fmschulz
@fmschulz
Public Skills
bio-gene-calling
by fmschulz
Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.
bio-stats-ml-reporting
by fmschulz
Aggregate results, train ML models, and produce reports with validated references.
jgi-lakehouse
by fmschulz
Query JGI Lakehouse (Dremio) for genomics metadata across GOLD/IMG/Mycocosm/Phytozome and download genome files via IMG taxon OIDs.
agent-browser
by fmschulz
Browser automation via agent-browser CLI for web navigation, form filling, screenshots, scraping, login flows, and UI testing.
bio-prefect-dask-nextflow
by fmschulz
Design and scaffold bioinformatics pipelines using Prefect+Dask for local/distributed execution or Nextflow for HPC schedulers.
tracking-taxonomy-updates
by fmschulz
Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance.
beautiful-data-viz
by fmschulz
Create publication-quality matplotlib/seaborn charts with readable axes, tight layout, and curated palettes.
notebook-ai-agents-skill
by fmschulz
Create/refactor reproducible analysis notebooks with Marimo (preferred) or Jupyter (minimal support). Use for interactive, narrative-first analyses.
bio-viromics
by fmschulz
Detect, classify, and QC viral contigs.
bio-binning-qc
by fmschulz
Perform metagenomic binning, refinement, and QC with completeness/contamination checks.
bio-annotation
by fmschulz
Functional annotation and taxonomy inference from sequence homology.
plotly-dashboard-skill
by fmschulz
Build production-ready Plotly Dash dashboards with consistent theming, clear layouts, and performant callbacks.
bio-protein-clustering-pangenome
by fmschulz
Cluster proteins into orthogroups and derive pangenome matrices.
bio-assembly-qc
by fmschulz
Assemble genomes/metagenomes and produce assembly QC artifacts.
polars-dovmed
by fmschulz
Search 2.4M+ full-text PubMed Central Open Access papers for literature reviews, trends, and data extraction.
bio-workflow-methods-docwriter
by fmschulz
Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.
bio-foundation-housekeeping
by fmschulz
Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.
bio-reads-qc-mapping
by fmschulz
Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
science-writing
by fmschulz
Write publication-quality scientific manuscripts with DOI validation and structured reference management.