> ## Documentation Index > Fetch the complete documentation index at: https://hubify.com/docs/llms.txt > Use this file to discover all available pages before exploring further. # MCP Tools Reference > All 48 Hubify MCP tools. Platform tools (unprefixed) drive lab data directly. Phase E ledger tools (hubify_* prefix) write to the agentEvents ledger and appear in the Hubify web app in real time. # MCP Tools Reference The Hubify MCP server exposes **48 tools** across two categories: | Category | Count | Prefix | Use for | | -------------------- | ----- | --------- | ----------------------------------------------------------- | | Platform tools | 31 | none | Reading and writing lab data directly | | Phase E ledger tools | 17 | `hubify_` | Writing to the agentEvents ledger; surfaces in Captain View | All tools work without authentication for both read and write operations when the MCP server is configured with `CONVEX_URL` and `HUBIFY_LAB_SLUG`. *** ## Platform Tools ### Lab Navigation #### `lab_create` Create a new lab and automatically provision a matching GitHub repository. If the user has a connected GitHub account, the repo is created in their own account. Otherwise it is created in the `Hubify-Projects` org. | Parameter | Type | Required | Description | | ------------- | ------- | -------- | --------------------------------------------------- | | `userId` | string | Yes | Convex user ID | | `name` | string | Yes | Lab name (used as repo name base) | | `description` | string | No | Short description | | `mission` | string | No | Mission statement | | `subdomain` | string | No | URL subdomain (auto-derived from name if omitted) | | `isPublic` | boolean | No | Whether the lab and repo are public (default: true) | Returns: `{ labId, repoUrl }` — `repoUrl` is `null` if GitHub repo creation failed (lab is still created). *** #### `lab_status` Get a snapshot of the current lab: experiment count, paper count, agent count, pod count, anomaly count. No parameters. *** #### `lab_list` List every lab on this Convex deployment with slug, name, status, and which is currently active. No parameters. *** #### `lab_switch` Hot-swap the active lab for the current MCP session without restarting. | Parameter | Type | Required | Description | | --------- | ------ | -------- | ------------------------------------------------------------------- | | `slug` | string | No | Lab slug to switch to. Omit to reset to the env-configured default. | *** ### Experiments #### `experiment_list` List experiments with status, title, and runtime. | Parameter | Type | Required | Description | | --------- | ------ | -------- | ------------------------------------------------------ | | `status` | string | No | Filter: `queued`, `running`, `pass`, `fail`, `blocked` | *** #### `experiment_create` Create and queue a new experiment (auto-generates `EXP-NNN` ID). | Parameter | Type | Required | Description | | ------------- | ------ | -------- | ---------------------------------------------- | | `title` | string | Yes | Experiment title | | `config` | string | No | JSON config string (hyperparameters, etc.) | | `template` | string | No | Template name to base the experiment on | | `computeMode` | string | No | `gpu`, `cpu`, or `distributed`. Default: `gpu` | *** #### `experiment_run` Dispatch a queued experiment to a GPU pod. Accepts `EXP-*` ID or Convex document `_id`. | Parameter | Type | Required | Description | | -------------- | ------ | -------- | --------------------------------------------------- | | `experimentId` | string | Yes | `EXP-BB-001` or Convex `_id` | | `podId` | string | No | Target pod ID. Auto-picks a running pod if omitted. | *** #### `experiment_queue` List queued and running experiments. No parameters. *** ### Papers #### `paper_list` List all papers with readiness percentages and status. No parameters. *** #### `paper_create` Create a new paper draft. | Parameter | Type | Required | Description | | ---------- | ------ | -------- | ------------------------------------------------------------- | | `title` | string | Yes | Paper title | | `abstract` | string | No | Paper abstract | | `target` | string | No | Target journal (e.g. `Physical Review D`, `MNRAS`) | | `status` | string | No | `draft`, `review`, `submitted`, `published`. Default: `draft` | *** #### `paper_review` Trigger