Post-process OrcaFlex simulation results using OPP (OrcaFlex Post-Process). Use for extracting summary statistics, linked statistics, range graphs, time series, histograms, and generating interactive HTML reports from .sim files.
Generate visualizations from OrcaFlex simulations including model views, time series plots, range graphs, and interactive HTML reports using Plotly for comprehensive analysis presentation.
Specialized knowledge for assisting with Chris Towles's blog. Use when users ask about blog posts, topics, or need help navigating content.
Use when researching markets, analyzing competitors, comparing technologies, or finding case studies. Ensures all findings include credible sources and URLs.
Process, transform, and analyze images using common operations
Orchestrates life sciences APIs to build knowledge graphs using the Fuzzy-to-Fact protocol, combining MCPs for nodes and curl for edges, then persisting to Graphiti. This skill should be used when the user asks to "build knowledge graphs", "find biological connections", "explore drug repurposing", "validate drug targets", or mentions traversing gene→protein→pathway→drug→disease paths, multi-API orchestration, or graph persistence workflows.
Comprehensive AI writing detection patterns and methodology. Provides vocabulary lists, structural patterns, model-specific fingerprints, and false positive prevention guidance. Use when analyzing text for AI authorship or understanding detection patterns.
Master LLM-as-a-Judge evaluation techniques including direct scoring, pairwise comparison, rubric generation, and bias mitigation. Use when building evaluation systems, comparing model outputs, or establishing quality standards for AI-generated content.
ChatGPT-style deep research strategy with problem decomposition, multi-query generation (3-5 variations per sub-question), evidence synthesis with source ranking, numbered citations, and iterative refinement. Use for complex architecture decisions, multi-domain synthesis, strategic comparisons, technology selection. Keywords: architecture, integration, best practices, strategy, recommendations, comparison.
Helps users discover patterns and insights in their Knowledge Graphs. Use when users ask about important entities, connections, patterns, or want to understand what they can do with their graph. Triggers proactively after extraction to show what's possible.
AI-powered web search and reasoning using Perplexity API through the scraper MCP server. Invoked when searching the web with AI synthesis, conducting research with citations, performing complex reasoning tasks, or answering questions requiring real-time information. Provides two tools for different query types.
Systematic analysis patterns for categorical AI papers (Gavranović, de Wynter, Bradley, Zhang). Use when analyzing academic papers on categorical deep learning, extracting categorical structures from AI research, mapping meta-prompting concepts to category theory, or building comprehensive literature reviews on categorical approaches to AI.
CC2.0 seven-function research workflow (observe, reason, create, orchestrate, learn, verify, deploy) for categorical AI research. Use when conducting systematic research on categorical AI topics, coordinating multi-stream research workflows, applying categorical foundations to research methodology, or implementing the L5 meta-prompting research framework.
This skill should be used when user wants to learn from their collected references, synthesize patterns across sources, or turn research into frameworks from curated reference collections (Are.na channels, bookmarks, saved articles).
Manage large-scale OrcaFlex batch processing with parallel execution, adaptive worker scaling, memory optimization, and progress tracking for efficient simulation campaigns.
Create educational documents that build understanding progressively with citations
Standard multi-source verification search strategy for moderate complexity research. 2-iteration workflow with source ranking, consensus identification, and citation transparency. Use for feature comparisons, moderate complexity topics, fact-checking. Keywords: compare, differences, features, fact-check, verify, what are.
Fast, targeted single-pass search strategy for simple factual lookups. 1-iteration workflow with authoritative source verification and minimal citations. Use for version lookups, documentation finding, simple definitions, existence checks. Keywords: what version, find docs, link to, what is, does X support.
Searches journal for past work related to current task, finding relevant context, solutions, and decisions
Queries clinical databases (Open Targets, ClinicalTrials.gov) via curl for target-disease associations, target tractability assessment, and clinical trial discovery. This skill should be used when the user asks to "validate drug targets", "find clinical trials", "assess target tractability", "discover disease associations", or mentions Open Targets scores, NCT identifiers, target-disease evidence, druggability assessment, or translational research workflows.
