Lord1Egypt
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- ▌ Pydantic Validation 2 · lord1egyptData validation, data parsing, configuration management, and type coercion using Pydantic.
- ▌ Regular Expressions 2 · lord1egyptDesigning, parsing, and searching string parameters using Python regular expressions.
- ▌ Semantic Versioning 2 · lord1egyptConfiguring release versions, package numbering schemes, and tracking dependency compatibilities.
- ▌ Stripe Payments API 2 · lord1egyptIntegrating Stripe payments, managing subscription billing checkout sessions, and validation signatures on webhooks.
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- ▌ Claude System Prompt 2 · lord1egyptOperational rules, safety instructions, reasoning guidelines, and behavioral patterns from the Claude 3.7 Sonnet system prompt.
- ▌ Dnanexus Integration 2 · lord1egypt bundleDNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
- ▌ Docker Compose Utils 2 · lord1egyptConfiguring, spinning up, and orchestrating multi-container local runtime environments with Docker Compose.
- ▌ Latchbio Integration 2 · lord1egypt bundleLatch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
- ▌ Linux Bash Scripting 2 · lord1egyptWriting automation scripts, file directory operations, and loop controls in Linux Bash shell.
- ▌ Neuropixels Analysis 2 · lord1egypt bundleNeuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
- ▌ Neuroscience Imaging 2 · lord1egyptNeuroimaging data analysis with nilearn, nibabel, and fMRIPrep outputs. Use for fMRI/MRI data loading, brain atlas parcellation, functional connectivity analysis, GLM-based task fMRI, resting-state network analysis, and publication-quality brain visualizations. Covers structural MRI, task fMRI, and rs-fMRI workflows.
- ▌ Statistical Analysis 2 · lord1egypt bundleGuided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic research reporting, test selection guidance. For implementing specific models programmatically use statsmodels.
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- ▌ Benchling Integration 2 · lord1egypt bundleBenchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
- ▌ Climate Data Analysis 2 · lord1egyptClimate and Earth system data analysis using xarray, cartopy, cfgrib, and CMIP6/ERA5 datasets. Use for loading NetCDF/GRIB climate data, computing climatologies, spatial aggregation, anomaly detection, bias correction, and publication-quality climate maps. Best for atmospheric, oceanic, and land surface data analysis.
- ▌ Hypothesis Generation 2 · lord1egypt bundleStructured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
- ▌ Metabolomics Analysis 2 · lord1egyptUntargeted and targeted metabolomics data analysis using pyMZML, mzTab-M processing, and metabolite identification. Use for LC-MS/GC-MS feature detection, metabolite annotation, differential metabolite analysis, pathway mapping, and metabolic flux visualization. Covers XCMS-compatible workflows in Python.
- ▌ Opentrons Integration 2 · lord1egypt bundleOfficial Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot.
- ▌ Pandas Data Wrangling 2 · lord1egyptCleaning, filtering, merging, and aggregating massive tabular data structures using Pandas.
- ▌ Performance Profiling 2 · lord1egyptMeasuring CPU performance metrics and memory bottlenecks in Python code blocks.
- ▌ Scientific Schematics 2 · lord1egypt bundleCreate publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
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- ▌ Tool Description Repl 2 · lord1egyptDescribes the REPL tool, a JavaScript programming interface for looping, branching, and composing Claude Code tool calls as async functions
- ▌ Beautifulsoup Scraping 2 · lord1egyptParsing HTML web structures, searching tags, and extracting text using BeautifulSoup4.
- ▌ Crispr Screen Analysis 2 · lord1egyptCRISPR genetic screen analysis using MAGeCK, CRISPRclean, and crispy. Use for pooled CRISPR knockout/activation screens, sgRNA count normalization, gene essentiality scoring, hit calling, pathway enrichment, and QC of CRISPR screen data. Supports both positive and negative selection screens.
- ▌ Data Tool Use Concepts 2 · lord1egyptConceptual foundations of tool use with the Claude API including tool definitions, tool choice, and best practices
- ▌ Labarchive Integration 2 · lord1egypt bundleElectronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
- ▌ Markdown Documentation 2 · lord1egyptStructuring technical markdown docs, wikis, and building clean developer layout grids.
- ▌ Python Requests Client 2 · lord1egyptPerforming synchronous HTTP requests, managing sessions, passing headers, and query parameters using Requests.
- ▌ Skill Computer Use MCP 2 · lord1egyptInstructions for using computer-use MCP tools including tool selection tiers, app access tiers, link safety, and financial action restrictions
- ▌ Tool Description Skill 2 · lord1egyptTool description for executing skills in the main conversation
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- ▌ Get Available Resources 2 · lord1egypt bundleThis skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.
