# Jean — Molecular Biology & Genomics (remote · jeanslabs.vercel.app)

Validated molecular biology tools: cloning, primers, CRISPR, Sanger, alignment, qPCR, phylogenetics

- Trust score: 72/100 (medium)
- Change this week: +4
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `jeanslabs.vercel.app`: 72/100 (this document), [markdown](https://verifymcp.io/servers/genmnz-jean/jeanslabs.md), [page](https://verifymcp.io/servers/genmnz-jean/jeanslabs)

## Channel facts

- Endpoint: `https://jeanslabs.vercel.app/mcp`
- Transports: `streamable-http`
- Auth: `none`
- Version: `1.0.2`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically against the live server, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Endpoint Security**: 63/100
  - The endpoint's TLS certificate is valid, in date, and uses a strong key.
  - Authorisation not fully verified: no authorisation is required to call this server, and 1 tool(s) never declared a destructiveHint. The MCP spec treats an absent hint as destructive by default, so we cannot call this surface safe.
  - HTTPS is enforced; there's no plaintext access path.
  - The HSTS (Strict-Transport-Security) header is present.
  - DNSSEC check failed: this domain isn't protected by DNSSEC.
- **Transport & Reachability**: 100/100
  - Verified streamable-http transport via a live MCP handshake.
- **Schema Quality & AI Usability**: 69/100
  - 100% of prompts and resources have a non-trivial description (not blank, and not just the item's name).
  - AI-judged instruction clarity (good).
  - Context-footprint check failed: tool/resource definitions use about 169415 tokens (~536/item across 316 items; 315 tools + 1 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 53/100
  - Stability observed for 16 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
  - Structured output schemas are declared (99% of tools); any adoption earns full credit.
- **Tool Safety**: 75/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - 0 of 1 tool(s) whose name or description implies an irreversible operation declare an MCP destructiveHint annotation; "consensus_from_traces" implies "merge" and declares readOnlyHint instead, contradicting what its own name says it does.
  - An AI judge read all 317 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a current MCP spec version (2026-07-28).
  - Supports UI / widget rendering.

## Install

### How do I install the Jean — Molecular Biology & Genomics MCP server?

Jean — Molecular Biology & Genomics is a hosted endpoint at https://jeanslabs.vercel.app/mcp, so there is nothing to install locally. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add --transport http genmnz-jean 'https://jeanslabs.vercel.app/mcp'
```

### Cursor

```json
{
  "mcpServers": {
    "genmnz-jean": {
      "url": "https://jeanslabs.vercel.app/mcp"
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "genmnz-jean": {
      "type": "http",
      "url": "https://jeanslabs.vercel.app/mcp"
    }
  }
}
```

### Codex

```toml
[mcp_servers.genmnz-jean]
url = "https://jeanslabs.vercel.app/mcp"
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "genmnz-jean": {
      "type": "remote",
      "url": "https://jeanslabs.vercel.app/mcp",
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add genmnz-jean --url 'https://jeanslabs.vercel.app/mcp' --transport streamable-http
```

### Hermes

```yaml
mcp_servers:
  genmnz-jean:
    url: "https://jeanslabs.vercel.app/mcp"
```

### Netclaw

```json
{
  "McpServers": {
    "genmnz-jean": {
      "Transport": "http",
      "Url": "https://jeanslabs.vercel.app/mcp"
    }
  }
}
```

### Vellum

```bash
assistant mcp add genmnz-jean -t streamable-http -u 'https://jeanslabs.vercel.app/mcp'
```

### Other

```json
{
  "mcpServers": {
    "genmnz-jean": {
      "type": "http",
      "url": "https://jeanslabs.vercel.app/mcp"
    }
  }
}
```

The mcpServers block is a cross-client convention. Remote transports vary, so check your client's docs.

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-05 (score 72, +1)

- [functional] This server's schema is too large to store in full, so we cannot compare its tools day to day

### 2026-11-04 (score 71, 0)

- [functional] This server's schema is too large to store in full, so we cannot compare its tools day to day

### 2026-11-03 (score 71, +1)

- [functional] This server's schema is too large to store in full, so we cannot compare its tools day to day

### 2026-11-02 (score 70, 0)

- [functional] This server's schema is too large to store in full, so we cannot compare its tools day to day

### 2026-11-01 (score 70, +1)

- [functional] This server's schema is too large to store in full, so we cannot compare its tools day to day

### 2026-10-31 (score 69, 0)

- [functional] This server's schema is too large to store in full, so we cannot compare its tools day to day

### 2026-10-30 (score 69, +1)

- [functional] This server's schema is too large to store in full, so we cannot compare its tools day to day

### 2026-10-29 (score 68, 0)

- [functional] This server's schema is too large to store in full, so we cannot compare its tools day to day

## MCP tools (315)

The latest capture was truncated, so this tool list may be partial.

### `list_workflow_templates` (~92 tokens)

Input parameters:

- `id` (string)

### `validate_workflow` (~281 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `graph` (object, required)

### `run_workflow` (~304 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `graph` (object, required)

### `get_open_record` (~142 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)

Output parameters:

- `circular` (boolean)
- `length` (number)
- `name` (string)
- `record` (object|null)
- `sequence` (string)

### `load_record` (~175 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string, required)

Output parameters:

- `circular` (boolean)
- `length` (number)
- `name` (string)
- `record` (object|null)
- `sequence` (string)

### `list_library` (~166 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `kind` (string)

Output parameters:

- `count` (number)
- `ids`
- `items`
- `names`

### `find_restriction_sites` (~181 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `enzymes` (array, required)

Output parameters:

- `sites`

### `find_star_sites` (~232 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `enzymes` (array, required)

Output parameters:

- `enzymes`
- `sites` (number)
- `unexamined` (number)

### `check_methylation_block` (~265 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `enzymes` (array, required)

Output parameters:

- `blocked` (number)
- `blockedEnzymes`
- `enzymes`
- `unexamined` (number)

### `digest_reaction_conditions` (~264 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `enzymes` (array, required)

Output parameters:

- `buffer` (string|null)
- `buffers`
- `cofactors`
- `heatInactivation`
- `singleTube` (boolean)
- `temperaturesC`
- `unknown`

### `enzyme_cut_counts` (~170 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `enzymes` (array, required)

Output parameters:

- `counts`
- `cutters` (number)
- `single` (number)
- `total` (number)
- `zero_cutters` (number)

### `export_map_svg` (~564 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `collapse_duplicate_labels` (boolean)
- `end` (number)
- `enzymes` (array)
- `font` (string)
- `layout` (string)
- `legend` (boolean)
- `show_bases` (boolean)
- `show_labels` (boolean)
- `show_sites` (boolean)
- `size` (number)
- `start` (number)
- `title` (string)
- `transparent` (boolean)

Output parameters:

- `height` (number)
- `rows` (number)
- `sites` (number)
- `svg` (string|null)
- `width` (number)

### `run_gel_lane` (~260 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `detail` (string)
- `product_bp` (number)
- `source` (string, required)

Output parameters:

- `bands`

### `draw_gel` (~886 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `agarose_percent` (number)
- `caption` (boolean)
- `dna_form` (string)
- `exposure` (string)
- `labels` (boolean)
- `ladder` (string)
- `lane_width` (number)
- `lanes` (array, required)
- `mobility_model` (string)
- `stain` (string)

Output parameters:

- `bandCount` (number)
- `calibratedBy` (string)
- `height` (number)
- `ladder` (string)
- `laneCount` (number)
- `offScale` (number)
- `svg` (string|null)
- `width` (number)

### `primer_check` (~301 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `primer` (string, required)
- `thresholds` (object)

Output parameters:

- `bestIdentityPct` (number)
- `bestTier` (string)
- `bindingCount` (number)
- `siteCount` (number)
- `sites`
- `thresholds`

