---
name: start
description: Orient a session on this plugin. BioNexus is a Scientific Reliability Layer for AI-Assisted Biology. Route completed single-cell DE to the pre-submission shadow review; check backend readiness before a requested analysis. Do not assign cell-type labels or run analyses from this skill.
---

# BioNexus start

BioNexus is a **Scientific Reliability Layer for AI-Assisted Biology**, not a generic bioinformatics toolbox. Its Capability Plane provides **reference implementations** to demonstrate and test evidence boundaries. It stops at **numeric clusters + marker tables** and does not annotate cell types.

## First laboratory use

For completed single-cell differential expression, use `single-cell-de-audit`.
Start with existing DE results, a sample sheet and the proposed claim. The core
table-review path does not require scientific backends or a new analysis run.
`bionexus audit-de --demo --bundle review-demo` demonstrates a synthetic review;
it deliberately returns a non-pass and never establishes laboratory benefit.

For other tasks, preserve the explicit user scope and use the routes below.

## Before backend execution

```bash
python scripts/doctor.py
```

Honor `tier`, `ready.scverse_ready` / `scvi_ready` / `spatial_ready`, `allowed_next_actions`, and `forbidden_claims`.

Install: `pip install -e .` (kernel). scRNA gold chain: `pip install -e ".[goldchain]"`. Spatial: `pip install -e ".[spatial]"`. Full scVI: `pip install -e ".[scverse]"`.

## Capability Plane: Reference Implementations

The capability plane provides reference execution pipelines (not an all-in-one bioinformatics suite):

| Priority | Tier | Skills (Reference Implementations) | When |
|---|---|---|---|
| 1 | **core** | `single-cell-rna-qc`, `spatial-transcriptomics` (squidpy), `scvi-tools`, `nextflow-development` | Default for real data |
| 2 | wrapper | Allotrope, provenance | Named lab-ops jobs |
| 3 | heuristic (not auto-discovered) | biologics, pLM, ACMG combiner, structure, multiome | Only if user asked **and** accepts grade C |
| 4 | outline | start, problem-selection | Planning only |

Heuristic skills live as `SKILL.legacy.md`. Do **not** open them for a generic “analyze my data” request. To opt in, rename that file back to `SKILL.md`.

## Core scRNA gold chain

```bash
python scripts/doctor.py
python skills/single-cell-rna-qc/scripts/scrna_inspect.py raw.h5ad
python skills/single-cell-rna-qc/scripts/scrna_convert.py 10x_dir/ -o raw.h5ad
python skills/single-cell-rna-qc/scripts/scrna_pipeline.py raw.h5ad -o clustered.h5ad
python skills/single-cell-rna-qc/scripts/scrna_plot.py clustered.h5ad -o figures/
python skills/single-cell-rna-qc/scripts/scrna_scrublet.py raw.h5ad -o raw_scrub.h5ad
python skills/single-cell-rna-qc/scripts/scrna_pseudobulk.py clustered.h5ad -o pb.csv --by sample condition --design pb_design.tsv
python skills/single-cell-rna-qc/scripts/scrna_deseq.py pb.csv --design pb_design.tsv --condition condition --reference control --contrast-level treated -o de.csv
```

## Core spatial gold chain (squidpy)

```bash
python skills/spatial-transcriptomics/scripts/spatial_inspect.py visium.h5ad
python skills/spatial-transcriptomics/scripts/spatial_pipeline.py visium.h5ad -o spatial_out.h5ad
```

Endpoint: clustered `.h5ad` + markers/SVG CSV. Clusters are numbers. Do not invent cell types.

## When **not** to use a core skill

| User has | Do not use | Use instead |
|---|---|---|
| Only FASTQs / need nf-core | `scrna_pipeline.py` | `nextflow-development` |
| Already-clustered object, just plots | full gold chain | `scrna_plot.py` / `spatial_inspect.py` |
| Technical batch that Harmony cannot fix | Harmony-only | `scvi-tools` on **counts** |
| Spatial without coordinates | spatial gold chain | refuse; do not invent `obsm['spatial']` |
| “What cell type is this?” | this plugin | stop; clusters stay numeric |

## MCP

Local server defaults to the BioNexus compatibility surface (UniProt, Ensembl, gnomAD, PDB, AF, Reactome, STRING, GEO, GTEx). Prefer dedicated Literature/Database peer plugins when the host provides them; BioNexus does not bundle those peers. Set `BIONEXUS_LOCAL_HOSTED_FALLBACKS=1` only for disaster recovery.