AI & ML

gptomics Bundle

Runs RNA-seq-specific post-alignment QC - strandedness inference, gene-body 5'-3' coverage, read distribution (exonic/intronic/intergenic), rRNA/globin/mitochondrial rate, transcript integrity (TIN), and saturation - with RSeQC, Qualimap, RNA-SeQC, and Picard. Use when validating RNA-seq libraries before quantification or differential expression, diagnosing degradation or gDNA contamination, or determining library strandedness. For raw-FASTQ QC use quality-reports; for UMI dedup use umi-processing.

ariffazil Skill

Hold the dissipative-transition paradox. Load when Arif or an agent talks entropy/gender-as-pattern/identity crisis/transition zone, tries to "resolve" meaning, treats F4 as heat, or maps absurdism/ Gödel/Sisyphus/AzwaOS onto the federation. Operating skill, not a new floor. Pointers to canon + C13/C14 + Gödel lock.

ariffazil Skill

Unified skill inventory, audit, mesh health, and cross-surface contrast. Multi-surface skill audit (10 agent homes) with cross-surface contrast, drift/orphan/dual-name detection. Check whether every agent in the federation has the same core skills at the same version. Multi-harness skill catalog unity — AAA catalog, Grok/Claude/Codex views, alias table, mesh-sync, BOOT gate.

ariffazil Skill

Stage and operate Nous hermes-agent-self-evolution (DSPy + GEPA) against arifOS Hermes skills. Use when Arif says evolve a skill, GEPA, DSPy self-evolution, or hermes-agent-self-evolution. Never auto-writes live skills. Never pip-installs into the production Hermes venv. 888_HOLD before any evolve run (paid API ~$2-10).

ariffazil Skill

Substrate primitive /init — establishes actor, session, lane, atlas expression, authority tier. EVERY autonomous agent MUST call this before any mutation. SESSION BOUND is the answer to "who is acting?"

ariffazil Skill

Provision nodes into the arifOS sovereign Headscale mesh and federate MCP clients to remote organs.

ariffazil Bundle

Diagnose and fix Hermes Telegram gateway image routing — Path B model override, supports_vision decision chain, and common failure modes when images don't reach the LLM.

oimiragieo Bundle

Entity and relation tracking skill using MCP memory server patterns and local knowledge graph storage. Build persistent knowledge graphs of entities, relationships, and observations across agent sessions. Covers the MCP memory server (@modelcontextprotocol/server-memory), local JSON-based graphs, and entity-relation querying patterns for long-running agents.

oimiragieo Bundle

AI-first security scanning with Medusa. 3,000+ detection patterns covering AI/ML, agents, MCP, RAG, prompt injection, and traditional SAST vulnerabilities. Wraps Medusa CLI with SARIF/JSON parsing, structured finding output, OWASP mapping, and remediation guidance.

oimiragieo Bundle

Shell out to OpenAI Codex CLI for headless code generation, analysis, and question-answering. Optimized for code tasks. Requires OPENAI_API_KEY env var.

ariffazil Bundle

mcporter — Universal MCP CLI for inspecting, calling, and debugging MCP servers from terminal.

ariffazil Skill

Unified APEX constitutional gate evaluator. Parameterized by gate_type to evaluate proposed actions against arifOS F1-F13 floors, scope boundaries, authority claims, reversibility requirements, audit coverage, and MCP tool approval routing. Merges: apex_floor_check, apex_scope_check, apex_authority_check, apex_reversibility_test, apex_audit_coverage_check, apex_tool_approval_gate.

ariffazil Skill

Identifies and recognizes the sovereign (Arif, F13) before any action that targets them, addresses them, or binds them. Prevents agent

gptomics Bundle

Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

gptomics Bundle

Dimensionality reduction and graph-based clustering for single-cell RNA-seq with Scanpy (Python) and Seurat (R). Resolves which algorithm to use (Leiden vs Louvain), how many PCs and neighbors to set, how to sweep and validate resolution, when a split is over-clustering, and why post-clustering marker p-values are not valid inference. Use when clustering cells, choosing a clustering resolution, deciding whether two clusters are one population, building a UMAP/tSNE, or judging whether clusters are real.

oimiragieo Bundle

Agent task delegation patterns — spawn protocols, handoff metadata, drain gate, parallel limits, and model selection for multi-agent orchestration

oimiragieo Bundle

LLM-as-judge evaluation framework with 5-dimension rubric (accuracy, groundedness, coherence, completeness, helpfulness) for scoring AI-generated content quality with weighted composite scores and evidence citations

ariffazil Skill

OpenClaw-native /forge — routes execution to a coding agent or A-FORGE. The execution primitive after /init establishes identity and /propose-seal establishes evidence. /forge = "go execute this mutation under my authority."

