Create publication-quality, aesthetically refined charts in Python/Jupyter (matplotlib/seaborn): readable axes, tight whitespace, and curated palettes…
Perform metagenomic binning, refinement, and QC with completeness/contamination checks.
Search bioRxiv preprints through the official bioRxiv API and locally filter titles, abstracts, and authors for keyword queries.
Aggregate results, train ML models, and produce reports with validated references.
Query the Crossref REST API for DOI validation, title search, citation metadata, and bibliography audits.
Run a Codex-native planning and implementation loop with docs/plans progress tracking, MEMORY.md failure memory, per-task git worktrees, and iterative verification until tasks…
Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance.
Build production-ready Plotly Dash dashboards with consistent theming, clear layouts, and performant callbacks.
Implement a research paper in a marimo notebook fully automatically without extra user input.
Evaluates scientific research rigor using systematic frameworks. Assesses methodology, statistics, biases, and evidence quality.
Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome. Downloads genome files from JGI filesystem using IMG taxon OIDs.
Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.
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…
Generate reproducible bioinformatics/data-science Methods + run documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including a top-of-doc workflow summary, exact…
Assess paper and journal impact using OpenAlex citation counts, optional Altmetric data, and curated journal impact-factor references.
Run a multi-agent scientific manuscript review with parallel specialist reviewers, disagreement checks, and an editor meta-review.
Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
Create/refactor reproducible analysis notebooks with Marimo (preferred) or Jupyter (minimal support). Use for interactive, narrative-first analyses.
Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.
Designs and scaffolds bioinformatics pipelines using Prefect (Python) with Dask for local/distributed task execution and Nextflow for HPC scheduler-native execution.
Structured, decision-ready review framework for AI/ML, computational biology, and bioscience proposals. Use when evaluating grant, project, or funding proposals.
Critically review, score, compare, and rank one or more AI scientist outputs for biology, bioinformatics, computational life science, or adjacent research tasks.
Write a marimo notebook in a Python file in the right format.
Functional annotation and taxonomy inference from sequence homology.
Cluster proteins into orthogroups and derive pangenome matrices.
Convert a Jupyter notebook (.ipynb) to a marimo notebook (.py).
Assemble genomes/metagenomes and produce assembly QC artifacts.
Generate anywidget components for marimo notebooks.
Build marker gene alignments and phylogenetic trees.
Detect, classify, and QC viral contigs.