a cross-model peer review on a paper via the orchestrator. | Parameter | Type | Required | Description | | ----------- | ------ | -------- | ------------------- | | `paperName` | string | Yes | Paper name or title | *** ### Tasks #### `task_list` List tasks with status and priority. | Parameter | Type | Required | Description | | --------- | ------ | -------- | ---------------------------------------------------------- | | `status` | string | No | Filter: `backlog`, `todo`, `in_progress`, `review`, `done` | *** #### `task_create` Create a new task. | Parameter | Type | Required | Description | | ------------- | ------ | -------- | ---------------------------------------------------- | | `title` | string | Yes | Task title | | `description` | string | No | Task details | | `priority` | string | No | `low`, `medium`, `high`, `urgent`. Default: `medium` | | `status` | string | No | Initial status. Default: `todo` | *** #### `task_update` Update task status or priority. | Parameter | Type | Required | Description | | ---------- | ------ | -------- | ----------------- | | `taskId` | string | Yes | Convex task `_id` | | `status` | string | No | New status | | `priority` | string | No | New priority | *** ### Memory & Knowledge #### `memory_search` Search across all 4 memory layers: user messages, agent learnings, knowledge wiki, and lab decisions. | Parameter | Type | Required | Description | | --------- | ------ | -------- | ------------------------------------------------------------- | | `query` | string | Yes | Search query | | `layer` | string | No | `user`, `agent`, `lab`, `decisions`, or `all`. Default: `all` | *** #### `memory_save` Save to the lab memory system. | Parameter | Type | Required | Description | | ----------- | ------ | ----------- | -------------------------------------- | | `type` | string | Yes | `preference`, `decision`, or `message` | | `key` | string | Conditional | Required for `preference` type | | `value` | string | Conditional | Required for `preference` type | | `title` | string | Conditional | Required for `decision` type | | `decision` | string | Conditional | Required for `decision` type | | `rationale` | string | Conditional | Required for `decision` type | | `content` | string | Conditional | Required for `message` type | | `summary` | string | No | One-line summary for `message` type | *** #### `knowledge_search` Full-text search across the lab's knowledge base: experiments, papers, agents, surveys, knowledge entries. | Parameter | Type | Required | Description | | --------- | ------ | -------- | ------------ | | `query` | string | Yes | Search query | *** #### `knowledge_add` Add an entry to the lab's knowledge wiki. | Parameter | Type | Required | Description | | ----------------- | --------- | -------- | --------------------------------------------------------------- | | `name` | string | Yes | Entry name (e.g. `Hellings-Downs Correlation`) | | `entityType` | string | Yes | `concept`, `entity`, `source`, `method`, `result`, or `dataset` | | `description` | string | No | Entry description | | `relatedEntities` | string\[] | No | Related entity names | *** #### `agent_learning_save` Save an operational or scientific learning to agent memory. | Parameter | Type | Required | Description | | ------------ | ------ | -------- | ----------------------------------------------------------------- | | `key` | string | Yes | Short unique key (e.g. `mcmc-convergence-criteria`) | | `insight` | string | Yes | What was learned — specific and actionable | | `type` | string | No | `operational`, `scientific`, `procedural`. Default: `operational` | | `confidence` | number | No | Confidence 0–1. Default: 0.7 | *** ### Contributions #### `contribution_list` List scientific contributions with novelty scores. | Parameter | Type | Required | Description | | --------- | ------ | -------- | ------------------------ | | `limit` | number | No | Max results. Default: 20 | *** #### `contribution_create` Log a scientific contribution. | Parameter | Type | Required | Description | | ------------- | ------ | -------- | ----------------------------------------------------------------------------------------------------- | | `title` | string | Yes | Contribution title | | `description` | string | Yes | What was discovered or contributed | | `type` | string | No | `prediction`, `measurement`, `method`, `catalog`, `constraint`, `null_result`. Default: `measurement` | *** ### Agents & Communication #### `agent_list` List all agents with roles, status, and models. No parameters. *** #### `chat` Send a message to the lab orchestrator and wait for its response. Shares history with the web chat and CLI surfaces. | Parameter | Type | Required | Description | | ----------- | ------ | -------- | ----------------------------------------------------------- | | `message` | string | Yes | Message to send | | `sessionId` | string | No | Existing session ID to resume. Pass `"new"` to start fresh. | | `waitMs` | number | No | Max wait for response in ms. Default: 90000 | *** ### Compute & Costs #### `pod_list` List GPU pods with status, GPU type, and cost. No parameters. *** #### `pod_create` Create a new GPU pod via RunPod API. | Parameter | Type | Required | Description | | --------- | ------ | -------- | ------------------------------------------------------- | | `gpuType` | string | No | GPU type (e.g. `H200`, `H100`, `A100`). Default: `H100` | | `name` | string | No | Pod name | *** #### `cost_summary` Get daily/weekly/monthly/all-time cost breakdown vs budget. No parameters. *** ### Misc #### `notification_list` List recent notifications (alerts, experiment completions, agent messages). | Parameter | Type | Required | Description | | ------------ | ------- | -------- | ----------------------------------------- | | `limit` | number | No | Max results. Default: 20 | | `unreadOnly` | boolean | No | Only unread notifications. Default: false | *** #### `survey_list` List astronomical surveys with anomaly counts and source statistics. No parameters. *** #### `figure_list` List all figures with titles, types, and image URLs. | Parameter | Type | Required | Description | | --------- | ------ | -------- | ------------------------ | | `limit` | number | No | Max results. Default: 20 | *** #### `standup_trigger` Trigger an agent standup. | Parameter | Type | Required | Description | | --------- | ------ | -------- | -------------------------------------------------- | | `type` | string | No | `morning`, `midday`, `evening`. Default: `morning` | *** #### `activity_list` List recent lab activity (experiment completions, agent actions, alerts). | Parameter | Type | Required | Description | | --------- | ------ | -------- | ------------------------ | | `limit` | number | No | Max results. Default: 20 | *** ## Phase E Ledger Tools (`hubify_*`) These tools write to the `agentEvents` ledger. Events appear in real time in the Hubify web app's Captain View and activity feed. Use these when Claude Code is acting as a local lab operator. ### Context & Session #### `hubify_get_context` Full lab snapshot as structured JSON: lab metadata, stats, recent events, contributions, papers. Use at session start. | Parameter | Type | Required | Description | | ------------- | ------ | -------- | ------------------------------------- | | `recentLimit` | number | No | Recent events to include. Default: 25 | *** #### `hubify_get_context_pack` Token-budgeted plain-text context pack for agent system prompts (lab state + in-flight experiments + recent events). | Parameter | Type | Required | Description | | ---------- | ------ | -------- | ------------------------------------------------------------------ | | `target` | string | No | Compaction style: `claude`, `codex`, `generic`. Default: `generic` | | `maxBytes` | number | No | Approximate output cap. Default: 8000 | *** #### `hubify_create_session_summary` Persist a session summary to the ledger. Use at the end of every Claude Code session. | Parameter | Type | Required | Description | | ------------ | ------ | -------- | ------------------------------------------------------ | | `summary` | string | Yes | Markdown or plain-text summary of what was done | | `sessionId` | string | No | Session identifier. Auto-generates a UUID if omitted. | | `durationMs` | number | No | Session duration in ms | | `surface` | string | No | Where the session ran: `claude-code`, `cli`, `sidebar` | *** ### Event Logging #### `hubify_log_event` Append a typed event to the agentEvents ledger. Idempotent on `clientEventId`. Common event types: `paper.section.drafted`, `experiment.completed`, `discovery.proposed`, `run.recorded`, `agent.woke`, `agent.sleeping`. | Parameter | Type | Required | Description | | --------------- | ------ | -------- | ------------------------------------------------------------------------------------- | | `type` | string | Yes | Dotted event type (e.g. `paper.section.drafted`) | | `clientEventId` | string | No | Idempotency key. Auto-generated if omitted. | | `actorKind` | string | No | `captain`, `agent`, `orchestrator`, `system`, `webhook`, `cli`, `mcp`. Default: `mcp` | | `actorLabel` | string | No | Human-readable actor name (e.g. `claude-code`) | | `entityType` | string | No | Entity the event is about (`paper`, `experiment`, `claim`) | | `entityId` | string | No | Convex `_id` or external ID of the entity | | `payload` | object | No | JSON-encodable body | | `severity` | string | No | `debug`, `info`, `warn`, `error`. Default: `info` | | `correlationId` | string | No | Links related events together | | `parentEventId` | string | No | Parent event for nested flows | *** #### `hubify_log_finding` Log a scientific finding. When `noveltyScore >= 6`, also creates a contributions row visible in the Contributions UI. | Parameter | Type | Required | Description | | -------------- | --------- | -------- | ----------------------------------------------------------- | | `summary` | string | Yes | One-paragraph summary of the finding | | `noveltyScore` | number | No | 1–10 novelty rating. Default: 5 | | `claimIds` | string\[] | No | Related claim IDs | | `experimentId` | string | No | Source experiment Convex `_id` | | `type` | string | No | `method`, `dataset`, `result`, `theorem`. Default: `result` | *** #### `hubify_sync_events` Batch-flush locally-buffered events in one round-trip. Idempotent on `clientEventId`. | Parameter | Type | Required | Description | | --------- | --------- | -------- | --------------------------------------------------------------------- | | `events` | object\[] | Yes | Array of event objects, each with `type` and `clientEventId` required | Each event in the array accepts: `type`, `clientEventId`, `actorKind`, `actorLabel`, `entityType`, `entityId`, `payload`, `severity`, `correlationId`, `occurredAt`. *** ### Run & Claims #### `hubify_record_run` Record a new run directory, tying paths to the originating experiment. Emits `run.recorded`. | Parameter | Type | Required | Description | | -------------- | --------- | -------- | -------------------------------------- | | `runId` | string | Yes | Run ID, e.g. `2026-04-29-mcmc-final` | | `paths` | string\[] | Yes | Files written (relative to repo root) | | `experimentId` | string | No | Source experiment `_id` | | `summary` | string | No | Brief summary of what the run produced | *** #### `hubify_create_claim` Create a scientific claim. Emits `claim.proposed` and creates a contributions row. | Parameter | Type | Required | Description | | -------------- | ------ | -------- | ------------------------------------- | | `text` | string | Yes | The claim — one falsifiable assertion | | `paperId` | string | No | Paper this claim belongs to | | `experimentId` | string | No | Source experiment `_id` | | `noveltyScore` | number | No | 1–10. Default: 5 | *** #### `hubify_update_claim` Update a claim's status. Emits `claim.upserted`, `claim.supported`, or `claim.refuted`. | Parameter | Type | Required | Description | | -------------- | --------- | -------- | -------------------------------- | | `claimId` | string | Yes | Claim contribution `_id` | | `action` | string | Yes | `upsert`, `support`, or `refute` | | `text` | string | No | New claim text (for `upsert`) | | `evidenceIds` | string\[] | No | Evidence IDs (for `support`) | | `refuterIds` | string\[] | No | Refuting IDs (for `refute`) | | `noveltyScore` | number | No | Updated novelty score | *** ### Status #### `hubify_compute_status` Current pod and compute status, cost totals, monthly budget, and budget headroom. No parameters. *** #### `hubify_repo_status` Lab GitHub repo wiring: URL, default branch, manifest schema version, auto-push state. No parameters. *** ### Paper Pipeline #### `hubify_get_paper_pipeline_status` Return pipeline state for a paper: title, status, readiness %, target venue, last-updated. | Parameter | Type | Required | Description | | --------- | ------ | -------- | ------------------ | | `paperId` | string | Yes | Paper Convex `_id` | *** #### `hubify_update_paper_stage` Move a paper to a new pipeline stage. Emits `paper.stage.changed` and updates the paper row. | Parameter | Type | Required | Description | | ----------- | ------ | -------- | ------------------------------------------------------------------------------------- | | `paperId` | string | Yes | Paper Convex `_id` | | `from` | string | Yes | Current stage (e.g. `drafting`) | | `to` | string | Yes | Target stage (e.g. `internal-review`) | | `newStatus` | string | No | New top-level status if it should change: `draft`, `review`, `submitted`, `published` | *** #### `hubify_update_paper_section` Record that a paper section was drafted, edited, or completed. Emits `paper.section.drafted`, `paper.section.edited`, or `paper.section.completed`. Note: does not write `.tex` content directly — the round-trip GitHub sync owns the file content. | Parameter | Type | Required | Description | | --------- | ------ | -------- | -------------------------------------------------------- | | `paperId` | string | Yes | Paper Convex `_id` | | `section` | string | Yes | Section name (e.g. `introduction`, `methods`, `results`) | | `action` | string | Yes | `draft`, `edit`, or `complete` | | `sha` | string | No | Git commit sha if known | | `summary` | string | No | Brief description of what changed | *** ### Adversarial Review #### `hubify_start_adversarial_review` Kick off a multi-model adversarial peer review for a paper. Emits `adversarial_review.started` and triggers parallel reviewer roles. | Parameter | Type | Required | Description | | ---------- | --------- | -------- | --------------------------------------------------------------------------------------- | | `paperId` | string | Yes | Paper Convex `_id` | | `roles` | string\[] | No | Reviewer roles (e.g. `["skeptic", "statistician"]`). Backend defaults apply if omitted. | | `abstract` | string | No | Override the stored abstract for this review round | *** #### `hubify_log_model_review` Record one model's verdict in an in-flight adversarial review. Creates a paperReviews row visible in the reviews UI. | Parameter | Type | Required | Description | | --------------- | --------- | -------- | ------------------------------------------------------- | | `paperId` | string | Yes | Paper Convex `_id` | | `role` | string | Yes | Reviewer role (`skeptic`, `statistician`, `generalist`) | | `model` | string | Yes | Model identifier (e.g. `claude-opus-4-8`) | | `verdict` | string | Yes | `approve`, `concern`, or `reject` | | `summary` | string | Yes | Review summary | | `findings` | string\[] | No | Specific findings | | `correlationId` | string | No | Correlation ID from `hubify_start_adversarial_review` | *** #### `hubify_create_review_consensus` Synthesize an adversarial review verdict. Emits `consensus.created` and triggers the synthesis action. | Parameter | Type | Required | Description | | --------------- | --------- | -------- | ----------------------------------------------------- | | `paperId` | string | Yes | Paper Convex `_id` | | `verdict` | string | Yes | `approve`, `minor`, `major`, or `reject` | | `blockers` | string\[] | No | Blocking issues that must be resolved | | `correlationId` | string | No | Correlation ID from `hubify_start_adversarial_review` | *** ## MCP Resources In addition to tools, the MCP server exposes read-only resources: | Resource URI | Contents | | ------------------- | --------------------------------------- | | `lab://status` | Lab stats as JSON | | `lab://experiments` | All experiments as JSON | | `lab://papers` | All papers as JSON | | `lab://agents` | All agents as JSON | | `lab://tasks` | All tasks as JSON | | `lab://memory` | Lab decisions + agent learnings as JSON | *** ## MCP Prompts Four built-in prompt templates available in any MCP client: | Prompt | Description | | --------------------- | --------------------------------------------------- | | `research-assistant` | Research assistant with full lab context injected | | `paper-reviewer` | Rigorous peer reviewer for a specific paper | | `experiment-designer` | Designs next experiments based on completed results | | `houston-method` | Post-experiment 9-step Houston Method checklist | | `standup-facilitator` | Facilitates agent standups with real lab data |