tools
Posts tagged “tools”.
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.
Automated lineage designation from viral genomic data
This study describes an automated framework for lineage designation from phylogenetic and genomic data, designed to scale to very large viral datasets while remaining consistent and interpretable.