Notes & Writing
Occasional notes on computational RNA biology, scientific software, reproducible research practice, and the wider RNA field. Longer methodological writing appears here; software releases and project updates are cross-posted from RNA Forecast.
SHAPE and chemical probing data in RNA structure prediction: how to fold with reactivities in ViennaRNA
How SHAPE reactivities go into RNAfold, what the three methods in ViennaRNA do with them, and what probing data change in a prediction and what they do not. Worked example with yeast tRNA-Phe, all...
Run Claude Code with Ollama: ollama launch claude, manual setup, context length, models
Ollama serves Anthropic's Messages API since version 0.14, so Claude Code connects to it directly. The one-command launcher, the manual setup on macOS and Linux, the context-length trap, measured memory needs, a...
Codex CLI with a local model: LM Studio and Ollama setup, models, troubleshooting
Codex CLI has a built-in local mode. This guide covers the flag and the config profile, which local models work for agentic coding and what they need, Ollama's one-command launcher, Linux GPU notes, and the errors...
Connect Claude Code to LM Studio: local LLM setup on Apple Silicon
Connect Claude Code to LM Studio's Anthropic-compatible endpoint and run a local model on Apple Silicon: setup, model choice, context length, and the errors you will actually meet.
How to compute normalized RNA-seq expression from multicov files
Why TPM is generally a better expression measure than RPKM, and how to compute normalized RNA-seq expression from multicov files.
The link between mRNA vaccine design and barbeque optimization
A short podcast appearance on optimization, data sharing, and what mRNA design can teach us about iterative engineering problems.
Functional RNAs in Virology Special Issue
A Viruses Special Issue on functional RNAs in virology, covering structured RNAs, RNA-protein interactions, and RNA-based regulation in viral infection.
Exploring RNA Biology with Deep Learning Algorithms
An RNA Biology article collection on deep learning methods in transcriptomics, RNA structure prediction, and molecular design.
What virus bioinformatics can and cannot tell us about RNA viruses
Virus bioinformatics helps us compare genomes, track outbreaks, and identify conserved RNA elements, but its value depends on careful interpretation rather than broad claims.
Paper announcements are listed on the publications page, which links each paper to its own page and DOI.