··on FP8 is ~100 tflops faster when the kernel name has "cutlass" in it
Thank you, perhaps the parent can be edited to use this URL instead
bede··on Why Android can't use CDC Ethernet (2023)
I assumed that the article must be about a frustrated CDC employee just trying to get internet access at work.
bede··on Spotify will reduce total headcount by approximately 17%
I also lost faith in certain scientists (and many more politicians) during the pandemic. But be wary of generalising about a such a large and interdisciplinary group of people. Voices amplified by the media (indeed like Robert Malone on Rogan's podcast) often grossly misrepresent scientific consensus.
bede··on Spotify will reduce total headcount by approximately 17%
Thanks for the recommendation
bede··on Spotify will reduce total headcount by approximately 17%
Thanks!
bede··on Spotify will reduce total headcount by approximately 17%
Not absolute, but pausing a sub with an explanation sends an immediate message. Which services would you recommend? I'm mostly after a broad and fresh electronic music catalogue.
bede··on Spotify will reduce total headcount by approximately 17%
Depth and breadth of electronic music catalogue and switching cost. Former is probably narrowing rapidly. What would you recommend? Building Apple's future streaming monopoly isn't particularly appealing. Small perhaps, but pausing a sub with explanation sends a clear signal.
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