### `design_oligo_plate_order` (~553 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `fill` (string)
- `format` (number)
- `mixed` (boolean)
- `names` (array, required)
- `oligos` (array, required)
- `pad_to_capacity` (boolean)
- `plate_name` (string)

Output parameters:

- `columns`
- `plateCount` (number)
- `reading` (string)
- `refused`
- `sheets`
- `tsv` (string)
- `wellNote` (string)

### `build_genbank_submission` (~660 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `collection_date` (string)
- `genbank` (string, required)
- `geo_loc_name` (string)
- `mol_type` (string)
- `organism` (string)
- `topology` (string)

Output parameters:

- `changes`
- `command` (string)
- `featureTable` (string)
- `files`
- `problems`
- `reading` (string)
- `written` (number)

### `build_ena_submission` (~521 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `collection_date` (string)
- `description` (string)
- `genbank` (string, required)
- `geo_loc_name` (string)
- `mol_type` (string)
- `organism` (string)
- `study` (string)
- `topology` (string)

Output parameters:

- `changes`
- `command` (string)
- `files`
- `flatFile` (string)
- `problems`
- `reading` (string)
- `written` (number)

### `screen_oligo_structure` (~556 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `dna_conc` (number)
- `dntp_conc` (number)
- `dv_conc` (number)
- `max_loop` (number)
- `mv_conc` (number)
- `names` (array)
- `oligos` (array, required)
- `temperature` (number)

Output parameters:

- `clean`
- `conditions`
- `flagged`
- `incompatibleCount` (number)
- `limits`
- `pairs`
- `perOligo`
- `provenance`
- `worstAnyTmC` (number)
- `worstEndTmC` (number)
- `worstHairpinTmC` (number)

### `check_manufacturability` (~394 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `feature` (string)
- `sequence` (string)
- `vendor` (string)

Output parameters:

- `checked` (number)
- `findings`
- `notGraded`
- `outside` (number)
- `profile`
- `reading` (string)
- `repeatScreens`
- `spans`
- `verdict` (string)

### `design_gene_fragment_order` (~479 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `feature` (string)
- `names` (array)
- `phosphorylate` (boolean)
- `plate_name` (string)
- `product` (string)
- `sequences` (array)

Output parameters:

- `columns`
- `plateCount` (number)
- `plateMinimum` (string)
- `profile`
- `reading` (string)
- `refused`
- `rows`
- `sheets`

### `classify_grammar_part` (~217 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)

Output parameters:

- `classification`
- `grammar` (string)
- `isVector` (boolean)
- `level` (number)
- `position` (string)
- `releaseCuts` (number)
- `releaseEnzyme` (string)
- `spans`

### `align_read` (~246 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `read` (string, required)
- `reference` (string)

Output parameters:

- `alignedRead` (string)
- `alignedReference` (string)
- `columns` (number)
- `identity` (number)
- `mismatches` (number)
- `referenceLength` (number)

### `trim_reads` (~669 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `adapter` (string)
- `adapter_kind` (string)
- `max_error_rate` (number)
- `min_length` (number)
- `min_overlap` (number)
- `phred_offset` (number)
- `quality_cutoff_back` (number)
- `quality_cutoff_front` (number)
- `reads` (string, required)

Output parameters:

- `basesRemovedByAdapter` (number)
- `basesRemovedByQuality` (number)
- `readsEmptied` (number)
- `readsWithAdapter` (number)
- `report`
- `trimmedFastq` (string)

### `fastq_qc` (~531 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `adapters` (string)
- `contaminants` (string)
- `grouping` (string)
- `phred_offset` (number)
- `reads` (string, required)

Output parameters:

- `failed` (number)
- `gcDeviationPercent` (number)
- `grades`
- `report`

### `map_reads` (~3634 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `bandwidth` (number)
- `bandwidth_long` (number)
- `base_alignment` (boolean)
- `consensus` (string)
- `consensus_ambiguity` (boolean)
- `consensus_args` (string)
- `consensus_fill_reference` (boolean)
- `consensus_min_depth` (number)
- `consensus_mode` (string)
- `consensus_positions` (string)
- `consensus_profile` (string)
- `consensus_region` (string)
- `consensus_show_deletions` (boolean)
- `consensus_show_insertions` (boolean)
- `depth` (string)
- `depth_count_deletions` (boolean)
- `depth_min_base_quality` (number)
- `depth_min_mapping_quality` (number)
- `depth_min_read_length` (number)
- `depth_remove_overlaps` (boolean)
- `end_bonus` (number)
- `gap_extend` (number)
- `gap_extend_long` (number)
- `gap_open` (number)
- `gap_open_long` (number)
- `homopolymer_compressed` (boolean)
- `k` (number)
- `mark_duplicates` (boolean)
- `markdup_mode` (string)
- `markdup_optical_distance` (number)
- `markdup_remove` (boolean)
- `markdup_supplementary` (boolean)
- `markdup_tag` (boolean)
- `match_score` (number)
- `mates` (string)
- `max_fragment_length` (number)
- `max_gap` (number)
- `max_intron` (number)
- `max_secondary` (number)
- `max_seed_occurrence` (number)
- `md_tag` (boolean)
- `min_chain_score` (number)
- `min_dp_score` (number)
- `min_minimizers` (number)
- `mismatch_penalty` (number)
- `noncanonical_penalty` (number)
- `output_format` (string)
- `preset` (string)
- `reads` (string, required)
- `reference` (string)
- `secondary_ratio` (number)
- `transition_penalty` (number)
- `variants` (boolean)
- `variants_adjust_mq` (number)
- `variants_args` (string)
- `variants_baq` (boolean)
- `variants_count_orphans` (boolean)
- `variants_full_baq` (boolean)
- `variants_gap_extend` (number)
- `variants_gap_open` (number)
- `variants_homopolymer` (number)
- `variants_indel_bias` (number)
- `variants_indel_size` (number)
- `variants_indels` (boolean)
- `variants_keep_reference` (boolean)
- `variants_max_depth` (number)
- `variants_max_indel_depth` (number)
- `variants_min_base_quality` (number)
- `variants_min_indel_fraction` (number)
- `variants_min_indel_reads` (number)
- `variants_min_mapping_quality` (number)
- `variants_overlap_adjustment` (boolean)
- `variants_prior` (number)
- `w` (number)
- `write_secondary` (boolean)
- `zdrop` (number)
- `zdrop_inversion` (number)

Output parameters:

- `calls`
- `consensus` (string)
- `consensusSummary`
- `coverage`
- `depth` (string)
- `flagstat` (string)
- `junctionTable`
- `junctions` (string)
- `mapped` (number)
- `mapq0` (number)
- `markdup` (string)
- `meanIdentity` (number|null)
- `options`
- `paf` (string)
- `properlyPaired` (number)
- `reading` (string)
- `sam` (string)
- `stats`
- `unmapped` (number)
- `variantSummary`
- `vcf` (string)

### `verify_read` (~328 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `aligned_read` (string, required)
- `aligned_ref` (string, required)
- `near_coverage_pct` (number)
- `near_ungapped_pct` (number)
- `read_name` (string)
- `target_len` (number, required)
- `target_name` (string)
- `verified_coverage_pct` (number)
- `verified_max_gaps` (number)
- `verified_ungapped_pct` (number)

Output parameters:

- `coveragePct` (number)
- `identity` (number)
- `indelEvents` (number)
- `mismatches` (number)
- `report`
- `result`
- `status` (string)

### `read_sequencing_qc` (~478 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `coverage_line` (number)
- `kind` (string)
- `step_window` (number)
- `text` (string, required)

Output parameters:

- `contaminationPct` (number|null)
- `contaminationSource` (string|null)
- `depthProfile` (object|null)
- `kind` (string)
- `largestStepFold` (number|null)
- `longestGap` (number|null)
- `minCoverage` (number|null)
- `perbase`
- `plasmidsaurus`
- `positionsAbove20x` (number|null)
- `reading` (string)
- `shape`

### `domesticate_part` (~434 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cds_end` (number, required)
- `cds_start` (number, required)
- `cds_strand` (number)
- `enzyme` (string)
- `sequence` (string)
- `table` (string)
- `table_tsv` (string)

Output parameters:

- `fixedCount` (number)
- `fixes`
- `outsideCds`
- `sequence` (string)

### `design_fusion_site_primers` (~346 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `buffer_bases` (string)
- `enzyme` (string)
- `left_overhang` (string, required)
- `right_overhang` (string, required)
- `sequence` (string)
- `target_tm` (number)

Output parameters:

- `forward` (string)
- `forwardTm` (number)
- `product` (string)
- `releasedPart` (string)
- `reverse` (string)
- `reverseTm` (number)

### `notebook_cross_refs` (~138 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `body_md` (string, required)

Output parameters:

- `actions`
- `gels`
- `plasmids`

### `history_protocol` (~126 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `root` (object, required)

Output parameters:

- `protocol` (string)