- ▌ Iso 13485 Certification 2 · lord1egypt bundleComprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.
- ▌ Ngs Pipeline Management 2 · lord1egyptNext-generation sequencing pipeline management with Snakemake and Nextflow. Use for building, running, and debugging reproducible NGS workflows for RNA-seq, WGS, ChIP-seq, ATAC-seq, and amplicon sequencing. Covers pipeline design patterns, HPC/cloud execution, containerization, and workflow optimization.
- ▌ Protocolsio Integration 2 · lord1egypt bundleIntegration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
- ▌ Spatial Transcriptomics 2 · lord1egyptSpatial transcriptomics data analysis with Squidpy, SpatialDE, and MERFISH/Visium/Xenium workflows. Use for spatial gene expression analysis, neighborhood enrichment, spatial variable gene detection, cell-cell communication with spatial context, and tissue domain identification. Complements Scanpy for spatially-resolved single-cell data.
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- ▌ Markdown Mermaid Writing 2 · lord1egypt bundleComprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams as the default documentation standard with full style guides (markdown + mermaid), 24 diagram type references, and 9 document templates.
- ▌ Scientific Brainstorming 2 · lord1egypt bundleCreative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation.
- ▌ Scientific Visualization 2 · lord1egypt bundleMeta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
- ▌ Skill Loop Slash Command 2 · lord1egyptParses user input into an interval and prompt, converts the interval to a cron expression, and schedules a recurring task
- ▌ Skill Run Skill Template 2 · lord1egyptTemplate file for the Run skill generator showing the frontmatter and section structure for a project-specific run skill
- ▌ System Prompt Git Status 2 · lord1egyptSystem prompt for displaying the current git status at the start of the conversation
- ▌ Clinical Decision Support 2 · lord1egypt bundleGenerate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis.
- ▌ Data Claude Model Catalog 2 · lord1egyptCatalog of current and legacy Claude models with exact model IDs, aliases, context windows, and pricing
- ▌ Exploratory Data Analysis 2 · lord1egypt bundlePerform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
- ▌ Skill Run Skill Generator 2 · lord1egyptSkill for authoring or improving a project-specific run skill that documents verified build, launch, runtime driving, and troubleshooting steps
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- ▌ Tool Description Computer 2 · lord1egyptMain description for the Chrome browser computer automation tool
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- ▌ Tool Description Workflow 2 · lord1egyptDescribes the Workflow tool for running deterministic multi-subagent orchestration scripts, including opt-in requirements, script metadata, agent hooks, concurrency, budgeting, quality patterns, and resume behavior
- ▌ Skill Run CLI Tool Example 2 · lord1egyptExample file for the Run app skill showing how to document building, invoking, and testing a CLI tool
- ▌ System Prompt Minimal Mode 2 · lord1egyptDescribes the behavior and constraints of minimal mode, which skips hooks, LSP, plugins, auto-memory, and other features while requiring explicit context via CLI flags
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- ▌ Agent Prompt Session Search 2 · lord1egyptSubagent prompt for searching past Claude Code conversation sessions by scanning .jsonl transcript files and returning matching session IDs
- ▌ Data Claude API Reference C 2 · lord1egyptC# SDK reference including installation, client initialization, basic requests, streaming, and tool use
- ▌ Data Cowork Plugin Examples 2 · lord1egyptReference examples of minimal, medium, and complex Cowork plugin structures with plugin metadata, skills, agents, hooks, MCP config, README, and connectors
- ▌ Skill Agent Design Patterns 2 · lord1egyptReference guide covering decision heuristics for building agents on the Claude API, including tool surface design, context management, caching strategies, and composing tool calls
- ▌ Skill Loop Self Pacing Mode 2 · lord1egyptInstructs Claude how to self-pace a recurring loop by arming event monitors as primary wake signals and scheduling fallback heartbeat delays between iterations
- ▌ Skill Model Migration Guide 2 · lord1egyptStep-by-step instructions for migrating existing code to newer Claude models, covering breaking changes, deprecated parameters, per-SDK syntax, prompt-behavior shifts, and migration checklists
- ▌ Skill Team Onboarding Guide 2 · lord1egyptTemplate for onboarding a new teammate to a team's Claude Code setup, walking them through usage stats, setup checklists, MCP servers, skills, and team tips in a warm conversational style
- ▌ System Prompt Learning Mode 2 · lord1egyptMain system prompt for learning mode with human collaboration instructions
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- ▌ Tool Description Croncreate 2 · lord1egyptDescribes the CronCreate tool for enqueuing one-shot or recurring cron-based jobs with jitter and off-minute scheduling guidance
- ▌ Tool Description Designsync 2 · lord1egyptDescribes the DesignSync tool for reading and updating claude.ai/design design-system projects, including project listing, plan finalization, file writes and deletes, and asset registration
- ▌ Tool Description Powershell 2 · lord1egyptDescribes the PowerShell command execution tool with syntax guidance, timeout settings, and instructions to prefer specialized tools over PowerShell for file operations
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- ▌ Agent Prompt General Purpose 2 · lord1egypt${"You are an agent for Claude Code, Anthropic's official CLI for Claude. Given the user's message, you should use the tools available to complete the task. Complete the task fully—don't gold-plate, but don't leave it half-done."} When you complete the task, respond with a concise report covering what was done and any key findings — the caller will relay this to the user, so it only needs the essentials.
