Frederik Schulz
Community@fmschulz · San Francisco
New Lineages of Life Discovery @ DOE JGI
Agent Skills by Frederik Schulz
Showing 22 vetted skills indexed across 1 GitHub repositories.
fmschulzagent-browser
Automate browser tasks via CLI for navigation, form filling, and data capture.
fmschulzbio-logic
Evaluate manuscripts and study designs for scientific rigor and bias.
fmschulzbio-gene-calling
Call genes in microbial genomes and generate GFF3, FAA, and FNA outputs.
fmschulzbio-prefect-dask-nextflow
Scaffold omics pipelines with Prefect+Dask or Nextflow for HPC schedulers.
fmschulzbio-annotation
Annotate protein functions and taxonomy from sequence homology using InterProScan, eggNOG-mapper, DIAMOND, and TaxonKit.
fmschulzscience-writing
Draft scientific manuscripts with DOI validation and structured references.
fmschulzbio-structure-annotation
Predict protein structures and annotate hits with Foldseek.
fmschulzbeautiful-data-viz
Automate publication-quality matplotlib/seaborn visualizations from tabular data in Python/Jupyter.
fmschulzplotly-dashboard-skill
Standardize Plotly Dash app theming, layout, and performance practices.
fmschulzbio-assembly-qc
Assemble bacterial, archaeal, and viral genomes with SPAdes or Flye and produce QUAST QC reports.
fmschulzpolars-dovmed
Search PMC Open Access papers full-text and extract metadata with snippets.
fmschulzbio-foundation-housekeeping
Create reproducible bioinformatics project scaffolds with Pixi, LinkML, and DuckDB.
fmschulzbio-phylogenomics
Extract marker genes, generate alignments, and infer phylogenetic trees.
fmschulzbio-stats-ml-reporting
Automates end-to-end ML reporting for omics analysis using DuckDB, scikit-learn, and XGBoost.
fmschulzbio-viromics
Detect viral contigs, classify taxonomy, and assess genome quality with geNomad, vConTACT3, and CheckV.
fmschulzjgi-lakehouse
Discover omics metadata across GOLD, IMG, Mycocosm, and Phytozome via SQL.
fmschulztracking-taxonomy-updates
Track taxonomy updates from NCBI, GTDB, ICTV, and UniEuk into versioned provenance reports.
fmschulzbio-workflow-methods-docwriter
Generate METHODS.md and run_manifest.yaml from Nextflow, Snakemake, and CWL workflow artifacts.
fmschulznotebook-ai-agents-skill
Orchestrate and validate narrative-first notebooks with Pixi environments and nbclient execution.
fmschulzbio-binning-qc
Coordinate binning, refinement, and QC to construct high-quality MAGs.
fmschulzbio-protein-clustering-pangenome
Cluster proteins from FASTAs into pan-genome presence/absence matrices using MMseqs2 or ProteinOrtho.
fmschulzbio-reads-qc-mapping
Ingest, QC, and map sequencing reads to generate coverage metrics.