### `scrub_restriction_sites` (~297 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `dna` (string, required)
- `protein` (string, required)
- `table` (string)
- `table_tsv` (string)

Output parameters:

- `dna` (string)
- `fixCount` (number)
- `fixes`

### `fold_rna` (~145 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `seq` (string, required)

Output parameters:

- `dg` (number|null)
- `dotBracket` (string|null)

### `pcr_amplify` (~865 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `conditions` (object)
- `dimer_threshold` (number)
- `dmso` (number)
- `dmso_model` (string)
- `end_length` (number)
- `forward` (string, required)
- `inner_forward` (string)
- `inner_reverse` (string)
- `limit` (number)
- `mismatches` (number)
- `nn_table` (string)
- `reverse` (string, required)

Output parameters:

- `annealingTempC` (number|null)
- `conditions`
- `crossDimerTmC` (number)
- `forwardTmC` (number)
- `primerDimerCutoff` (number|null)
- `primerDimerRisk` (boolean)
- `primerDimerScore` (number|null)
- `primerDimerVerdict` (boolean|null)
- `productCount` (number)
- `record` (object|null)
- `reverseTmC` (number)
- `round1ProductCount` (number|null)
- `sequence` (string)

### `design_mutagenesis_primers` (~572 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cds` (string, required)
- `codon_usage_tsv` (string)
- `mutation` (string, required)
- `tm_model` (string)

Output parameters:

- `candidates`
- `edgeCase`
- `mutCodon` (string)
- `ntChanges` (number)
- `ntPosition` (number)
- `outer`
- `wtCodon` (string)

### `design_saturation_primers` (~1795 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cds` (string, required)
- `compute_hairpin_homodimer` (boolean)
- `degenerate_codon` (string)
- `dnac1` (number)
- `dnac2` (number)
- `dntp` (number)
- `exclude_flanking_primers` (boolean)
- `five_end_flank` (string)
- `forward_primer` (string)
- `gc_content_weight` (number)
- `hairpin_temperature_weight` (number)
- `k` (number)
- `max_five_end_size` (number)
- `max_gc_content` (number)
- `max_overlap_size` (number)
- `max_overlap_temperature` (number)
- `max_primer_size` (number)
- `max_three_end_size` (number)
- `max_three_end_temperature` (number)
- `mg` (number)
- `min_five_end_size` (number)
- `min_gc_content` (number)
- `min_overlap_size` (number)
- `min_overlap_temperature` (number)
- `min_primer_size` (number)
- `min_three_end_size` (number)
- `min_three_end_temperature` (number)
- `na` (number)
- `oligo_prefix` (string)
- `overlap_temp_range` (number)
- `overlap_temp_range_step` (number)
- `overlap_temp_weight` (number)
- `precision` (number)
- `primer_dimer_temperature_weight` (number)
- `reverse_primer` (string)
- `salt_correction` (string)
- `separate_forward_reverse_temperatures` (boolean)
- `sites` (string, required)
- `solver` (string)
- `three_end_flank` (string)
- `three_end_size_weight` (number)
- `three_end_temp_range` (number)
- `three_end_temp_range_step` (number)
- `three_end_temp_weight` (number)
- `tris` (number)

Output parameters:

- `forwardTemperature` (number)
- `foundCount` (number)
- `fullSequence` (string)
- `overlapTemperature` (number)
- `pairs`
- `reverseTemperature` (number)
- `search`
- `siteCount` (number)

### `design_multisite_primers` (~1194 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cds` (string, required)
- `codon_usage_frequency_threshold` (number)
- `dntp` (number)
- `five_end_flank` (string)
- `five_end_size_weight` (number)
- `gc_content_weight` (number)
- `gc_value_set` (string)
- `hairpin_temperature_weight` (number)
- `k` (number)
- `max_five_end_size` (number)
- `max_gc_content` (number)
- `max_primer_size` (number)
- `max_temperature` (number)
- `max_three_end_size` (number)
- `mg` (number)
- `min_five_end_size` (number)
- `min_gc_content` (number)
- `min_primer_size` (number)
- `min_temperature` (number)
- `min_three_end_size` (number)
- `mutation_coverage_weight` (number)
- `mutations` (string, required)
- `na` (number)
- `non_overlapping_primers` (boolean)
- `organism` (string)
- `precision` (number)
- `primer_dimer_temperature_weight` (number)
- `primer_size_weight` (number)
- `seed` (number)
- `temp_range_size` (number)
- `temp_threshold_step` (number)
- `temp_weight` (number)
- `three_end_flank` (string)
- `three_end_size_weight` (number)
- `tris` (number)
- `use_degeneracy_codon` (boolean)
- `use_primer3` (boolean)

Output parameters:

- `failureCount` (number)
- `fullSequence` (string)
- `mutationCoverage` (number)
- `oligos`
- `reactionTemperature` (number)
- `seed` (number)

### `reverse_complement` (~137 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)

Output parameters:

- `record` (object|null)
- `sequence` (string)

### `translate_sequence` (~310 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cds` (boolean)
- `feature` (string)
- `reverse` (boolean)
- `table` (number)
- `to_stop` (boolean)

Output parameters:

- `length` (number)
- `protein` (string)
- `region` (string)

### `find_orfs` (~159 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alternative_starts` (boolean)
- `min_size` (number)

Output parameters:

- `count` (number)
- `longest` (number)
- `orfs`

### `digest_fragments` (~216 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `enzymes` (array, required)
- `fragment_index` (number)

Output parameters:

- `count` (number)
- `fragments`
- `lengths`
- `parentSpan`
- `record` (object|null)

### `gc_content` (~144 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `window` (number)

Output parameters:

- `gc` (number)
- `plot` (object|null)
- `profile`

### `record_composition` (~276 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `doubleStranded` (boolean)

Output parameters:

- `atPercent` (number|null)
- `composition`
- `extinction`
- `gcPercent` (number|null)
- `isoelectricPoint` (number|null)
- `length` (number)
- `molecularWeight` (number)
- `nonStandard`
- `standardCount` (number)
- `strands` (number)

### `protein_properties` (~770 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cystineConvention` (string)
- `gravyScale` (string)
- `momentWindow` (number)
- `pH` (number)
- `protein` (string, required)

Output parameters:

- `a280` (number|null)
- `aliphatic` (number|null)
- `aromaticity` (number|null)
- `atoms` (number|null)
- `boman` (number|null)
- `charge` (number|null)
- `composition`
- `compositionPercent`
- `elements`
- `extinctionCystines` (number|null)
- `extinctionReduced` (number|null)
- `formula` (string)
- `gravy` (number|null)
- `gravyHydrophobicEnd` (string|null)
- `gravyScale` (string|null)
- `gravyZeroIsMeaningful` (boolean|null)
- `halfLifeEcoli` (string)
- `halfLifeMammalian` (string)
- `halfLifeYeast` (string)
- `helix` (number|null)
- `instability` (number|null)
- `length` (number|null)
- `momentHelix` (number|null)
- `momentSheet` (number|null)
- `momentWindow` (number|null)
- `monoisotopicMw` (number|null)
- `mw` (number|null)
- `nTerminal` (string)
- `nonStandard`
- `pI` (number|null)
- `scaleNonStandard`
- `sheet` (number|null)
- `stable` (boolean|null)
- `turn` (number|null)

### `protein_profile` (~1963 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `edge` (number)
- `kind` (string)
- `normalize` (boolean)
- `protein` (string, required)
- `scale` (string)
- `scaleId` (string)
- `weightVariation` (string)
- `window` (number)

Output parameters:

- `centres`
- `label` (string)
- `normalized` (boolean)
- `peak` (number)
- `peakResidue` (number)
- `plot` (object|null)
- `reference` (string)
- `trough` (number)
- `troughResidue` (number)
- `values`
- `weightVariation` (string)
- `window` (number)

### `protein_signal_peptide` (~334 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `kingdom` (string)
- `minWeight` (number)
- `protein` (string, required)

Output parameters:

- `cleavageAfter` (number)
- `matrix` (string)
- `maturePeptide` (string)
- `score` (number)
- `scores`
- `signalPeptide` (string)
- `siteCount` (number)
- `sites`

### `protein_membrane_profile` (~256 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `angle` (number)
- `minWindows` (number)
- `protein` (string, required)
- `window` (number)

Output parameters:

- `hydrophobicity`
- `moment`
- `plot` (object|null)
- `position`
- `segments`
- `transmembrane` (number)

### `protein_topology` (~290 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `decoding` (string)
- `protein` (string, required)

Output parameters:

- `decoding` (string)
- `helices` (number)
- `logProb` (number)
- `path` (string)
- `posterior`
- `segments`
- `summary` (string)

### `protein_disorder` (~747 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `chargeModel` (string)
- `countHistidine` (boolean)
- `pH` (number)