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- ▌ Data Managed Agents Outcomes 2 · lord1egyptReference documentation for Managed Agents outcomes, including user.define_outcome events, rubrics, outcome evaluation events, deliverables, and interaction rules
- ▌ Data Managed Agents Overview 2 · lord1egyptProvides the agent with a comprehensive overview of the Managed Agents API architecture, mandatory agent-then-session flow, beta headers, documentation reading guide, and common pitfalls
- ▌ Data Managed Agents Webhooks 2 · lord1egyptReference documentation for Managed Agents webhooks, including endpoint registration, signature verification, payload envelopes, supported event types, delivery behavior, and pitfalls
- ▌ Protein Structure Prediction 2 · lord1egyptProtein structure prediction and analysis using AlphaFold2, ESMFold, RoseTTAFold, and ColabFold. Use for 3D structure prediction from amino acid sequences, structure quality assessment, binding site identification, and structural comparison. Best for proteins without experimental structures.
- ▌ Scientific Critical Thinking 2 · lord1egypt bundleEvaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.
- ▌ Skill Create Verifier Skills 2 · lord1egyptPrompt for creating verifier skills for the Verify agent to automatically verify code changes
- ▌ Skill Insights Report Output 2 · lord1egyptFormats and displays the insights usage report results after the user runs the /insights slash command
- ▌ Agent Prompt Memory Synthesis 2 · lord1egyptSubagent that reads persistent memory files and returns a JSON synthesis of only the information relevant to each query, with cited filenames
- ▌ Agent Prompt Quick Git Commit 2 · lord1egyptStreamlined prompt for creating a single git commit with pre-populated context
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- ▌ Data Token Counting Reference 2 · lord1egyptReference documentation for counting Claude model tokens with the Messages count_tokens endpoint and Anthropic SDK or CLI examples, including warnings against OpenAI tokenizers
- ▌ Skill Cowork Plugin Authoring 2 · lord1egyptSkill instructions for creating or customizing Cowork plugins, including mode selection, research, implementation, packaging, connector replacement, and plugin delivery
- ▌ Skill Run Library Sdk Example 2 · lord1egyptExample file for the Run app skill showing how to document building, testing, and smoke-checking a library or SDK at its public package boundary
- ▌ System Prompt Emoji Avoidance 2 · lord1egyptInstructs Claude to avoid using emojis unless the user explicitly asks for them
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- ▌ Tool Description Bash Timeout 2 · lord1egyptYou may specify an optional timeout in milliseconds (up to ${GET_MAX_TIMEOUT_MS()}ms / ${GET_MAX_TIMEOUT_MS()/60000} minutes). By default, your command will timeout after ${GET_DEFAULT_TIMEOUT_MS()}ms (${GET_DEFAULT_TIMEOUT_MS()/60000} minutes).
- ▌ Tool Description Browserbatch 2 · lord1egyptTool description for BrowserBatch, which executes multiple browser tool calls sequentially in one round trip
- ▌ Tool Description Exitplanmode 2 · lord1egyptDescription for the ExitPlanMode tool, which presents a plan dialog for the user to approve
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- ▌ Tool Description Notebookedit 2 · lord1egyptTool description for editing Jupyter notebook cells by replacing, inserting, or deleting a cell using cell IDs from the read tool
- ▌ Tool Description Senduserfile 2 · lord1egyptDescribes the SendUserFile tool for surfacing generated deliverable files to the user, with optional captions and normal or proactive status
- ▌ Tool Description Teammatetool 2 · lord1egyptTool for managing teams and coordinating teammates in a swarm