Run the full experiment lifecycle — design, sanity check, full sweep, synthesize, and claim review. Given a hypothesis, proposes sweep matrix, runs the experiment, generates artifacts, and updates the research log.
Audit NVCA recipe quality: check file inventory, metadata schema, field-to-replacement coverage, ambiguous keys, smart quotes, test fixtures, and fill quality. Produces a structured scorecard per recipe with maturity tier classification. Use when user says "audit recipe quality," "check recipe coverage," "recipe scorecard," or "NVCA recipe quality."
Opentrons Flex Gripper - automated labware movement between deck locations, modules, waste chute, and off-deck storage with precise positioning and offset control for hands-free plate transfers
Opentrons Absorbance Plate Reader Module for Flex - on-deck microplate spectrophotometry with single/multi-wavelength reading (380-740nm in 10nm increments), automated lid control, and CSV data export for ELISA, cell growth, and colorimetric assays
Opentrons Temperature Module - precise heating and cooling (4-95°C) for sample storage, enzyme reactions, and temperature-sensitive protocols with aluminum block adapters for plates, tubes, and PCR strips
Opentrons Heater-Shaker Module - temperature control (37-95°C) with orbital mixing (200-3000 rpm) for cell culture, enzymatic reactions, and sample preparation requiring simultaneous heating and agitation
Opentrons Magnetic Block for Flex - unpowered magnetic bead separation using gripper-based labware movement with high-strength neodymium magnets for DNA/RNA purification, immunoprecipitation, and bead-based workflows
Evaluate a skill's effectiveness by running test cases and grading results. Use when you want to test whether a skill produces correct guidance, validate skill improvements, or benchmark a skill before release.
Synchronize dev and main branches for LAMB releases, including merging changes, creating version tags, and bumping version numbers in code. Use this skill when creating a new release, syncing branches, or tagging a version.
Retrieves, organizes, and interprets laboratory Observation resources with clinical context. Use when user asks to "interpret labs", "review lab results", "what do these labs mean", "explain my bloodwork", "check labs", "lab trends", "abnormal labs", or needs clinical interpretation of laboratory values. Do NOT use for vital signs, imaging results, pathology reports, or non-laboratory Observations.
Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.
Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools. Use when analyzing repertoire diversity, finding shared clonotypes, or comparing immune profiles between conditions.
Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC. Use when assessing acquisition quality or identifying problematic samples before analysis.
Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality.
Quality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use when assessing data quality before analysis or troubleshooting problematic acquisitions.
Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound biological signals.
Estimates required sample sizes for differential expression, ChIP-seq, methylation, and proteomics studies. Use when budgeting experiments, writing grant proposals, or determining minimum replicates needed to achieve statistical significance for expected effect sizes.
Mass spectrometry raw data quality control using PTXQC, rawTools, or MSstatsQC.
Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy. Use when improving assembly accuracy with polishing tools.
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation. Ensure models meet SBML standards and produce biologically meaningful predictions. Use when improving draft models or preparing models for publication.
