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Scientific computing and academic tools.

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lab-tools
14

feedback

Gather shot feedback, analyze extraction, recommend adjustments, and record results. Use when user says: "/feedback", "I just pulled a shot", "how was that", "it tasted [sour/bitter/flat/good]", provides a star rating, shares taste observations, or asks "what should I adjust" after a shot. Owns the full shot feedback loop: gathering, analysis, tasting notes, and drink format.

julianleopold
julianleopold
research
open
lab-tools
14

text-classification

Guides LLM-based text classification for survey and experimental text data. Covers codebook design, learning regime selection, model choice, human-LLM hybrid workflows, and validation. Use when (1) designing an LLM classification scheme for open-ended survey responses, (2) writing a codebook for LLM text annotation, (3) choosing between zero-shot, few-shot, fine-tuning, or instruction-tuning, (4) selecting a model for classification, (5) validating LLM classifications against human-coded ground truth, (6) implementing hybrid human-LLM workflows, (7) addressing reproducibility concerns, or (8) reporting LLM classification methods and results.

scdenney
scdenney
research
open
lab-tools
14

cross-national-design

Guides the design of cross-national comparative survey experiments. Use when (1) selecting countries for a multi-country study, (2) localizing experimental instruments across languages and institutional contexts, (3) calibrating origin-country stimuli for immigration experiments, (4) conducting per-country power analyses, or (5) planning a cross-national analytical strategy with pooled and per-country models. Covers case selection, instrument localization, ecological validity, power management, and sensitivity bias auditing.

scdenney
scdenney
research
open
lab-tools
14

diagnose

Diagnose espresso extraction issues by correlating machine telemetry with taste feedback. Use when user says: "what went wrong", "analyze that shot", "why did it taste [sour/bitter/flat]", "my shots are inconsistent", or asks about pressure spikes, flow issues, or extraction problems. Fetches shot data via analyze_shot MCP tool, interprets patterns, and provides actionable recommendations.

julianleopold
julianleopold
research
open
lab-tools
14

list-experiment

Guides design, estimation, and diagnostics for list experiments (item count technique, ICT). Use when (1) deciding whether a list experiment is warranted for a sensitive question, (2) designing the control list or choosing baseline items, (3) selecting between design variants (single, double, placebo), (4) choosing an estimator (difference-in-means, multivariate NLSreg/MLreg, combined), (5) testing the identifying assumptions (no design effect, no floor/ceiling), (6) assessing or diagnosing mechanical inflation or artificial deflation, or (7) interpreting list experiment results in relation to direct question estimates. Covers the full pipeline from pre-design sensitivity assessment through statistical inference and power analysis.

scdenney
scdenney
research
open
lab-tools
14

pylabrobot

Laboratory automation toolkit for controlling liquid handlers, plate readers, pumps, heater shakers, incubators, centrifuges, and analytical equipment. Use this skill when automating laboratory workflows, programming liquid handling robots (Hamilton STAR, Opentrons OT-2, Tecan EVO), integrating lab equipment, managing deck layouts and resources (plates, tips, containers), reading plates, or creating reproducible laboratory protocols. Applicable for both simulated protocols and physical hardware control.

jackspace
jackspace
research
open
lab-tools
14

mutation-testing

Diff-scoped mutation testing to verify test quality beyond coverage metrics. Detects language, selects the appropriate tool (Stryker, mutmut, cargo-mutants, PIT, gremlins), and runs mutations only on changed code. Use when asked to run mutation testing, check test quality, find weak tests, verify test coverage is meaningful, or "are my tests actually catching bugs?". Also use after TDD cycle completes or when bugmagnet identifies test coverage gaps. Triggers on: mutation testing, mutant, test quality, weak tests, test effectiveness, "do my tests catch bugs", "are these tests good enough", "verify test quality", "mutation score".

pvillega
pvillega
research
open
lab-tools
14

anti-fabrication

Validate claims through tool execution, avoid superlatives and unsubstantiated metrics. Use when reviewing codebases, analyzing systems, reporting test results, or making any factual claims about code or capabilities.

vinnie357
vinnie357
research
open
lab-tools
14

medication-reminder

Manages medication schedules, tracks adherence (doses taken vs. due), identifies missed dose patterns, and monitors refill timelines. Use when the user logs medications, asks about adherence, or needs a medication schedule.

vitaclaw
vitaclaw
research
open
scientific-computing
14

dataset-query

Query-first dataset access with @domoinc/query including filters, grouping, date grains, and performance constraints.

stahura
stahura
research
open
scientific-computing
14

etetoolkit

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

jackspace
jackspace
research
open
scientific-computing
14

deeptools

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

jackspace
jackspace
research
open
scientific-computing
14

hmdb-database

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

jackspace
jackspace
research
open
scientific-computing
14

cobrapy

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

jackspace
jackspace
research
open
scientific-computing
14

biopython

Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

jackspace
jackspace
research
open
scientific-computing
14

pump-token-lifecycle

Full token lifecycle from creation through bonding curve trading, graduation detection, AMM migration, fee collection, and volume tracking on Solana using PumpSdk and OnlinePumpSdk.

x402agent
x402agent
research
open
scientific-computing
14

tooluniverse

Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages. Use when searching for scientific tools, executing computational biology workflows, composing multi-step research pipelines, accessing databases like OpenTargets/PubChem/UniProt/PDB/ChEMBL, performing tool discovery for research tasks, or integrating scientific computational resources into LLM workflows.

jackspace
jackspace
research
open
scientific-computing
14

matchms

Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.

jackspace
jackspace
research
open
scientific-computing
14

neurokit2

Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.

jackspace
jackspace
research
open
scientific-computing
14

pymatgen

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

jackspace
jackspace
research
open
scientific-computing
13

market-research-and-competitive-analysis

TAM/SAM/SOM calculation, competitor analysis, and market trends identification. Use when analyzing markets, validating business ideas, or entering new markets.

ShunsukeHayashi
ShunsukeHayashi
research
open
computational-chemistry
13

model-evaluation-benchmark

Automated reproduction of comprehensive model evaluation benchmarks following the Benchmark Suite V3. Auto-activates for model benchmarking, comparison evaluation, or performance testing between AI models.

rysweet
rysweet
research
open
scientific-computing
13

causal-loop-microsim-generator

This skill generates interactive Causal Loop Diagram (CLD) MicroSims using the vis-network JavaScript library. Use this skill when users need to create causal loop diagrams for systems thinking education, showing feedback loops, reinforcing and balancing dynamics. The skill creates a complete MicroSim package with index.md, main.html, JavaScript, JSON data, and CSS files in the /docs/sims/ directory. This skill should be used when users request creating CLDs, causal diagrams, feedback loop visualizations, or systems thinking diagrams.

dmccreary
dmccreary
research
open
academic
13

chapter-content-generator

This skill generates comprehensive chapter content for intelligent textbooks after the book-chapter-generator skill has created the chapter structure. Use this skill when a chapter index.md file exists with title, summary, and concept list, and detailed educational content needs to be generated at the appropriate reading level with rich non-text elements including diagrams, infographics, and MicroSims. (project, gitignored)

dmccreary
dmccreary
research
open
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