Critically review, score, compare, and rank one or more AI scientist outputs for biology, bioinformatics, computational life science, or adjacent research tasks. Trigger when the user asks to evaluate notebooks, code, figures, analyses, manuscripts, software, or final reports produced by AI scientists; compare multiple AI scientists on the same task; judge publication readiness; or audit rigor, reproducibility, novelty, and task completion. Do not use this skill to perform the original research task itself unless the user is explicitly asking for a reviewer-style audit of already produced outputs.

Functional annotation and taxonomy inference from sequence homology.

Assemble genomes/metagenomes and produce assembly QC artifacts.

Curate, validate, and standardize FASTA/FAA sequence databases: standardize headers, merge databases, remove duplicates, convert GenBank to FASTA, and generate statistics. Use when preparing reference databases for HMM searches, MMseqs2, BLAST, and other bioinformatics workflows.

Evaluate scientific rigor, methods, biases, and evidence quality for claims, papers, and study designs.

Design and scaffold bioinformatics pipelines using Prefect+Dask for local/distributed execution or Nextflow for HPC schedulers.

Cluster proteins into orthogroups and derive pangenome matrices.

Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.

Aggregate results, train ML models, and produce reports with validated references.

Structure prediction and structure-based annotation.

Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.

Search bioRxiv preprints through the official bioRxiv API and locally filter titles, abstracts, and authors for keyword queries. Use when you need recent biology preprints, bioRxiv-native metadata, date-range scans, DOI lookups, or author shortlists that may not yet appear in peer-reviewed literature indexes.

Query the Crossref REST API for DOI validation, title search, citation metadata, and bibliography audits. Use when you need DOI lookup, title-to-DOI matching, or reference metadata cleanup.

Extract a CSAG (Conditional Scientific Argumentation Graph) from a manuscript using the canonical argumentation spine (Assertions, EvidenceItems, EvidenceLinks, InferenceSteps) while enforcing CSAG conditionality (no assertion without at least one Context). Also generates paper-grounded Q&A items using bundled QA templates.

Fetch current API and SDK documentation with the chub CLI. Use when writing or reviewing code against fast-changing APIs, especially when the user asks for the latest or current docs.

Run a multi-agent scientific manuscript review with parallel specialist reviewers, disagreement checks, and an editor meta-review. Use when reviewing a manuscript, preprint, revision, or rebuttal in Codex or Claude Code.

Convert any PDF (or DOCX/PPTX/XLSX/image) to clean Markdown. For scientific papers, produce the canonical paper-to-md bundle (Markdown plus section_audit.json and article.json) using the remote OCR API when an OCR key is available, or LiteParse v2 locally when it is not. For any non-paper PDF, defer to a fast, local, no-API-key LiteParse v2 conversion. Use when turning a PDF or manuscript into Markdown, extracting article structure, or preparing input for csag-extraction.

Assess paper and journal impact using OpenAlex citation counts, optional Altmetric data, and curated journal impact-factor references. Use when comparing papers, journals, or literature shortlists by reach and influence.

Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance.