# Install the Tahoe plugin

> **Connected to Tara before 14 Oct 2026? Remove that connection and add it again.** Connections made before then were issued by the old sign-in and stop working. Run `claude mcp remove tahoe-public` (Claude Code) or `codex mcp remove tahoe-public` (Codex), then install again below.

This document is written for an agent to follow. The agent installs Tara and starts the sign-in; the user completes it in the browser. After the install, start the client's own login flow if authentication is missing, without another permission question; the user completes the sign-in and host-required approvals (such as sandbox escalation) still apply. In Codex, first check with `codex mcp list` (the Auth column) and run `codex mcp login tahoe-public` only if tahoe-public is not logged in; it opens the system browser itself, and if the sandbox blocks the local callback listener or the browser launch, request escalation rather than skipping the step. Claude Code's agent cannot start OAuth, so tell the user to run /mcp, choose tahoe-public, and Authenticate (or it prompts on first use). The user completes the sign-in in the browser that opens. The agent must never open or drive a browser itself, never use Computer Use, and never print or inspect credentials. Then tell the user what comes next. Claude Code: run /mcp, choose tahoe-public, Authenticate — no restart needed. Codex: run `codex mcp login tahoe-public` if needed, then start a new session. An agent with no UI
(a terminal/CLI agent) follows Path 2.

Tahoe Public MCP exposes Tahoe's Frontier Scale Datasets to your AI agent: expression and differential expression, pathway scores,
phenotype readouts, embedding distances, perturbation markers, drug and
cell-line annotations, and guarded read-only SQL.

## 1. Install — pick one path

Add Tahoe's plugin marketplace and install the `tara` plugin.

### Path 1 — an app or desktop agent (it has a UI)

Paste this one-liner into the agent:

    Use curl to read https://tara.tahoebio.io/install.md and perform the setup to install Tara

### Path 2 — a terminal (Codex CLI, Claude Code CLI)

Claude Code:

    claude plugin marketplace add tahoebio/tahoe-public-plugins
    claude plugin install tara@tahoe-public

Then run /mcp, choose tahoe-public, and Authenticate: no restart needed.

Codex:

    codex plugin marketplace add tahoebio/tahoe-public-plugins
    codex plugin add tara@tahoe-public
    codex mcp login tahoe-public

Then start a new Codex session.

## 2. Sign in

> **After you finish signing in, go back to your agent. Claude Code: run /mcp, choose tahoe-public, Authenticate — no restart needed. Codex: run `codex mcp login tahoe-public` if needed, then start a new session.**

Sign in with your email address or Google when prompted — Claude Code asks on first use. Claude Code: run /mcp, choose tahoe-public, Authenticate — no restart needed. Codex: run `codex mcp login tahoe-public` if needed, then start a new session. A connection added before 14 Oct 2026 must be removed and re-added.

Open preview: any verified email address, or a Google account.

If your browser shows 'site can't be reached' after you sign in or verify your email, your app has already finished or stopped waiting: run the sign-in again (`codex mcp login tahoe-public`, or /mcp in Claude Code) — your account is already created.

## Tools don't appear after signing in?

Claude Code reconnects by itself after you sign in, so it needs no restart. Codex keeps its
signed-out state in a session that was already open, so it needs a new one.

1. Claude Code: run /mcp, choose tahoe-public, and Authenticate. No restart needed.
2. Codex: run `codex mcp list` and check the Auth column. If tahoe-public is not logged
   in, run `codex mcp login tahoe-public`; then start a new session.
3. If you added the server before 14 Oct 2026, remove it and add it again (see the note at the
   top of this page).


## 3. Advanced: connect the server directly

Skip the plugin and add the MCP server itself.

Claude Code:

    claude mcp add --transport http --scope user tahoe-public https://tara.tahoebio.io/mcp

Codex:

    codex mcp add tahoe-public --url https://tara.tahoebio.io/mcp

## Tools

### Find & resolve

Pin a release, then find the drugs, doses, cell lines and genes to ask about.

Example: Which MEK and RAF inhibitors are in Tahoe's data? 4 MEK (Binimetinib, Cobimetinib, TAK-733, Trametinib) and 3 RAF (Dabrafenib, Encorafenib, Vemurafenib).

- `list_releases`: Available dataset releases and supported tools. Call this first.
- `search_conditions`: Find conditions — drug, dose and cell line — in the index.
- `resolve_genes`: Resolve gene symbols and Ensembl ids; exact, ambiguous or not_found, never a guess.
- `list_cell_lines`: The cell lines: Cellosaurus id, name, DepMap id, organ and driver annotations.
- `get_drug_info`: Drug annotations: targets, mechanism class, approval status; filter by drug, moa or target.

### Expression

Gene expression for drugs × cell lines, against matched vehicle controls.

Example: Which genes does trametinib change most versus vehicle in a melanoma cell line, and is DUSP6 among the top down-regulated? DUSP6 is down-regulated by trametinib in C32 at 0.5 µM on both plates (log2 fold change −5.24 and −0.95), though not among the top genes returned by adjusted p-value.

- `get_expression_slice`: Pseudobulk expression for genes × conditions, with matched controls and the release and request it answered.
- `get_differential_expression`: Drug-versus-vehicle differential expression per contrast, with the release and request it answered.
- `get_perturbation_markers`: The genes a classifier found most important for one drug × cell line condition.

### Pathways

Pathway-level (VISION) scores in place of single genes.

Example: Does binimetinib up- or down-regulate KRAS signaling? Down-regulates: the median Hallmark KRAS score is negative at every dose.

- `search_gene_sets`: Find gene sets (pathways) by name or collection, to pass to get_pathway_scores.
- `get_pathway_scores`: Differential VISION pathway scores per drug × cell line, with the release and request it answered.
- `get_validated_signatures`: The validated readout for a cancer process, with its evidence and caveats, when that panel is enabled.

### Phenotypes & embeddings

Whole-cell readouts and how far a drug moves a cell line's state.

Example: Which drugs most deplete skin (melanoma) lines relative to the other pooled lines, and do they also move cells furthest from vehicle? Epirubicin in SK-MEL-2 at 5 µM has a relative-depletion score of −2.61 (not absolute viability); among these sampled conditions, depletion and embedding-distance rankings differ.

- `get_phenotype_scores`: Survival, cell-cycle, heterogeneity and separability readouts for drugs × cell lines.
- `get_embedding_distance`: How far a drug moves a cell line's state from vehicle, in the release's embedding space.

### SQL & guidance

Your own read-only queries, the analysis guide, and a liveness check.

Example: Which MOA most raises the interferon α/β response at the highest dose? MEK inhibitors (Hallmark interferon-alpha response, 5 µM).

- `run_sql`: Read-only SQL over the approved tables, guarded and cost-bounded; the exact SQL is returned.
- `get_guide`: How to analyse and interpret the data: controls, units, coverage traps.
- `health`: Liveness, the served release, and the response contract version.

## Every answer shows its work

- Completed analysis results name the data release and record the request they answered.
- SQL is read-only and checked before it runs; the exact SQL is returned so you can inspect and re-run it.
- If a result was trimmed to fit, it says so, names the reason and states how many rows it returned.
- Sign in with your email address or Google; data licences vary by dataset.

## Free during preview — fair-use limits

- 10,000 queries per day per user (run_sql counts as 1; fetching a pending result counts as 1).
- Up to 5 queries running at once per user.
- Results arrive in seconds, or as a handle to fetch later (kept about 12 hours).
- Each result holds up to 1,000 rows and 40 KB.
- Open preview: any verified email address, or a Google account.

## FAQ

**Why does my client keep saying I'm signed out?** If your client keeps asking you to sign in again — Codex especially — remove the tahoe-public connection and add it again. The stored sign-in cannot be refreshed, so retrying the connection does not clear it.

**Who can use it?** Anyone with an email address or a Google account.

**What data is in it?** Tahoe's Frontier Scale Datasets — single-cell perturbation data across drugs and cell lines; not DepMap or PRISM. DepMap ids appear only as cell-line labels. More datasets are planned.

**What is the licence?** Data licences depend on the selected dataset; see the terms page. Call list_releases for available datasets and get_guide for attribution. VISION signatures retain their source terms; guidance is all rights reserved.

**What are the limits?** 10,000 queries per day per user, up to 1,000 rows and 40 KB per result. See the fair-use limits above.

**What if the tools don't appear?** Restart your session after signing in.

## License

Data: dataset-specific licences. Guidance: All rights reserved.

## Links

- [Terms](https://tara.tahoebio.io/terms)
- [Privacy](https://tara.tahoebio.io/privacy)
- [Data licences by dataset](https://tara.tahoebio.io/terms)
- [Guidance: All rights reserved](https://tara.tahoebio.io/terms)