- `pKaSet` (string)
- `protein` (string, required)
- `window` (number)

Output parameters:

- `boundary` (number)
- `chargeModel` (string)
- `disorderedFraction` (number)
- `disorderedWindows` (number)
- `meanHydropathy` (number)
- `meanNetCharge` (number)
- `overall` (number)
- `pKaSetName` (string)
- `plot` (object|null)
- `positions`
- `scores`
- `segments`
- `unfolded` (boolean)
- `window` (number)
- `windowCount` (number)
- `windows`

### `protein_disorder_metapredict` (~506 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `convert` (boolean)
- `gapClosure` (number)
- `minimumFoldedDomain` (number)
- `minimumIdrSize` (number)
- `protein` (string, required)
- `threshold` (number)
- `version` (string)

Output parameters:

- `converted` (number)
- `disorderedResidues` (number)
- `foldedDomains`
- `idrResidues` (number)
- `idrs`
- `percentDisordered` (number)
- `scores`
- `threshold` (number)
- `version` (string)

### `protein_digest` (~1449 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `charges` (array)
- `customCleave` (array)
- `customExceptions` (array)
- `customRegex` (string)
- `cysteine` (string)
- `enzyme` (string)
- `enzymes` (array)
- `keilExceptions` (boolean)
- `massMax` (number)
- `massMin` (number)
- `maxLength` (number)
- `metOxidation` (string)
- `minLength` (number)
- `missedCleavages` (number)
- `mode` (string)
- `protein` (string, required)
- `semi` (boolean)

Output parameters:

- `count` (number)
- `coverage` (number)
- `peptides`
- `results`
- `sites`
- `totalPeptides` (number)

### `peptide_mass` (~302 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `charges` (array)
- `ionType` (string)
- `sequence` (string, required)

Output parameters:

- `average` (number|null)
- `monoisotopic` (number|null)
- `mz`

### `fragment_ions` (~280 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `ionTypes` (array)
- `maxCharge` (number)
- `sequence` (string, required)

Output parameters:

- `count` (number|null)
- `ions`

### `isotopic_composition` (~159 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `sequence` (string, required)

Output parameters:

- `abundance` (number|null)
- `composition`

### `isotope_envelope` (~276 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `charge` (number)
- `formula` (string)
- `maxIsotope` (number)
- `sequence` (string)

Output parameters:

- `peaks`

### `score_spectrum` (~282 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `intensity` (array, required)
- `mz` (array, required)
- `peptide` (string, required)
- `precursorCharge` (number)
- `tolerance` (number)
- `toleranceUnit` (string)

Output parameters:

- `detail`
- `matches`
- `score` (number|null)

### `read_mgf` (~207 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `text` (string, required)
- `title` (string)

Output parameters:

- `count` (number|null)
- `spectra`

### `read_mzml` (~249 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `id` (string)
- `msLevel` (number)
- `text` (string, required)

Output parameters:

- `count` (number|null)
- `spectra`

### `infer_proteins` (~656 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `aggregation` (string)
- `chargeVariantsSeparate` (boolean)
- `coverageOf` (string)
- `database` (string, required)
- `greedyGroupResolution` (boolean)
- `higherIsBetter` (boolean)
- `ilEquivalent` (boolean)
- `maxAmbiguousResidues` (number)
- `minPeptides` (number)
- `modificationVariantsSeparate` (boolean)
- `peptideProteinResolution` (boolean)
- `psms` (string, required)
- `scoreColumn` (string)
- `scoresArePep` (boolean)
- `useSharedPeptides` (boolean)

Output parameters:

- `ambiguityGroups`
- `count` (number)
- `coverageMap` (string|null)
- `groups`
- `method` (string|null)
- `proteins`
- `scoreColumn` (string|null)

### `bayesian_protein_inference` (~589 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `appendReversedDecoys` (boolean)
- `beta` (number)
- `database` (string, required)
- `decoyPrefix` (string)
- `gamma` (number)
- `gridSearch` (boolean)
- `ilEquivalent` (boolean)
- `maxAmbiguousResidues` (number)
- `peptidePrior` (number)
- `psmCutoff` (number)
- `psms` (string, required)
- `scoreColumn` (string)

Output parameters:

- `count` (number)
- `grid`
- `groups`
- `proteins`
- `psmPosteriors`

### `target_decoy_qvalues` (~336 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `correction` (number)
- `formula` (number)
- `higherIsBetter` (boolean)
- `isDecoy` (array, required)
- `ratio` (number)
- `scores` (array, required)
- `threshold` (number)

Output parameters:

- `accepted` (number|null)
- `decoys` (number|null)
- `fdr` (number|null)
- `q`
- `targets` (number|null)
- `threshold` (number|null)

### `crispr_design_guides` (~403 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `min_stem` (number)
- `nuclease` (string)
- `region_end` (number)
- `region_start` (number)
- `restriction_enzymes` (array)

Output parameters:

- `count` (number)
- `guides`
- `region`
- `topSpacer` (string)
- `totalCandidates` (number)

### `crispr_design_library` (~961 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `barcode_id` (number)
- `custom_prefix` (string)
- `custom_suffix` (string)
- `exclude_graf` (boolean)
- `exclude_poly_t` (boolean)
- `guides_per_target` (number)
- `moi` (number)
- `nuclease` (string)
- `rank` (string)
- `reads_per_oligo` (number)
- `representation` (number)
- `restriction_enzymes` (array)
- `target_type` (string)
- `transduction_efficiency` (number)

Output parameters:

- `count` (number)
- `coverage`
- `distinctSpacers` (number)
- `oligoLength` (number)
- `oligos`
- `perTarget`

### `crispr_analyze_screen` (~666 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `control_columns` (array, required)
- `equalise_replicates` (number)
- `essential_genes` (string, required)
- `fdr_cut` (number)
- `min_reads` (number)
- `non_essential_genes` (string, required)
- `pseudo_count` (number)
- `read_counts` (string, required)
- `sample_columns` (array)

Output parameters:

- `curve`
- `fit`
- `genes`
- `hitBf` (number)
- `hits` (number)
- `training`

### `design_knockout_package` (~981 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `arm_length` (number, required)
- `guides` (number)
- `insert` (string)
- `insert_name` (string)
- `max_mismatches` (number)
- `nuclease` (string)
- `primer_tm` (number)
- `replace_target` (boolean)
- `restriction_enzymes` (array)
- `screen_flank` (number, required)
- `subject` (string)
- `target_end` (number, required)
- `target_name` (string)
- `target_start` (number, required)

Output parameters:

- `chosen`
- `donor`
- `guides`
- `marks`
- `offTargets`
- `order`
- `record` (object|null)
- `report` (string)
- `screening`
- `steps` (array)

### `screen_guides` (~362 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `backbone` (string)
- `gg` (boolean)
- `pre_g` (boolean)
- `spacers` (array, required)

Output parameters:

- `backboneLabel` (string)
- `clean`
- `counts`
- `screened`

### `search_off_targets` (~549 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `circular` (boolean)
- `dna_bulge` (number)
- `limit` (number)
- `max_mismatches` (number)
- `nuclease` (string)
- `rna_bulge` (number)
- `spacer` (string, required)
- `subject` (string)

Output parameters:

- `byMismatch`
- `cfdSpecificity` (number|null)
- `hits`
- `mitSpecificity` (number|null)
- `scored` (boolean)
- `total` (number)

### `survey_off_targets` (~516 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `circular` (boolean)
- `dna_bulge` (number)
- `max_mismatches` (number)
- `nuclease` (string)
- `rna_bulge` (number)
- `spacers` (array, required)
- `subject` (string)

Output parameters:

- `cleanest` (string)
- `counted` (number)
- `searched` (string)
- `skipped`
- `spacers`

### `fold_guide` (~402 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `nuclease` (string)
- `sg_rna` (boolean)
- `spacer` (string, required)

Output parameters:

- `scaffoldIntact` (boolean|null)
- `scaffoldName` (string|null)
- `sgRna`
- `spacer`
- `spacerScaffoldPairs` (number|null)
- `unavailable` (string|null)

### `list_sgrna_scaffolds` (~152 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)

Output parameters:

- `count` (number)
- `scaffolds`

### `scan_splice_sites` (~465 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `max_results` (number)
- `min_maxent` (number)
- `sequence` (string)
- `strand` (string)

Output parameters:

- `count` (number)
- `sites`
- `strongest`
- `strongestMaxEnt` (number|null)

### `scan_motif_sites` (~302 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `motifs` (array, required)
- `sequence` (string)

Output parameters:

- `count` (number)
- `perMotif`
- `sites`

