fmschulz
- 34 skills
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- 1 week ago last updated
- ▌ Bio Prefect Dask Nextflow · fmschulz bundleDesign reproducible bioinformatics pipelines with Prefect plus Dask or Nextflow. Use when scaffolding local, distributed, or scheduler-backed workflows.
- ▌ Exploratory Data Analysis · fmschulz bundleInspect scientific data and generate a Markdown structure-and-quality report. Use when triaging tabular, array, sequence, HDF5, JSON, or raster files before downstream analysis.
- ▌ Manuscript Review Council · fmschulz bundleProduce 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.
- ▌ Tracking Taxonomy Updates · fmschulz bundleTrack 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.
- ▌ Bio Fasta Database Curator · fmschulz bundleCurate and validate FASTA or FAA databases. Use when standardizing headers, merging references, deduplicating sequences, converting GenBank files, or preparing BLAST, MMseqs2, and HMM inputs.
- ▌ Bio Foundation Housekeeping · fmschulz bundleAdd 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.
- ▌ Scientific Impact Assessment · fmschulz bundleAssess research reach with OpenAlex citations, optional Altmetric data, and journal context. Use when comparing papers, journals, or literature shortlists by influence.
- ▌ Bio Workflow Methods Docwriter · fmschulz bundleGenerate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands, versions, parameters, QC gates, provenance, and outputs.
- ▌ Bio Protein Clustering Pangenome · fmschulz bundleCluster proteins into orthogroups and build pangenome matrices. Use when comparing gene-family presence, absence, expansion, contraction, or core and accessory content across genomes.
- ▌ Bio Viromics · fmschulz bundleDetect, quality-control, and classify viral contigs. Use when identifying viruses in assemblies, checking viral completeness and contamination, or assigning viral taxonomy.
- ▌ Polars Dovmed · fmschulz bundleSearch 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.
- ▌ Bio Annotation · fmschulz bundleAnnotate genes or proteins and infer taxonomy from sequence homology. Use when assigning functions, domains, or taxonomic labels to genomes, contigs, or protein sets.
- ▌ Bio Binning Qc · fmschulz bundleBin and refine metagenomic contigs, then assess MAG quality. Use when recovering genomes with QuickBin and checking completeness, contamination, and bin consistency.
- ▌ Biorxiv Search · fmschulz bundleSearch 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.
- ▌ Bio Assembly Qc · fmschulz bundleAssemble genomes or metagenomes and assess assembly quality. Use when turning sequence reads into contigs and reporting completeness, continuity, and contamination evidence.
- ▌ Crossref Lookup · fmschulz bundleQuery Crossref for DOI validation, title matching, citation metadata, and bibliography audits. Use when resolving references or cleaning citation records.
- ▌ Csag Extraction · fmschulz bundleExtract 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.
- ▌ Proposal Review · fmschulz bundleEvaluate 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.
- ▌ Bio Gene Calling · fmschulz bundlePredict 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.
- ▌ Public DB Lookup · fmschulz bundleFetch 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.
- ▌ Bio Phylogenomics · fmschulz bundleBuild and validate marker-gene alignments and phylogenetic trees. Use when inferring evolutionary relationships, choosing models, or checking tree support and contamination.
- ▌ Beautiful Data Viz · fmschulz bundleCreate publication-quality static charts with matplotlib or seaborn. Use when scientific figures need readable axes, accessible palettes, tight layouts, and high data-ink design.
- ▌ Scientific Writing · fmschulz bundleDraft 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.
- ▌ Bio Interdomain Hgt · fmschulz bundleDetect 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.
- ▌ Bio Reads Qc Mapping · fmschulz bundleIngest, quality-control, and map sequencing reads with reproducible outputs. Use when processing raw reads, removing contaminants, or calculating mapping and coverage statistics.
- ▌ AI Scientist Evaluator · fmschulz bundleScore 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.
- ▌ Bio Stats Ml Reporting · fmschulz bundleAnalyze biological results with statistics or machine learning and produce validated reports. Use when aggregating features, testing hypotheses, training models, or reporting performance.
- ▌ Bioinformatics Project · fmschulz bundleStructure 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.
- ▌ Plotly Dashboard Skill · fmschulz bundleBuild production-ready Plotly Dash dashboards. Use when scientific data needs an interactive, consistently themed layout with clear and performant callbacks.
- ▌ Bio Structure Annotation · fmschulz bundlePredict 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.
- ▌ Bio Logic · fmschulz bundleAssess 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.
- ▌ Notebooks · fmschulz bundleAuthor, execute, validate, and convert reproducible marimo or Jupyter notebooks. Use when delivering an analysis notebook with all cells run and figures embedded.
- ▌ PDF To Md · fmschulz bundleConvert 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.
- ▌ Arxiv Search · fmschulz bundleSearch 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.