How to SNIFF out Good Scientific Software
New PLOS Computational Biology paper: "Ten Quick Tips to SNIFF Out Sustainable and Secure Scientific Software"...
Turn new data into Quarto reports automatically
The {watcher} R package monitors your filesystem and run arbitrary code when files change. You can use this to automate things like creating parameterized Quarto reports....
Closing my tabs, July 10, 2026
Off switches for dual-use knowledge, the PhD admissions drop, a Brown cheating mess, the end of reading, AI labs at the bench, and planning for a "Bio Mythos" moment. 1.7k words, 8 min reading time....
The Simulator That Isn't There
Okay, this is one of those cases where I kvetch about other people not having built the tools I want to use - perhaps a bit of a insufferably egotistical position. I mean, what gives me the chutzpah ...
Dorado v2.0.0 part 3: methylation
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Countable Labs Raises Funds, Heads to Clinic
<div>I caught up by teleconference recently with Countable Labs CEO Giovanna Prout, fresh off Countable Labs' $26M equity fundraising - a round which was oversubscribed. Top on my agenda: what is Pro...
My Comment on OMB-2026-0034
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Fewer Rungs on the Ladder
Automating the analyst's work doesn't turn analysts into principal scientists...
Minibwa is the new bwa-mem
<p>Preprinted <a href="https://arxiv.org/abs/1303.3997">in 2013</a>, <a href="https://github.com/lh3/bwa">bwa-mem</a> is a popular mapper for 100+ bp short reads. It is often the first choice in varia...
Alex Hastie Returns to BioNano, Takes CSO Reins
An interesting news item this week is that BioNano Genomics has appointed Alex Hastie as Chief Scientific Officer. Hastie is an obvious choice for CSO, as for many years he was very much the public s...