### `scan_sigma70_promoters` (~501 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `both_strands` (boolean)
- `max_dg` (number)
- `max_results` (number)
- `region_end` (number)
- `region_start` (number)
- `sequence` (string)

Output parameters:

- `count` (number)
- `offset` (number)
- `promoters`
- `strongest`
- `strongestDg` (number|null)

### `scan_intrinsic_terminators` (~476 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `both_strands` (boolean)
- `max_results` (number)
- `region_end` (number)
- `region_start` (number)
- `sequence` (string)

Output parameters:

- `count` (number)
- `offset` (number)
- `strongest`
- `strongestHairpin` (number|null)
- `terminators`

### `score_rbs` (~220 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `mrna` (string)
- `start_pos` (number, required)

Output parameters:

- `dgHybrid` (number|null)
- `dgMrna` (number)
- `dgTotal` (number|null)
- `relStrength` (number)
- `sdLength` (number|null)
- `sdStart` (number|null)
- `spacing` (number|null)
- `structure` (string)
- `structureStart` (number)

### `assemble_operon` (~393 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cds` (array, required)
- `include_subject` (boolean)
- `leader` (string)
- `promoter` (string)
- `target_strength` (number)
- `target_strengths` (array)
- `terminator` (string)

Output parameters:

- `genes`
- `layout`
- `onTarget` (boolean)
- `record` (object|null)
- `sequence` (string)

### `codon_usage_analysis` (~630 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `enc_bg_correction` (boolean)
- `enc_pairs` (boolean)
- `feature` (string)
- `organism` (string)
- `rare_threshold` (number)
- `rcbs_directional` (boolean)
- `rcbs_mean` (string)
- `reverse` (boolean)
- `table` (string)

Output parameters:

- `cai` (number|null)
- `caiAvailable` (boolean)
- `codonMap` (object|null)
- `codons` (number)
- `enc` (number)
- `gc` (number)
- `rareBasis` (string)
- `rareFraction` (number)
- `rareHits`
- `rcbs` (number)
- `referenceTable` (string)
- `region` (string)
- `report`
- `strandSource` (string)

### `codon_usage_distance` (~316 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `feature` (string)
- `reverse` (boolean)
- `synonymous` (boolean)

Output parameters:

- `ceiling` (number)
- `compared` (number)
- `furthest` (string)
- `nearest` (string)
- `nearestDistance` (number)
- `neighbours`
- `region` (string)
- `skipped`
- `strandSource` (string)
- `synonymous` (boolean)

### `check_invariants` (~485 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cai_organism` (string)
- `forbid_sites` (array)
- `gc_window` (number)
- `max_gc` (number)
- `max_length` (number)
- `min_cai` (number)
- `min_gc` (number)
- `min_length` (number)
- `preserve_protein_of` (string)
- `require_frame` (boolean)
- `require_start` (boolean)
- `require_stop` (boolean)
- `sequence` (string)
- `table` (number)

Output parameters:

- `admissible` (boolean)
- `checked` (number)
- `failed` (number)
- `summary` (string)
- `verdicts`

### `design_expression_variants` (~1052 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `avoid_patterns` (array)
- `cds` (string)
- `feature` (string)
- `gc_max` (number)
- `gc_min` (number)
- `gc_window` (number)
- `genetic_table` (string)
- `host_table` (string)
- `host_table_name` (string)
- `host_table_tsv` (string)
- `native_table` (string)
- `native_table_tsv` (string)
- `postures` (array, required)
- `rare_below` (number)
- `seed` (number)
- `upstream` (string)

Output parameters:

- `best_cai` (string)
- `distinct` (number)
- `least_structured` (string)
- `protein` (string)
- `records`
- `region` (string)
- `report` (string)
- `skipped`
- `variants`

### `optimize_sequence` (~558 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `candidates` (number)
- `constraints` (array)
- `objectives` (array)
- `randomization_threshold` (number)
- `seed` (number)

Output parameters:

- `caiAfter` (number|null)
- `candidates`
- `distinct` (number)
- `gcAfter` (number)
- `gcProfile` (object|null)
- `nEdits` (number)
- `record` (object|null)
- `sequence` (string)
- `success` (boolean)

### `design_rbs` (~226 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cds` (string)
- `target_strength` (number, required)
- `upstream` (string)

Output parameters:

- `achievableMax` (number|null)
- `achievableMin` (number|null)
- `dgTotal` (number|null)
- `full` (string)
- `onTarget` (boolean)
- `relStrength` (number)
- `sd` (string)
- `spacing` (number)
- `utr` (string)

### `design_lamp_primers` (~1310 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `amplified_span_max` (number)
- `amplified_span_min` (number)
- `end_stability_dg` (number)
- `end_stability_nt` (number)
- `gc_max` (number)
- `gc_min` (number)
- `length_max` (number)
- `length_min` (number)
- `loop_primers` (boolean)
- `loop_span_max` (number)
- `loop_span_min` (number)
- `max_sets` (number)
- `outer_gap_max` (number)
- `outer_gap_min` (number)
- `region_end` (number)
- `region_start` (number)
- `tm_inner_max` (number)
- `tm_inner_min` (number)
- `tm_loop_max` (number)
- `tm_loop_min` (number)
- `tm_outer_max` (number)
- `tm_outer_min` (number)

Output parameters:

- `b3` (string)
- `bip` (string)
- `constraints`
- `f3` (string)
- `fip` (string)
- `offset` (number)
- `penaltyTerms`
- `setCount` (number)
- `sets`
- `targetClass` (string)

### `design_codehop` (~838 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alignment` (array)
- `alignment_fasta` (string)
- `base_cutoff` (number)
- `block_index` (number)
- `clamp_tm` (number)
- `conditions` (object)
- `core_lengths` (array)
- `genetic_code_id` (number)
- `max_clamp_length` (number)
- `max_core_degeneracy` (number)
- `max_run` (number)
- `strand` (string)
- `table` (string, required)
- `weighting` (string)

Output parameters:

- `blockCount` (number)
- `forward` (string)
- `primerCount` (number)
- `primers`
- `rejections`
- `reverse` (string)
- `table` (string)

### `design_degenerate_primers` (~745 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `algorithm` (string)
- `alignment` (array)
- `alignment_fasta` (string)
- `exhaustive_mer_limit` (number)
- `iterations` (number)
- `length` (number)
- `limit` (number)
- `max_degeneracy` (number)
- `max_product` (number)
- `min_depth` (number)
- `min_fraction_matching` (number)
- `min_product` (number)
- `seed` (number)
- `skip` (number)
- `trim_cutoff` (number)

Output parameters:

- `degeneracyCoerced` (boolean)
- `forward` (string)
- `keptColumns`
- `maxDegeneracyUsed` (number)
- `pairCount` (number)
- `pairs`
- `reverse` (string)
- `windows`

### `design_bisulfite_primers` (~1045 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `assay` (string)
- `criteria` (string)
- `design_in_island` (number)
- `island_min_length` (number)
- `island_min_obs_exp` (number)
- `island_min_percent` (number)
- `island_window` (number)
- `max_cpg_distance_from_3` (number)
- `max_gc` (number)
- `max_length` (number)
- `max_results` (number)
- `max_tm` (number)
- `min_cpg` (number)
- `min_gc` (number)
- `min_length` (number)
- `min_non_cpg_c` (number)
- `min_tm` (number)
- `opt_length` (number)
- `opt_tm` (number)
- `product_max` (number)
- `product_min` (number)
- `region_end` (number)
- `region_start` (number)

Output parameters:

- `assay` (string)
- `count` (number)
- `forward` (string)
- `islandCount` (number)
- `islands`
- `methylatedPairs`
- `pairs`
- `reverse` (string)
- `unmethylatedPairs`

### `design_sequencing_primers` (~531 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `both_strands` (boolean)
- `dead_zone` (number)
- `min_length` (number)
- `overlap` (number)
- `read_length` (number)
- `region_end` (number)
- `region_start` (number)
- `target_tm` (number)

Output parameters:

- `authority`
- `complete` (boolean)
- `coverage`
- `doubleStranded` (boolean)
- `gaps`
- `primers`
- `readCount` (number)
- `reads`
- `singleStranded`
- `skipped`
- `used`

### `design_primers` (~304 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `conditions` (object)
- `forward_primer` (string)
- `limit` (number)
- `reverse_primer` (string)
- `target_tm` (number)

Output parameters:

- `forward` (string)
- `forwardTm` (number)
- `productLen` (number)
- `productTm` (number)
- `program` (string)
- `reverse` (string)
- `reverseTm` (number)
- `ta` (number)

### `align_sequences` (~1236 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `affine_gap` (boolean)
- `align_matrix` (string)
- `engine` (string)
- `gap` (number)
- `gap_extend` (number)
- `gap_open` (number)
- `gap_penalty` (number)
- `global_align` (boolean)
- `guide_tree` (string)
- `include_subject` (boolean)
- `match` (number)
- `mismatch` (number)
- `score_matrix` (string)
- `sequences` (array)
