Omics Skills

Assess a scientific claim, study design, method, or interpretation against its evidence. Use when testing causal reasoning, finding methodological bias, weighing alternative explanations, or revising hypotheses.

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

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.

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.

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

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.

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

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

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.

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

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

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.

Evaluate a proposed AI/ML, computational-biology, or bioscience research project for a funding decision. Use when reviewing a grant, research proposal, or funding application against sponsor criteria, feasibility, budget, and risks.

Predict coding sequences and screen assemblies for non-coding RNA features. Use when calling genes in prokaryotic, viral, or eukaryotic assemblies, or when a tRNA, rRNA, or other ncRNA census is needed before functional annotation.

Fetch bounded JSON records from UniProt, NCBI Entrez, NCBI Datasets, MGnify, InterPro, AlphaFold DB, STRING, or ENA over HTTP GET. Use when looking up an accession, taxon, entry, or structure record from a public database.

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

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.

Draft or edit scientific prose while preserving its claims and evidence. Use when writing manuscript sections, proposal narratives, rebuttals, or response letters, or when checking sentence-level clarity and style.

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.

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

Score completed AI-generated biology or bioinformatics work against its original task and required artifacts. Use when auditing or comparing AI scientist submissions for task completion, scientific validity, and reproducibility.

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

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.

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

Predict protein or complex structures and annotate proteins by structural similarity. Use when predicting a fold, judging prediction confidence, or finding structural homologs for proteins with weak sequence evidence.

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

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.

Produce a journal-style peer review of a scientific manuscript with specialist reports and an editor decision. Use when assessing publication readiness, or whether a revision or author response resolves scientific objections.

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.

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.

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.

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

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

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