openscientist-io/openscientist
Instructions file
Instructions for openscientist-io/openscientist, covering openscientist development guide, project structure, development setup, install dependencies and set up environment variables (see .env.example).
openscientist-io/openscientist
Skill Claude CodeCodex
Skills for querying the JGI Dremio Lakehouse containing GOLD and IMG genomics databases. Use this when users want to explore JGI databases, query GOLD (Genomes OnLine Database), IMG (Integrated Microbial Genomes), or run SQL queries against JGI genomics data. Triggers on mentions of JGI, GOLD database, IMG database…
openscientist-io/openscientist
Skill Claude CodeCodex
Skills for querying the KBase/BERDL Datalake via the MCP REST API. Use this when users want to explore KBase databases, list tables, get schemas, sample data, or run SQL queries against the KBase data lake. Triggers on mentions of KBase, BERDL, or requests to query biological/microbiome data stored in KBase.
openscientist-io/openscientist
Skill Claude CodeCodex
Statistical analysis strategies and data exploration techniques.
openscientist-io/openscientist
Skill Claude CodeCodex
Genomics and transcriptomics analysis strategies.
openscientist-io/openscientist
Skill Claude CodeCodex
Metabolomics-specific analysis strategies and domain knowledge.
openscientist-io/openscientist
Skill Claude CodeCodex
Reference of available Phenix commands for structural biology analysis.
openscientist-io/openscientist
Skill Claude CodeCodex
Generate testable hypotheses from data patterns and literature.
openscientist-io/openscientist
Skill Claude CodeCodex
Decide what to investigate next when you have multiple options.
openscientist-io/openscientist
Skill Claude CodeCodex
Interpret statistical results and decide what to do next.
openscientist-io/openscientist
Skill Claude CodeCodex
Decide when to stop investigating and prepare final report.