Bio Phylogenomics
Build marker gene alignments and phylogenetic trees.
Beautiful Data Viz
Create publication-quality matplotlib/seaborn charts with readable axes, tight layout, curated palettes, and Tufte-style high-data-ink design.
Pdf To Md
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Bio Viromics
Detect, classify, and QC viral contigs.
Csag Extraction
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Bio Reads Qc Mapping
Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
Polars Dovmed
Search the PMC Open Access literature with polars-dovmed. Author structured JSON queries directly, then use the hosted API when an API key is available or fall back to local dovmed scan over PMC, bioRxiv, or both parquet corpora.
Bio Assembly Qc
Assemble genomes/metagenomes and produce assembly QC artifacts.
Get Api Docs
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.
Bio Fasta Database Curator
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.
Bio Annotation
Functional annotation and taxonomy inference from sequence homology.
Bio Gene Calling
Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.
Bio Prefect Dask Nextflow
Design and scaffold bioinformatics pipelines using Prefect+Dask for local/distributed execution or Nextflow for HPC schedulers.
Proposal Review
Structured, decision-ready review framework for AI/ML, computational biology, and bioscience proposals. Use when evaluating grant, project, or funding proposals.
Crossref Lookup
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.
Notebooks
Author, execute, and deliver reproducible analysis notebooks in marimo (default) or Jupyter, with all cells run end-to-end and figures embedded. Also converts between marimo and Jupyter on request.
Bio Protein Clustering Pangenome
Cluster proteins into orthogroups and derive pangenome matrices.
Biorxiv Search
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.
Ai Scientist Evaluator
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Bio Logic
Evaluate scientific rigor, methods, biases, and evidence quality for claims, papers, and study designs.
Bio Binning Qc
Perform metagenomic binning with QuickBin, refinement, and QC with completeness/contamination checks.
Tracking Taxonomy Updates
Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance.
Bio Stats Ml Reporting
Aggregate results, train ML models, and produce reports with validated references.
Manuscript Review Council
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.
Arxiv Search
Search arXiv preprints through the official arXiv API and turn arXiv IDs into local Markdown summaries. Use when you need CS, math, physics, or quantitative biology preprints, especially recent submissions that may not yet appear in peer-reviewed literature indexes.
Bio Structure Annotation
Structure prediction and structure-based annotation.
Jgi Lakehouse
Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome. Downloads genome files from JGI filesystem using IMG taxon OIDs and links JGI taxon OIDs to read files through PMO/GOLD identifiers and JAMO. Use when working with JGI data, GOLD projects, IMG annotations, or downloading genomes.
Bio Foundation Housekeeping
Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.
Bio Interdomain Hgt
Detect and polarize interdomain horizontal gene transfer (virus <-> eukaryote/bacteria/archaea, and cross-cellular HGT) using reciprocal best hits, transfer-direction inference, a genomic-context contamination guard, and per-gene phylogenetic confirmation. Use when asked about HGT, lateral gene transfer, gene flow between domains, virus-host gene exchange, endogenous viral elements, or host-deriv…
Exploratory Data Analysis
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Cover…
Plotly Dashboard Skill
Build production-ready Plotly Dash dashboards with consistent theming, clear layouts, and performant callbacks.
Bio Workflow Methods Docwriter
Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.
Scientific Writing
Draft, review, and iteratively revise scientific manuscripts with a provider-agnostic multi-agent workflow for Codex and Claude Code. Use for new manuscripts, section rewrites, rebuttals, response letters, manuscript QA, or sentence-level writing reviews when claims must stay grounded in supplied artifacts.
Scientific Impact Assessment
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.