GitHub
lenia-core
Core Lenia engine API, stable parameters, multi-species presets, and growth functions. Use when working on the simulation engine, configuring organisms, or debugging parameter issues.
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databases bioinformatics AI Skills
Discover databases bioinformatics skills, compare source repositories and read the instructions for each workflow.
Categories: databases bioinformatics
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literature-search
Search PubMed for RNAi/dsRNA research on target genes or species (utility skill - use anytime)
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GitHub
design-dsrna
Design dsRNA candidates using sliding window algorithm
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GitHub
blast-screen
Screen dsRNA candidates for off-target matches in human and honeybee
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GitHub
full-workflow
Execute the complete dsRNA design workflow with human confirmation at each step
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identify-genes
Match essential genes in target genome using orthology and literature
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fetch-genome
Download CDS sequences from NCBI RefSeq for a target species
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context-map
Fast repository indexing for RLM workflows. Use before analysis to reduce context drift.
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GitHub
aind-infrastructure
Knowledge about AIND data infrastructure including MongoDB/DocumentDB access patterns, S3 asset storage, collection schemas, and query patterns. Use when working with AIND analysis results, querying metadata, o...
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vision-analytics
Advanced visibility analysis using head pose, face mesh, and temporal patterns. Use for face-visible vs body-only breakdowns.
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GitHub
face-alignment
Face alignment, landmark extraction, and quality gating. Use when debugging alignment issues, reviewing rejected faces, or tuning quality thresholds.
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GitHub
pipeline-insights
AI-powered pipeline diagnostics. Explains why faces weren't detected, tracked, embedded, or clustered using OpenAI GPT-4o analysis. Use when debugging pipeline issues, reviewing unclustered tracks, or understan...
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GitHub
security-agent
Deep security analysis with high reasoning effort for threat detection
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data-analyst
Analyze data, identify trends, and generate visualization recommendations
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rlm-patterns
Library of Recursive Language Model analysis patterns. Reference when designing analysis strategies for large documents.
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GitHub
alphafold-database
Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
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GitHub
weaver
Map-Reduce system for comprehensive reports and literature reviews. Breaks topic into chapters, researches each in parallel, then weaves into unified document. Use for deep research, reports, and synthesis.
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GitHub
balkan-family-tree
Comprehensive skill for working with Balkan Family Tree JS libraries (V1 and V2). Use when creating family tree visualizations, genealogy applications, org charts with family relationships, or when migrating be...
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GitHub
galaxy-automation
BioBlend and Planemo expertise for Galaxy workflow automation. Galaxy API usage, workflow invocation, status checking, error handling, batch processing, and dataset management. Essential for any Galaxy automati...
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GitHub
bioinformatics-fundamentals
Core bioinformatics concepts including SAM/BAM format, sequencing technologies (Hi-C, HiFi, Illumina), quality metrics, and common data processing patterns. Essential for debugging alignment, filtering, and pai...
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GitHub
dem-pipeline
Run DEM lineament analysis to identify unmapped fault structures. Use when visually confirming orphan earthquake clusters, mapping fault extensions, or finding dark earthquake sources. Triggers on "DEM analysis...
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GitHub
time-to-event-methods
Survival analysis methods including weighted logrank, MaxCombo, RMST, and milestone tests. Use when analyzing TTE data or choosing analysis methods for non-proportional hazards.
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GitHub
nma-methodology
Deep methodology knowledge for network meta-analysis including transitivity, consistency assessment, treatment rankings, and model selection. Use when conducting or reviewing NMA.
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GitHub
tidy-itc-workflow
Master tidy modelling patterns for ITC analyses following TMwR principles. Covers workflow structure, consistent interfaces, reproducibility best practices, and data validation. Use when setting up ITC analysis...
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