Bede Constantinides
@bede
Research fellow at the University of Birmingham interested in infectious disease informatics. Also cycling, photography, active travel.
As requested, Deacon 0.17.0 adds BINSEQ CBQ support. CBQ is a binary sequence format by @noamteyssier.bsky.social that’s tiny on disk, fast to decode, and supports Ns. With CBQ, Deacon can filter sequences at >5 Gbp/s on a laptop (faster than uncompressed FASTA) github.com/bede/deacon/...
I get that airlines oversell flights, but should it not be illegal to pretend that check-in failed due to "technical issues" rather than running out of seats due to overselling? And then to advise checking in at airport when there's negligible chance of flying. Easyjet.
Ever wanted to quickly check host content of DNA sequences? bede.im/sapiometer
Air conditioning is not ventilation. Crisp and dry conditioned air feels fresh but often isn't. Beware of this sensory trickery.
"I'm sorry Dave, I'm afraid I can't …Summarise a document about genomic surveillance"
With lab work done, sequencing and bioinformatics made up the final days of the @artic.network workshop in Ghana
The Viral Sequencing and Bioinformatics workshop in Accra, Ghana is underway! @artic.network
Also presta valves have fiddly removable valve cores. Even if not bent these will leak if loose. Can tighten with pliers if careful. PTFE tape on threads can help too. A drop of water will reveal a leak here.
"Makes no sense for any road users". What about the owners of these six bicycles locked up on Thursday evening @maryoxford.bsky.social ? Are they not road users? Popular already and in spite of damage.
Only took a week for a driver to smash into new bike racks opposite White Hart. Clearly popular though. Bigger bollard needed?
Remarkably swift response from @anneliesedoddsmp.bsky.social and team – thank you
Tip for hybrid Teams meetings: disable background noise suppression so that quiet voices aren't silenced
Deacon can now run in the browser using WebAssembly. Sequence data never leaves your machine. It currently supports FASTA/Q filtering using indexes up to 1GB in size. Demo: bede.im/deacon
TLDR: don't tell an agent that it's deity theshamblog.com/an-ai-agent-...
How AI Impacts Skill Formation arxiv.org/abs/2601.20245 Studied by challenging mostly university-educated Python programmers to use async Python (Trio), so likely quite conceptually challenging. LLM users were barely faster but with a large deficit in skill acquisition. Ouch.
That favourite burger place of yours… ratings.food.gov.uk/business/269...
Great to meet IRL! Thanks for your talk and chats with us in Birmingham too
TIL Deacon decompresses fastq.gz 3x faster than GNU coreutils gzip/zcat. You can decompress, dehost and recompress fastq.gz using Deacon in less time than only decompressing using coreutils gzip/zcat or pigz.
Deacon 0.9.0 can filter FASTA at well over 2Gbp/s on an AMD CPU from 2021. Compression is very limiting, but I suspect ~1Gbp/s is possible for fastq.gz with a modern CPU. Thanks @curiouscoding.nl for a monumental perf PR! Release 0.9.0 github.com/bede/deacon/... www.biorxiv.org/content/10.1...
Dehosting compressed FASTQ at 150Mbp/s on a MacBook github.com/bede/deacon