- `terminal_penalty` (boolean)

Output parameters:

- `alignedSequences` (array)
- `consensus` (string)
- `conservation` (string)
- `count` (number)
- `engine` (string)
- `figure` (string|null)
- `fit`
- `guideTreeNewick` (string)
- `length` (number)
- `rows`
- `scores`

### `draw_alignment` (~446 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cell_width` (number)
- `columns` (number)
- `conservation` (boolean)
- `from` (number)
- `name_chars` (number)
- `row_height` (number)
- `rows` (array, required)
- `ruler` (boolean)
- `scheme` (string)

Output parameters:

- `alphabet` (string)
- `columns` (number)
- `conservedColumns` (number)
- `firstColumn` (number)
- `height` (number)
- `lastColumn` (number)
- `meanIdentity` (number)
- `rows` (number)
- `scheme` (string)
- `svg` (string|null)
- `width` (number)

### `alignment_redundancy` (~274 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `from` (number)
- `rows` (array, required)
- `threshold` (number)
- `to` (number)

Output parameters:

- `kept`
- `redundant`
- `rows`
- `summary` (string)

### `alignment_pca` (~309 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `components` (number)
- `model` (string)
- `rows` (array, required)

Output parameters:

- `coordinates`
- `eigenvalues`
- `similarity` (array)
- `summary` (string)

### `read_structure_consensus` (~333 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `text` (string, required)

Output parameters:

- `alphabet` (string)
- `columns` (number)
- `medianSupport` (number)
- `pairList`
- `pairTable`
- `pairs` (number)
- `roles`
- `rows` (number)
- `support`

### `gibson_assemble` (~455 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `expect_no_unused_parts` (boolean)
- `fragments` (array)
- `include_subject` (boolean)
- `max_constructs` (number)
- `max_homology_bp` (number)
- `max_tm` (number)
- `min_homology_bp` (number)
- `min_tm` (number)
- `preserve_backbone_origin` (boolean)
- `topology` (string)

Output parameters:

- `errors`
- `productCount` (number)
- `products`
- `record` (object|null)
- `warnings`

### `assemble_multiple_inserts` (~399 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `backbone` (string)
- `enzymes` (array, required)
- `inserts` (array, required)
- `max_constructs` (number)
- `max_homology_bp` (number)
- `min_homology_bp` (number)

Output parameters:

- `arcs`
- `cutCounts`
- `insertionPoints` (number)
- `placements`
- `reading` (string)
- `record` (object|null)

### `design_gibson_primers` (~449 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `circular` (boolean)
- `conditions` (object)
- `fragments` (array)
- `include_subject` (boolean)
- `min_footprint` (number)
- `overlap` (number)
- `synthesis_scale` (string)
- `target_tm` (number)

Output parameters:

- `amplicons`
- `circular` (boolean)
- `conditions`
- `cost`
- `costTotal` (number)
- `overlap` (number)
- `primerCount` (number)
- `primers`

### `golden_gate_assemble` (~339 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `connectors` (array)
- `enzyme` (string)
- `expect_no_unused_parts` (boolean)
- `expected_constructs` (number)
- `include_subject` (boolean)
- `max_constructs` (number)
- `parts` (array)

Output parameters:

- `enzyme` (string)
- `errors`
- `overhangs`
- `productCount` (number)
- `products`
- `record` (object|null)
- `warnings`

### `check_golden_gate_parts` (~233 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `enzyme` (string)
- `include_subject` (boolean)
- `parts` (array)

Output parameters:

- `internalSiteCount` (number)
- `needsDomestication`
- `parts`
- `ready` (boolean)

### `score_overhang_fidelity` (~561 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `dataset` (string)
- `enzyme` (string)
- `overhangs` (array, required)
- `remedies` (boolean)
- `replacements_per_junction` (number)

Output parameters:

- `atMeasurementCeiling` (boolean)
- `dataset` (string)
- `fidelity` (number)
- `flags`
- `junctions`
- `meaningful` (boolean)
- `percent` (number)
- `repair`
- `replacements`
- `worst`

### `design_split_sites` (~809 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alien_overhangs` (array)
- `dataset` (string)
- `efficiency_weight` (number)
- `exclude_from` (number)
- `exclude_to` (number)
- `fidelity_weight` (number)
- `fragments` (number)
- `max_length` (number)
- `max_overhang_identity` (number)
- `min_length` (number)
- `sequence` (string)
- `traces` (number)

Output parameters:

- `alternatives`
- `breaks`
- `candidates` (number)
- `dataset` (string)
- `fragment_count` (number)
- `fragments`
- `net_efficiency` (number)
- `net_fidelity` (number)
- `overhangs`
- `report`
- `score` (number)

### `design_overhang_set` (~608 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `candidate_pool` (number)
- `dataset` (string)
- `enzyme` (string)
- `fixed` (array)
- `size` (number)
- `start_from` (array)

Output parameters:

- `dataset` (string)
- `fidelity` (number)
- `fixed`
- `from` (string)
- `overhangs`
- `percent` (number)

### `assembly_plan_simulate` (~367 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `include_subject` (boolean)
- `method` (string)
- `parts` (array)
- `plan` (string, required)

Output parameters:

- `built` (number)
- `cancelled` (number)
- `constructs`
- `failed` (number)
- `leafParts`
- `levels`
- `record` (object|null)

### `melt_profile` (~296 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `ions` (number)
- `max_temp` (number)
- `min_temp` (number)
- `region_end` (number)
- `region_start` (number)
- `step` (number)

Output parameters:

- `curve`
- `derivative`
- `domainCount` (number)
- `hrmPlot` (object|null)
- `meltPlot` (object|null)
- `tm50` (number|null)
- `transitions`

### `design_ish_probes` (~1255 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alignment_sam` (string)
- `dnac1` (number)
- `dnac2` (number)
- `filter_by` (string)
- `filter_threshold` (number)
- `formamide` (number)
- `hybridization_temperature` (number)
- `kmer_canonical` (boolean)
- `kmer_dump` (string)
- `kmer_length` (number)
- `kmer_reference` (string)
- `kmer_threshold` (number)
- `max_gc` (number)
- `max_length` (number)
- `max_off_target_probability` (number)
- `max_tm` (number)
- `min_gc` (number)
- `min_length` (number)
- `min_tm` (number)
- `oligos_per_probe` (number)
- `origin` (number)
- `overlap` (boolean)
- `probes` (number)
- `prohibited` (string)
- `rank_by` (string)
- `screen_mode` (string)
- `sodium` (number)
- `spacing` (number)

Output parameters:

- `coverage`
- `coveredFraction` (number)
- `explanation`
- `kmer`
- `oligoCount` (number)
- `oligos`
- `probes`
- `stages`

### `design_padlock_probes` (~469 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `arm_length` (number)
- `barcode` (string)
- `blast_csv` (string)
- `interval` (number)
- `linker_downstream` (string)
- `linker_upstream` (string)
- `max_tm` (number)
- `min_tm` (number)
- `variants` (string)

Output parameters:

- `explanation`
- `packed`
- `padlockCount` (number|null)
- `padlocks`
- `targetsFasta` (string)

### `design_hcr_probes` (~632 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alignment_sam` (string)
- `channel` (string)
- `dtm_filter` (boolean)
- `dtm_max` (number)
- `max_gc` (number)
- `max_gibbs` (number)
- `max_hairpin_tm` (number)
- `max_probes` (number)
- `max_run_length` (number)
- `max_run_mismatches` (number)
- `min_gc` (number)
- `min_gibbs` (number)
- `num_hits_allowed` (number)
- `target_gibbs` (number)
- `tile_size` (number)

Output parameters:

- `explanation`
- `orderTable` (string)
- `pairCount` (number)
- `pairs`
- `stages`
- `tilesFasta` (string)

### `design_merfish_probes` (~1009 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `barcode` (string)
- `cross_talk_k` (number)
- `expression` (string)
- `formamide` (number)
- `forward_primer` (string)
- `max_gc` (number)
- `max_readout_ot_increase` (number)
- `max_rtrna_ot` (number)
- `max_tm` (number)
- `min_gc` (number)
- `min_specificity` (number)
- `min_tm` (number)
- `one_bit_per_probe` (boolean)
- `probe_nm` (number)
- `probes_per_transcript` (number)
- `readout_assignment` (string)
- `readouts` (string)
- `readouts_per_probe` (number)
- `reverse_primer` (string)
- `rtrna_k` (number)
- `rtrna_reference` (string)
- `seed` (number)
- `sodium_mm` (number)
- `spacer` (string)
- `specificity_k` (number)
- `t7_length` (number)
- `target_id` (string)
- `target_length` (number)
- `transcriptome` (string)
- `trials` (number)

Output parameters:

- `explanation`
- `orderTable` (string)
- `probeCount` (number)
- `probes`
- `report`
- `stages`

### `design_xenium_probes` (~680 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `arm_length` (number)
- `blast_csv` (string)
