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.
Claude Code, Codex, OpenCode and pi against ten local models on a two-Mac exo cluster
I ran Claude Code, Codex, OpenCode and pi against the ten models that are downloaded on my exo cluster (two Mac minis with 24 GB each), with the same one-line editing task for all of them, one...
ViennaRNA 2.8.0: cross-linking data, global probabilities, modified RNA
ViennaRNA 2.8.0 was released on 6 November 2026. Cross-linking experiments can now guide a structure prediction through interval-pair constraints, equilibrium probabilities for base pairs, unpaired stretches and...
RNAplfold tutorial: accessibility in long RNAs
How to compute the accessibility of a region with RNAplfold in the ViennaRNA Package, i.e. the probability that a stretch of nucleotides is unpaired, how to read the _lunp file, how to choose the right maximum base...
Claude Code for data analysis with a cloud model and gpt-oss:20b on Ollama
How to get a reproducible analysis of a small CSV file out of Claude Code, once with a cloud model and once with gpt-oss:20b on a local Ollama server, and how to check the result independently of the agent. Both runs...
RNAfold tutorial: MFE, pair probabilities and ensemble output
How to read the output of RNAfold in the ViennaRNA Package, i.e. the minimum free energy structure, the pair probabilities, the centroid and MEA structures, the suboptimal structures from RNAsubopt, and how to tell...
SHAPE and chemical probing tutorial: folding with reactivities in RNAfold
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 commands included.
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, Ollama and exo 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, exo for pooling several machines...
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.
AI for RNA structure prediction: what deep learning models learn
What neural networks trained on known RNA structures actually learn, why the usual benchmarks overstate their accuracy, what a test on synthetic data revealed about their outputs, and what has changed since 2022.
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.
ViennaRNA training and workshops for researchers, starting in 2027
A series of practical ViennaRNA training modules and workshops is in preparation at RNA Forecast, planned to begin in early 2027. The training is for researchers who use RNA structure prediction in their own work and...
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.