ariffazil Skill

OpenCode-native /forge — execution primitive. After identity is established via /init, /forge mutates code under the agent's authority band. The flow: /init → /forge → /propose-seal.

ariffazil Skill

Comprehensive multi-engine search engine API & structured SERP extractor via SerpApi MCP server (mcp.serpapi.com). Supports Google, Bing, Yahoo, DuckDuckGo, YouTube, eBay, Google Scholar, stock market, and weather data.

ariffazil Bundle

Probe any MCP server (local or HTTPS) using MCPJam CLI or SDK. Discover protocol version, tool/resource/prompt surface, OAuth conformance, and stateless transport (2026-07-28) support. Use this skill whenever an MCP server endpoint needs to be verified — whether it is the federation organs, a public HTTPS MCP server, or a third-party vendor endpoint.

ariffazil Skill

Persistent conversational memory, semantic code search, dependency graph mapping, pre-compaction session capture, and workspace Q&A via ContextStream MCP server (mcp.contextstream.io/mcp).

oimiragieo Bundle

Byzantine consensus voting for multi-agent decision making. Implements voting protocols, conflict resolution, and agreement algorithms for reaching consensus among multiple agents.

oimiragieo Bundle

Google Workspace integration skill for Gmail, Calendar, Drive, Docs, and Sheets via Python client libraries and MCP servers

oimiragieo Bundle

Shell out to Cursor Agent CLI for headless IDE-aware code tasks. Supports multi-model routing (auto mode routes to Claude, Gemini, GPT). Requires Cursor Pro/Business subscription.

oimiragieo Bundle

Use when the user wants to use Google Gemini for analysis, large files or codebases, sandbox execution, or brainstorming. Uses headless Gemini CLI scripts (no MCP). Triggers on "use Gemini", "analyze with Gemini", "large file", "sandbox", "brainstorm with Gemini".

oimiragieo Bundle

Use when building, debugging, or documenting Telegram bot polling flows that need safe agent routing, state tracking, and final-only replies without webhooks.

oimiragieo Bundle

Creates multi-agent orchestration workflows for complex tasks. Handles enterprise workflows, operational procedures, and custom orchestration patterns. Use when user needs to automate multi-phase processes with agent coordination.

ariffazil Skill

How to test any MCP server — use MCPJam Inspector, not coding agents

gptomics Bundle

Frames PTM/phosphoproteomics analysis as three stacked inference layers on a biased enrichment - chemistry selection, site localization (FLR), and protein-level-adjusted quantification with MSstatsPTM - plus kinase-activity and functional triage. Covers MaxQuant Phospho (STY)Sites multiplicity expansion, localization-probability filtering (class I, Ascore, ptmRS, DIA EG.PTMLocalizationProbabilities, DIA-NN PTM.Site.Confidence), false localization rate (LuciPHOr/DeepFLR), motif analysis with experiment-matched backgrounds, diGly/K-GG ubiquitin specificity, acetyl/glyco traps, and KSEA/PTM-SEA. Use when localizing and quantifying phosphorylation, acetylation, ubiquitination, or glycosylation sites from enrichment-based runs and deciding whether an apparent site change is real after subtracting protein abundance. Peptide ID and open/variable-mod search is peptide-identification; underlying protein-level quant is quantification and differential-abundance; DIA acquisition mechanics is dia-analysis.

gptomics Bundle

Analyze Perturb-seq / CROP-seq single-cell CRISPR screens. Use when assigning guides as a mixture problem, removing non-perturbed escaper cells with Mixscape, choosing a calibrated test (SCEPTRE conditional resampling) over naive DE, quantifying effect size with E-distance, separating compositional shifts from within-state expression change, or judging whether a perturbation-prediction foundation model actually beats a baseline.

oimiragieo Bundle

The Agent Tool Contract — 5 principles for designing tools agents call reliably: predictable signature, rich errors, token-efficient output, idempotency, graceful degradation. Includes anti-pattern table with 8 common mistakes.

ariffazil Skill

AI-powered web scraping, multi-format page extraction, async crawling, schema generation, and monitoring via ScrapeGraph AI MCP server (scrapegraph-mcp).

ariffazil Bundle

Health probe and auto-recovery for constitutional federation MCP servers

ariffazil Skill

Substrate primitive /propose-seal — proposes a sealed candidate to 888-APEX. NEVER self-seals. The flow: agent proposes → 888 judges → F13 authorizes → 999 executes (append to VAULT999).

ariffazil Skill

Enforce Δ·Ω·Ψ multimodal cognition rules. Every AAA agent that reasons about multimodal inputs (images, audio, video, seismic, well logs, market data) MUST load this skill. Constitutional rule: multimodal perception without Δ-substrate metabolism is not cognition. LLM is tri-witness, never judge.