- `gene_accessions` (string)
- `junctions` (string)
- `max_arm_tm` (number)
- `max_full_tm` (number)
- `max_g_run` (number)
- `min_arm_tm` (number)
- `min_full_tm` (number)
- `min_mismatches` (number)
- `prefer_cds` (boolean)
- `probes_per_gene` (number)
- `spacing` (number)
- `tm_rule` (string)

Output parameters:

- `explanation`
- `probeCount` (number|null)
- `probes`
- `stages`
- `targetsFasta` (string)

### `design_genetic_circuit` (~444 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `groups` (string)
- `library` (string)
- `logic` (string)
- `max_assignments` (number)
- `reporters` (string)
- `sensors` (string)

Output parameters:

- `assignment`
- `curves`
- `curvesFigure` (string|null)
- `dna`
- `explanation`
- `libraries`
- `netlist`
- `placement`
- `score` (number)
- `sequence` (string)
- `toxicity`
- `truthTable`

### `dot_plot` (~770 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `best_path_only` (boolean)
- `convert_wobbles` (boolean)
- `dedupe` (boolean)
- `engine` (string)
- `matrix` (string)
- `matrix_text` (string)
- `max_cells` (number)
- `max_unknown_percent` (number)
- `min_matches` (number)
- `nucleotide` (boolean)
- `other` (string)
- `reverse_complement` (boolean)
- `shift` (number)
- `step` (number)
- `threshold` (number)
- `word_size` (number)

Output parameters:

- `coverage` (number)
- `longestForward` (number)
- `plot`
- `stats`

### `dot_plot_grid` (~512 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `best_path_only` (boolean)
- `convert_wobbles` (boolean)
- `gap` (number)
- `include_subject` (boolean)
- `max_residues` (number)
- `max_sequences` (number)
- `max_unknown_percent` (number)
- `nucleotide` (boolean)
- `reverse_complement` (boolean)
- `sequences` (array, required)
- `word_size` (number)

Output parameters:

- `grid`
- `memberCount` (number)
- `sequences`
- `sharingPairs` (number)
- `summary`

### `build_tree` (~3134 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `bayesian_brlen_rate` (number)
- `bayesian_burn_in` (number)
- `bayesian_chains` (number)
- `bayesian_clock` (string)
- `bayesian_clock_sd` (number)
- `bayesian_gamma_categories` (number)
- `bayesian_iterations` (number)
- `bayesian_kappa` (number)
- `bayesian_min_part_freq` (number)
- `bayesian_model` (string)
- `bayesian_runs` (number)
- `bayesian_sample_frequencies` (boolean)
- `bayesian_sample_frequency` (number)
- `bayesian_sample_kappa` (boolean)
- `bayesian_sample_shape` (boolean)
- `bayesian_seed` (number)
- `bayesian_shape` (number)
- `bayesian_temp` (number)
- `bayesian_theta_prior_mean` (number)
- `bayesian_theta_shape` (number)
- `bayesian_theta_start` (number)
- `bootstrap` (number)
- `bootstrap_measure` (string)
- `bootstrap_seed` (number)
- `fastme_nni` (boolean)
- `fastme_spr` (boolean)
- `gamma` (number)
- `include_subject` (boolean)
- `ladderize` (boolean)
- `method` (string)
- `midpoint_root` (boolean)
- `ml_gamma_categories` (number)
- `ml_invariant` (number)
- `ml_model` (string)
- `ml_optimise_base_frequencies` (boolean)
- `ml_optimise_invariant` (boolean)
- `ml_optimise_rates` (boolean)
- `ml_optimise_shape` (boolean)
- `ml_optimise_topology` (boolean)
- `ml_rearrangement` (string)
- `ml_shape` (number)
- `model` (string)
- `pairwise_deletion` (boolean)
- `parsimony_rearrangement` (string)
- `sequences` (array)
- `sh_replicates` (number)
- `support_method` (string)

Output parameters:

- `bayesian`
- `branchSupport`
- `clockDeviationInBranches` (number|null)
- `distanceMap` (object|null)
- `distanceMatrix`
- `gamma` (number|null)
- `gammaP` (number|null)
- `newick` (string)
- `statistics`
- `tipCount` (number)
- `transfer`
- `warnings`

### `select_substitution_model` (~363 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `criterion` (string)
- `gamma_categories` (array)
- `include_invariant` (boolean)
- `include_subject` (boolean)
- `models` (array)
- `sequences` (array, required)

Output parameters:

- `best` (string)
- `candidates` (number)
- `fits`
- `startingTree` (string)
- `weight` (number)

### `transform_tree` (~457 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `ascending` (boolean)
- `max_length` (number)
- `min_support` (number)
- `newick` (string, required)
- `operation` (string)
- `position` (number)
- `taxa` (array)

Output parameters:

- `newick` (string)
- `statistics`
- `tipCount` (number)

### `draw_tree` (~510 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `branch_lengths` (boolean)
- `font_size` (number)
- `height` (number)
- `layout` (string)
- `length_unit` (string)
- `min_support` (number)
- `newick` (string, required)
- `support` (boolean)
- `tip_labels` (boolean)
- `unrooted_method` (string)
- `width` (number)

Output parameters:

- `height` (number)
- `pixelsPerUnit` (number)
- `svg` (string|null)
- `tipCount` (number)
- `width` (number)

### `compare_trees` (~319 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cutoff` (number)
- `mode` (string)
- `sharedTaxaOnly` (boolean)
- `trees` (array, required)

Output parameters:

- `comparedTaxa` (number)
- `consensus` (string)
- `distances`
- `normalized` (number)
- `prunedTaxa`
- `rf` (number)
- `treeCount` (number)

### `tree_statistics` (~182 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `newick` (string, required)

Output parameters:

- `ltt`
- `lttPlot` (object|null)
- `patristic`
- `patristicMap` (object|null)
- `statistics`
- `tipCount` (number)

### `tree_taxon_annotations` (~210 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `nexml` (string, required)

Output parameters:

- `annotations`
- `count` (number)
- `properties`

### `export_tree` (~251 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `format` (string)
- `name` (string)
- `tree` (string, required)

Output parameters:

- `sourceFormat` (string)
- `text` (string)

### `audit_barcodes` (~299 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `barcodes` (array, required)
- `metric` (string)
- `prune_to_errors` (number)
- `required_distance` (number)

Output parameters:

- `analysis`
- `audit`
- `baseComposition` (object|null)
- `distanceHistogram` (object|null)
- `distanceMap` (object|null)
- `dropped` (number)
- `gcHistogram` (object|null)
- `kept`
- `matrices`
- `neighbourHistogram` (object|null)
- `statistics`

### `demultiplex_reads` (~238 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `barcodes` (array, required)
- `metric` (string)
- `reads` (array, required)

Output parameters:

- `ambiguous` (number)
- `assigned` (number)
- `hits`

### `export_barcodes` (~460 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `adapter_3` (string)
- `adapter_5` (string)
- `barcodes` (array, required)
- `format` (string)
- `idt_purification` (string)
- `idt_scale` (string)
- `prefix` (string)
- `primer` (string)

Output parameters:

- `count` (number)
- `oligos`
- `text` (string)
- `warnings`

### `design_barcodes` (~459 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `filter_gc` (boolean)
- `filter_self_complementary` (boolean)
- `filter_triplets` (boolean)
- `heuristic` (string)
- `iterations` (number)
- `length` (number)
- `metric` (string)
- `min_distance` (number)
- `population` (number)
- `seed` (number)

Output parameters:

- `analysis`
- `barcodes`
- `count` (number)
- `guarantee`
- `warnings`

### `design_qpcr_assay` (~1122 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `amplicon_max` (number)
- `amplicon_min` (number)
- `conditions` (object)
- `max_poly_x` (number)
- `max_results` (number)
- `primer_max_gc` (number)
- `primer_max_length` (number)
- `primer_max_tm` (number)
- `primer_min_gc` (number)
- `primer_min_length` (number)
- `primer_min_tm` (number)
- `primer_opt_length` (number)
- `primer_tm_opt` (number)
- `probe_chemistry` (string)
- `probe_locked_positions` (string)
- `probe_max_gc` (number)
- `probe_max_length` (number)
- `probe_max_tm` (number)
- `probe_min_gc` (number)
- `probe_min_length` (number)
- `probe_min_tm` (number)
- `probe_opt_length` (number)
- `probe_tm_offset_min` (number)
- `probe_tm_opt` (number)
- `region_end` (number)
- `region_start` (number)
- `structure_check` (boolean)

Output parameters:

- `assays`
- `best`
- `conditions`
- `count` (number)
- `forward` (string)
- `offset` (number)
- `probe` (string)
- `probe_ordered` (string)
- `reverse` (string)

### `check_scorpion_stem` (~592 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `conditions` (object)
- `margin` (number)
- `probe` (string, required)
- `stem_length` (number)
- `target` (string, required)

Output parameters:

- `clearsMargin`
- `difference` (number|null)
- `marginSource` (string)
- `notes`
- `probeTm` (number|null)
- `stemGcPercent` (number|null)
- `stemTm` (number|null)

