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Microbiologists

Life, Physical, and Social Science Occupations · Job Skills & Competencies · SOC 19-1022 · 367 skills

Occupation context

These O*NET tasks describe the occupation. They provide context for this SOC mapping, but do not mean every listed Skill performs every task.

  • Isolate and maintain cultures of bacteria or other microorganisms in prescribed or developed media, controlling moisture, aeration, temperature, and nutrition.
  • Provide laboratory services for health departments, community environmental health programs, and physicians needing information for diagnosis and treatment.
  • Monitor and perform tests on water, food, and the environment to detect harmful microorganisms or to obtain information about sources of pollution, contamination, or infection.

O*NET task statements are shown in their source language (English). Task data excerpted from the O*NET® 29.1 Database (USDOL/ETA) and used under CC BY 4.0.

Representative sources

A bounded sample of popular skills mapped to this occupation, with at most one Skill from each GitHub repository. The complete mapped list follows.

analytical-method-validation
38.4k
K-Dense-AIK-Dense-AI/scientific-agent-skills
Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include "method validation", "analytical method validation", "AMV", "validation protocol", "acceptance criteria", "linearity", "reportable range", "accuracy and precision", "repeatability", "intermediate precision", "recovery", "LOD", "LOQ", "detection limit", "quantitation limit", "specificity", "robustness", "method transfer", "method comparison", "Deming", "Passing-Bablok", "Bland-Altman", "equivalence testing", "OOS investigation", "ICH Q2", "Q2(R2)", "Q14", "USP 1225", "ICH M10", "incurred sample reanalysis", "ISR", "CLSI EP", and any request to show that an assay works.
ngs-shotgun-metagenomics
5.3k
openaiopenai/plugins
Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN.
microbial-dynamics
3.4k
synthetic-sciencessynthetic-sciences/openscience
Microbial population dynamics modeling and analysis. Bacterial growth curve fitting (logistic, Gompertz, Baranyi), Lotka-Volterra community dynamics, Gillespie stochastic simulation, biofilm quantification, CFU enumeration, and genome annotation. For metabolic modeling use cobrapy; for sequence analysis use biopython.
bio-epidemiological-genomics-amr-surveillance
3.0k
FreedomIntelligenceFreedomIntelligence/OpenClaw-Medical-Skills
Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.

All mapped skills

Browse the complete catalog mapping by repository popularity or latest source activity.

Skill names and descriptions remain in the language supplied by their source repository.

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analytical-method-validation
38.4k
K-Dense-AIK-Dense-AI/scientific-agent-skills
Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include "method validation", "analytical method validation", "AMV", "validation protocol", "acceptance criteria", "linearity", "reportable range", "accuracy and precision", "repeatability", "intermediate precision", "recovery", "LOD", "LOQ", "detection limit", "quantitation limit", "specificity", "robustness", "method transfer", "method comparison", "Deming", "Passing-Bablok", "Bland-Altman", "equivalence testing", "OOS investigation", "ICH Q2", "Q2(R2)", "Q14", "USP 1225", "ICH M10", "incurred sample reanalysis", "ISR", "CLSI EP", and any request to show that an assay works.
pathogen-variant-surveillance
38.4k
K-Dense-AIK-Dense-AI/scientific-agent-skills
Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry. Use whenever a question depends on the current state of a pathogen population rather than on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence has moved week to week. Triggers include "variant surveillance", "genomic surveillance", "what variant is circulating", "dominant variant", "Pango lineage", "lineage prevalence", "growth advantage", "SARS-CoV-2 variant", "XFG", "clade 2.3.4.4b", "H5N1 genotype", "influenza clade", "RSV/mpox/measles/dengue lineage", "CoV-Spectrum", "LAPIS", "Nextclade", "pango-designation", and any request to report what a pathogen population looks like today.
tooluniverse-natural-product-dereplication
1.7k
mims-harvardmims-harvard/ToolUniverse
Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer "is [compound] a known natural product", "what microbe/organism produces [compound]", "what chemical class is [compound]", "dereplicate this metabolite (by formula/exact mass/InChIKey/SMILES)", or "classify this molecule into ChemOnt". Searches NPAtlas for known microbial natural products (producing organism + literature reference), assigns the ChemOnt kingdom→superclass→class→subclass hierarchy via ClassyFire, resolves systematic IUPAC names to structure via OPSIN, and cross-references identity in PubChem. NOT for general drug/compound identity or ADMET (use tooluniverse-chemical-compound-retrieval / tooluniverse-small-molecule-discovery) and NOT for metabolomics pathway/enrichment analysis (use tooluniverse-metabolomics skills).
tooluniverse-microbial-genome-characterization
1.7k
mims-harvardmims-harvard/ToolUniverse
Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCBI Datasets. Resolves an organism name or taxid to assemblies, picks the reference/representative or best-quality assembly, pulls assembly QC metrics (total length, contig/scaffold N50, contig count, GC%, assembly level, RefSeq category), enumerates chromosomes and plasmids via per-replicon sequence reports, and compares candidate assemblies on quality. Use for "what genomes are available for [organism]", "assembly stats / N50 / GC content for [GCF_/GCA_ accession]", "how many plasmids does [strain] have", "compare assemblies for [species]", "find the reference genome for [taxon]", "is this assembly Complete Genome or just contigs". NOT for gene-level orthology/synteny (use tooluniverse-comparative-genomics), plant gene structure (use tooluniverse-plant-genomics), de novo assembly from raw reads (no tool exists), or taxonomy-only name/lineage lookups.

12 skills are now shown.