Ben Jeffery @benjeffery
Recovering particle physicist, currently in a forest of tree sequences for genomics at the Big Data Institute in Oxford. Oxford, England Joined February 2009-
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Ben Jeffery retweeted
New from @jeromekelleher group aiding the analysis large-scale genetic variation data directly from cloud-based object stores Analysis-ready VCF at Biobank scale using Zarr doi.org/10.1093/gigasc…
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Ben Jeffery retweeted
Very happy to announce that the VCF Zarr paper is now published at GigaScience! academic.oup.com/gigascience/ar… See below for a tweetorial based on the preprint.
Very happy to announce that the VCF Zarr paper is now published at GigaScience! academic.oup.com/gigascience/ar… See below for a tweetorial based on the preprint.
Ben Jeffery retweeted
🎉 tskit 0.6.0 is released! 🎉 Thanks to our wonderful contributors, this is a bumper release. Read all about it at: tskit.dev/news/20241106-…
Finally our pilgrimage is complete. 🙏 And yes, it is surprisingly cooked! @thewheatgerm @adamhchase @wendoverpro
Really interesting, cooling with tropospheric SO2 release.
Really interesting, cooling with tropospheric SO2 release.
Ben Jeffery retweeted
Rome had centuries of per capita income growth, advances in hydraulics, metallurgy, agriculture, transportation, and stable governance that respected property rights But they never industrialized Why not? What was the binding constraint on a Roman industrial revolution?
Unbelievable, only took over 100 years
Unbelievable, only took over 100 years
Today: 300 leaflets, 212 doors knocked, 4 hours of telling. I am fried! Whatever happens: Witney you were wonderful.
Just pushed a big numbers update to witneypolls.com with all the pollsters final predictions for Witney!
Witney is a close race, so your vote really matters. I've made witneypolls.com to bring together all the latest predictions to help you choose.
Ben Jeffery retweeted
Excited to share my latest preprint (with a stellar band of collaborators), where we map the VCF data model into an efficient, cloud-native storage format. Thread follows: biorxiv.org/content/10.110…
Ben Jeffery retweeted
There's a 1.5 year postdoc position working on msprime/background selection models open in my group in Oxford: my.corehr.com/pls/uoxrecruit… Closing date is **June 12th**, so please do get in contact if you're interested, or send on to anyone who might be interested!
Really enjoying Claude's frustration with its inability to not think about the golden gate bridge.
Ben Jeffery retweeted
I think there is a huge benefit to standardizing a chunked on-disk binary typed arrays (e.g. Zarr) to store VCF data. Then, build bioinformatics and population genomics software on top of this format. bio2zarr is alpha but I'm very excited: github.com/sgkit-dev/bio2…
Finally!
Ben Jeffery retweeted
We have released Python 3.12.0 finally! 🎉🎉🎉🐍 In the CPython release team, we have put a lot of effort into making 3.12 the best version of Python possible. Better f-strings, faster Python, better typing, easier debugging and much more. Get it here: discuss.python.org/t/python-3-12-…
Nice summary of CPU cache effects with pretty graphs: igoro.com/archive/galler…
Attach a profiler to any running python process without code modification. 🤯 github.com/benfred/py-spy I just profiled a long-running process that had started before I even installed py-spy! Thanks @benfrederickson!
Ben Jeffery retweeted
Tweetorial on the recent preprint on inferring ARGs for SARS-Cov-2 with @shingheizhan, @ana_ignatieva, @DrYanWong, @ktmeaton, @benjeffery, @astheeggeggs, @cl_murall and @sarperotto 🧵👇 biorxiv.org/content/10.110…
Ben Jeffery retweeted
How to load 1.27 million Covid genomes, and their complex ancestry, into your laptop in ~1 second. If you're into #bioinformatics, help us improve our new software: virological.org/t/towards-pand…
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