omics-skills

ai-scientist-evaluator

Review, score, compare, and rank AI-generated biology or bioinformatics research artifacts. Use when auditing AI-scientist notebooks, code, figures, analyses, manuscripts, or reports for rigor, reproducibility, novelty, and task completion.

arxiv-search

Search arXiv through its official API and save local Markdown summaries. Use when finding recent CS, math, physics, or quantitative-biology preprints or resolving arXiv IDs.

beautiful-data-viz

Create publication-quality static charts with matplotlib or seaborn. Use when scientific figures need readable axes, accessible palettes, tight layouts, and high data-ink design.

bio-annotation

Annotate genes or proteins and infer taxonomy from sequence homology. Use when assigning functions, domains, or taxonomic labels to genomes, contigs, or protein sets.

bio-assembly-qc

Assemble genomes or metagenomes and assess assembly quality. Use when turning sequence reads into contigs and reporting completeness, continuity, and contamination evidence.

bio-binning-qc

Bin and refine metagenomic contigs, then assess MAG quality. Use when recovering genomes with QuickBin and checking completeness, contamination, and bin consistency.

bio-fasta-database-curator

Curate and validate FASTA or FAA databases. Use when standardizing headers, merging references, deduplicating sequences, converting GenBank files, or preparing BLAST, MMseqs2, and HMM inputs.

bio-foundation-housekeeping

Add schema-backed metadata validation, normalized Parquet tables, and a DuckDB catalog to a bioinformatics project. Use when an analysis needs LinkML/Pydantic records or a queryable data catalog.

bio-gene-calling

Call genes and annotate basic sequence features. Use when predicting prokaryotic, viral, or eukaryotic coding sequences before downstream annotation.

bio-interdomain-hgt

Detect and polarize interdomain horizontal gene transfer with homology, context, and phylogenetic checks. Use when studying lateral gene transfer, virus-host gene exchange, endogenous viral elements, or donor direction.

bio-logic

Evaluate scientific claims, methods, biases, and evidence strength. Use when stress-testing a study design, paper, analysis, or causal interpretation.

bio-phylogenomics

Build and validate marker-gene alignments and phylogenetic trees. Use when inferring evolutionary relationships, choosing models, or checking tree support and contamination.

Show all 34 bundled skills

Web & Frontend Listed

bio-prefect-dask-nextflow

Design reproducible bioinformatics pipelines with Prefect plus Dask or Nextflow. Use when scaffolding local, distributed, or scheduler-backed workflows.

bio-protein-clustering-pangenome

Cluster proteins into orthogroups and build pangenome matrices. Use when comparing gene-family presence, absence, expansion, contraction, or core and accessory content across genomes.

bio-reads-qc-mapping

Ingest, quality-control, and map sequencing reads with reproducible outputs. Use when processing raw reads, removing contaminants, or calculating mapping and coverage statistics.

bio-stats-ml-reporting

Analyze biological results with statistics or machine learning and produce validated reports. Use when aggregating features, testing hypotheses, training models, or reporting performance.

bio-structure-annotation

Predict protein structures and perform structure-based annotation. Use when sequence evidence is insufficient or structural similarity, confidence, domains, or complexes matter.

bio-viromics

Detect, quality-control, and classify viral contigs. Use when identifying viruses in assemblies, checking viral completeness and contamination, or assigning viral taxonomy.

bio-workflow-methods-docwriter

Generate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands, versions, parameters, QC gates, provenance, and outputs.

API & Backend Listed

bioinformatics-project

Structure reproducible bioinformatics projects with canonical layouts, restartable drivers, pinned environments, provenance, and lab notebooks. Use when starting or reorganizing a genomics project or making a sequencing analysis rerunnable.

API & Backend Listed

biorxiv-search

Search bioRxiv through its official API and filter title, abstract, and author metadata. Use when finding recent biology preprints, scanning date ranges, resolving DOIs, or building author shortlists.

crossref-lookup

Query Crossref for DOI validation, title matching, citation metadata, and bibliography audits. Use when resolving references or cleaning citation records.

csag-extraction

Extract a Conditional Scientific Argumentation Graph and grounded Q&A from a manuscript. Use when representing assertions, contexts, evidence links, and inference steps in machine-readable form.

exploratory-data-analysis

Inspect scientific data and generate a Markdown structure-and-quality report. Use when triaging tabular, array, sequence, HDF5, JSON, or raster files before downstream analysis.

jgi-lakehouse

Query JGI Lakehouse metadata and retrieve JGI genome or read files. Use when linking GOLD, IMG, MycoCosm, Phytozome, PMO, or JAMO identifiers and datasets.

Code & Development Listed

manuscript-review-council

Run a multi-agent manuscript critique with specialist reports, disagreement checks, and editor synthesis. Use for scientific review, revision assessment, or judging whether an author response resolves prior concerns.

notebooks

Author, execute, validate, and convert reproducible marimo or Jupyter notebooks. Use when delivering an analysis notebook with all cells run and figures embedded.

pdf-to-md

Convert PDFs and office documents to clean Markdown, with structured bundles for scientific papers. Use when extracting article structure, preparing a manuscript for analysis, or creating CSAG input.

plotly-dashboard-skill

Build production-ready Plotly Dash dashboards. Use when scientific data needs an interactive, consistently themed layout with clear and performant callbacks.

polars-dovmed

Search PMC Open Access and bioRxiv corpora with polars-dovmed. Use when structured, reproducible literature queries should run through the hosted API or local parquet indexes.

Code & Development Listed

proposal-review

Produce structured, decision-ready reviews of AI/ML, computational-biology, or bioscience proposals. Use when evaluating grants, projects, or funding applications.

DevOps & Infrastructure Listed

scientific-impact-assessment

Assess research reach with OpenAlex citations, optional Altmetric data, and journal context. Use when comparing papers, journals, or literature shortlists by influence.

DevOps & Infrastructure Listed

scientific-writing

Draft, review, and revise scientific manuscripts with grounded multi-agent checks. Use when writing sections, rebuttals, response letters, manuscript QA, or sentence-level reviews.

tracking-taxonomy-updates

Track taxonomy changes and triage sequence assignments across NCBI, GTDB, ICTV, and eukaryotic frameworks. Use when comparing releases, resolving renamed taxa, or routing genomes, bins, and contigs by domain.