Results for “update”

Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and transfer-vs-de-novo validation. Use when annotating a new assembly of a species with an existing reference, harmonizing coordinates across builds, or mapping annotations across related species.

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Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid, downloading prebuilt NCBI databases via update_blastdb.pl, choosing -task variants (megablast/dc-megablast/blastn/blastn-short), tuning soft/hard masking, scaling threads, or extracting hits with blastdbcmd. Encodes BLAST v5 vs v4 database format, taxonomy filtering, makeblastdb pitfalls.

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Run OpenSpec backlog delivery — validate BACKLOG.md, plan TaskCards, orchestrate agents by phase, review gate, and update backlog state.

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Memory consolidation pass: orient on existing memories, gather signal from logs/transcripts, merge updates into topic files, prune index. Use on 'dream', 'consolidate memory', 'clean up memories', 'prune memories', 'memory maintenance', or when memories feel stale.

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Automate BambooHR tasks via Rube MCP (Composio): employees, time-off, benefits, dependents, employee updates. Always search tools first for current schemas.

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Build real-time web applications with Azure Web PubSub SDK for Java. Use when implementing WebSocket-based messaging, live updates, chat applications, or server-to-client push notifications.

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This skill should be used when the user asks to "create AGENTS.md", "update AGENTS.md", "maintain agent docs", "set up CLAUDE.md", or needs to keep agent instructions concise. Enforces research-backed best practices for minimal, high-signal agent documentation.

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Create or update a Markdown blog draft from recent work and export it with `YYYY-MM-DD_slug.md` naming. Output directory can be set via environment variable or CLI option; if missing, ask the user and pass it explicitly.

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Cascade merge changes through a chain of dependent branches. Use when updating stacked/chained PRs, propagating changes from a parent branch to all downstream branches, or when the user mentions "cascade merge", "propagate changes", "update dependent branches", or "merge to downstream branches".

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Synchronize recent research learnings across all affected theses, sector notes, and macro documents. Use after a research session or when user says "sync", "propagate", or "update everything".

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Rename a thesis file when company name changes. Atomically updates filename, all inbound wikilinks across the vault, graph adjacency entry header, sector note Active Theses entry, snapshot snapshot_of references, and _hot.md mentions. Use when company changes name (FB → META, Square → Block, etc.), or when correcting a typo in a thesis filename.

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Refresh the Key Metrics table in a thesis with current data from Financial Modeling Prep, with a Quartr standardized-statement tie-break for Revenue Growth / Gross Margin gaps (Step 4b-Q) and a scoped web-search fallback (Step 4b) when FMP has no data or resolved the wrong company. Use when user says "numbers", "refresh metrics", "update key metrics", or "refresh [TICKER]" with no other action implied. Surgical edit only — does NOT create research notes or propagate via /sync. Also flags (never auto-edits) stale price/valuation framing in the thesis Summary — see Step 10b.

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Weekly sweep of ALL transcript-bearing spoken events (earnings calls, conference firesides, CMDs, investor days, AGMs, investor updates) for every active thesis, via the Quartr watchlist. Produces a triage digest in Daily Intel/ flagging thesis-touching mentions and recommending deep reads. Use when user says "event sweep", "what did my companies say this week", "conference sweep", or on the weekly schedule. Also `--setup` (build/rebuild the Quartr watchlist from active theses) and `[N]` (window override in days, default 8).

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Refresh the Key Metrics table in a thesis with current data from Financial Modeling Prep, with a scoped web-search fallback (Step 4b) when FMP has no data or resolved the wrong company. Use when user says "numbers", "refresh metrics", "update key metrics", or "refresh [TICKER]" with no other action implied. Surgical edit only — does NOT create research notes or propagate via $sync. Also flags (never auto-edits) stale price/valuation framing in the thesis Summary — see Step 10b.

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Edit EcoSIM PFT-parameter NetCDF files such as ecosim_pftpar_20260303.nc with the ParEditor class from applications/notebooks/scripts/ParamEditor.py. Use when asked to modify, scale, copy, compare, or delete PFT parameter records for a plant functional type (six-character pfts code such as gr3s43 or ndlf34), update microbe parameter NetCDF values, or maintain the JSONL change log that records past parameter changes. Never modify plant_trait.*.desc files; they are read-only references.

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Entry point for new work. Determines the best action path or work decomposition (update existing spec, create new spec, mixed decomposition, or no spec needed) and refines ideas through structured dialogue.

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Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.

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Add descriptions for new models from the HuggingFace router to chat-ui configuration. Use when new models are released on the router and need descriptions added to prod.yaml and dev.yaml. Triggers on requests like "add new model descriptions", "update models from router", "sync models", or when explicitly invoking /add-model-descriptions.

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Edit PDFs with natural-language instructions using the nano-pdf CLI. Modify text, fix typos, update titles, and make content changes to specific pages without manual editing.

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Notion API for creating and managing pages, databases, and blocks via curl. Search, create, update, and query Notion workspaces directly from the terminal.

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Monitor blogs and RSS/Atom feeds for updates using the blogwatcher CLI. Add blogs, scan for new articles, and track what you've read.

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Manage Linear issues, projects, and teams via the GraphQL API. Create, update, search, and organize issues. Uses API key auth (no OAuth needed). All operations via curl — no dependencies.

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Use when: User wants to run Archon workflows, CREATE workflows or commands, set up Archon, or manage Archon configuration. Triggers (run): "use archon to", "run archon", "archon workflow", "use archon for", "have archon", "let archon", "ask archon to". Triggers (create): "create a workflow", "write a workflow", "make a command", "author a workflow", "new workflow", "new command", "archon workflow yaml". Triggers (setup): "set up archon", "install archon", "how to use archon", "configure archon", "archon setup", "get started with archon". Triggers (config): "change my archon config", "modify archon config", "archon config", "change archon settings", "update my config", "help me change my config", "edit archon config", "archon configuration". Triggers (init): "initialize archon", "set up .archon", "archon init", "add archon to repo". Capability: Runs AI workflows in isolated git worktrees for parallel development. Also: Creates and manages workflow YAML files, command files, and configuration. NOT for: Direct Claude Code work - only for delegating to Archon CLI.

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Use when the user wants to change an existing PRD — 'refinar o PRD', 'adicionar requisito', 'atualizar escopo do PRD', 'update the PRD' — through targeted questions, bumping the version and re-opening approval. Do NOT use to create a PRD (prd-create).

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