### `simulate_taqman_curve` (~1045 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `amplicon` (string, required)
- `annealing_temperature` (number)
- `annealing_time` (number)
- `beta` (number)
- `cycles` (number)
- `denaturation_time` (number)
- `forward_primer` (string, required)
- `forward_primer_molar` (number)
- `k_deg` (number)
- `primer_dimer_dg` (number)
- `probe` (string, required)
- `probe_molar` (number)
- `reverse_primer` (string, required)
- `reverse_primer_molar` (number)
- `template_copies` (number)

Output parameters:

- `cq` (number|null)
- `curvePlot` (object|null)
- `estimators`
- `fluorescence`
- `notes`
- `plateau` (number|null)
- `probeConsumed` (number|null)

### `call_cq` (~1342 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `amounts` (string)
- `auto_model` (boolean)
- `baseline_from` (number)
- `baseline_scan` (number)
- `baseline_to` (number)
- `cq_method` (string)
- `criterion` (string)
- `curves` (string, required)
- `max_ratio_baseshift` (number)
- `max_ratio_smooth` (boolean)
- `model` (string)
- `outlier_method` (string)
- `shift` (number)
- `threshold` (number)

Output parameters:

- `amplificationPlot` (object|null)
- `count` (number)
- `cqMethod` (string)
- `errorNote` (string|null)
- `failed` (number)
- `meanEfficiency` (number)
- `methods`
- `model` (string)
- `modelChosen` (string|null)
- `modelTable`
- `outlierStat` (string)
- `outliers`
- `rows`
- `threshold` (number|null)
- `zeroCrossing`

### `relative_expression` (~1487 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `amounts` (string)
- `assess_efficiency` (boolean)
- `ct_table` (string, required)
- `groups` (string, required)
- `lm_conf_level` (number)
- `lm_formula` (string)
- `lm_mode` (string)
- `lm_variables` (string)
- `model` (string)
- `reference_gene` (string)
- `reference_group` (string, required)
- `sig_test` (string)
- `standard_ct_table` (string)
- `tube` (string)
- `wilcox_alternative` (string)
- `wilcox_conf_level` (number)
- `wilcox_correct` (string)
- `wilcox_exact` (string)

Output parameters:

- `count` (number)
- `design`
- `efficiency`
- `genes`
- `groups`
- `model` (string)
- `referenceGene` (string|null)
- `rows`
- `standardPoints`
- `test`
- `trend`

### `rank_reference_genes` (~392 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cq_table` (string, required)
- `normfinder_arm` (string)

Output parameters:

- `genormM`
- `grouped` (string)
- `mostStable` (string)
- `pairwiseV`
- `perMethod`
- `ranking`
- `recommendedCount` (number)

### `read_rdml_run` (~469 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `rdml_xml` (string, required)
- `run` (number)
- `table` (string)

Output parameters:

- `groups` (string)
- `omitted`
- `rows` (number)
- `runs`
- `table` (string)
- `version` (string)

### `quantify_dpcr` (~1024 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `ci_method` (string)
- `conf_level` (number)
- `dilution_factor` (number)
- `merge_replicates` (boolean)
- `partition_volume_nl` (number)
- `ratio_reference` (string)
- `ratio_target` (string)
- `reaction_volume_ul` (number)
- `reference_copies` (number)
- `template_volume_ul` (number)
- `volume_cv` (number)
- `volume_model` (string)
- `wells` (string, required)

Output parameters:

- `ciMethod` (string)
- `confLevel` (number|null)
- `count` (number)
- `flagged` (number)
- `partitionVolumeNl` (number)
- `ratios`
- `rows`
- `volumeCvPercent` (number)
- `volumeModel` (string)

### `gate_droplets` (~804 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cutoff_iqr` (number)
- `cutoff_sd` (number)
- `droplet_volume_ul` (number)
- `empty_lambda_high` (number)
- `empty_lambda_low` (number)
- `files` (string, required)
- `random_seed` (number)
- `top_percent` (number)
- `total_drops_t` (number)
- `x_var` (string)
- `y_var` (string)

Output parameters:

- `count` (number)
- `outlierCutoff`
- `params`
- `rejected` (number)
- `totalDroplets` (number)
- `verdicts`
- `wells`

### `classify_droplets` (~1656 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `ch1_nn` (number)
- `ch1_np` (number)
- `ch1_pn` (number)
- `ch1_pp` (number)
- `ch2_nn` (number)
- `ch2_np` (number)
- `ch2_pn` (number)
- `ch2_pp` (number)
- `constant_control` (string)
- `distance_param` (number)
- `droplets` (string, required)
- `k` (number)
- `markers` (string)
- `method` (string)
- `prob` (number)
- `random_seed` (number)
- `sam_seed` (number)
- `sensitivity` (number)
- `template` (string)
- `training` (string)

Output parameters:

- `centres`
- `classes`
- `confidence` (number)
- `copies_per_droplet`
- `counts`
- `members`
- `method` (string)
- `normalised`
- `params`
- `total` (number)
- `wells`

### `analyze_melt_curves` (~1567 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `all_peaks` (boolean)
- `artifact_peak_width` (number)
- `bilin_high_start_temp` (number)
- `bilin_high_stop_temp` (number)
- `bilin_low_start_temp` (number)
- `bilin_low_stop_temp` (number)
- `cut_area` (number)
- `engine` (string)
- `expected_tm` (number)
- `expo_high_temp` (number)
- `expo_low_temp` (number)
- `extremum` (string)
- `fluor_source` (string)
- `melt_table` (string, required)
- `norm_method` (string)
- `peak_cutoff` (number)
- `peak_high_temp` (number)
- `peak_low_temp` (number)
- `peak_max_width` (number)
- `replicate_percent` (boolean)
- `replicate_robust` (boolean)
- `resample` (boolean)
- `second_derivative` (boolean)
- `span_peaks` (number)
- `span_smooth` (number)
- `true_peak_width` (number)
- `window_ceiling` (number)

Output parameters:

- `classified` (string)
- `count` (number)
- `derivativePlot` (object|null)
- `engine` (string)
- `meanTm` (number)
- `meltPlot` (object|null)
- `noPeak` (number)
- `reactions`
- `replicateSpread`
- `targets`

### `propagate_uncertainty` (~858 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `conf_level` (number)
- `dist_sim` (string)
- `do_perm` (boolean)
- `do_sim` (boolean)
- `expression` (string, required)
- `input` (string)
- `nperm` (number)
- `nsim` (number)
- `second_order` (boolean)
- `seed` (number)
- `ties` (string)
- `use_cov` (boolean)
- `variables` (string, required)

Output parameters:

- `confLower` (number|null)
- `confUpper` (number|null)
- `contributions`
- `firstOrderMean` (number|null)
- `gradient`
- `permPValues`
- `permuted`
- `propagatedMean` (number|null)
- `propagatedSd` (number|null)
- `secondOrderMean` (number|null)
- `simulated`
- `variables`

### `bootstrap_cq` (~883 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `conf_level` (number)
- `cq_method` (string)
- `curves` (string, required)
- `drop` (number)
- `include_readouts` (boolean)
- `iterations` (number)
- `model` (string)
- `reaction` (string)
- `scheme` (string)
- `seed` (number)

Output parameters:

- `coefficients`
- `confLevel` (number)
- `converged` (number)
- `iterations` (number)
- `model` (string)
- `reaction` (string)
- `readouts`
- `rmse`
- `rss`

### `miqe_checklist` (~328 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `answers` (object)

Output parameters:

- `answered` (number)
- `incomplete` (number)
- `notes`
- `reading` (string)
- `rows`
- `total` (number)
- `tsv` (string)

### `calculate_power` (~1394 tokens)

Input parameters:

- `N` (number)
- `_files` (array)
- `_subject` (object)
- `alternative` (string)
- `between_var` (number)
- `df` (number)
- `difference` (number)
- `effect` (number)
- `effect_size` (string)
- `groups` (number)
- `k` (number)
- `n` (number)
- `n1` (number)
- `n2` (number)
- `p1` (number)
- `p2` (number)
- `power` (number)
- `sd` (number)
- `sig_level` (number)
- `solve_for` (string)
- `strict` (boolean)
- `test` (string, required)
- `type` (string)
- `u` (number)
- `v` (number)
- `within_var` (number)

Output parameters:

- `power` (number|null)
- `powerCurve` (object|null)
- `rCall` (string)
- `solved` (string)
- `value` (number|null)
- `values`
- `warnings`
- `wholeUnits`

### `estimate_effect_size` (~655 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alternative` (string)
- `ci` (number)
- `estimator` (string)
- `group` (string)
- `group_column` (string)
- `groups` (string)
- `paired` (boolean)
- `pooled_sd` (boolean)
- `power` (number)
- `reference` (string)
- `sig_level` (number)
- `subtract` (string)
- `table` (string, required)
- `value` (string, required)

Output parameters:

- `design`
- `estimate` (number|null)
- `groups`
- `interval`
- `sizing`

### `calculate_rnaseq_power` (~539 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (array)
- `cv` (array)
- `cv2` (array)
- `depth` (array, required)
- `effect` (array)
- `n` (array)
- `n2` (array)
- `power` (array)
- `solve_for` (string)

Output parameters:

- `curve` (object|null)
- `grid`
- `rCall` (string)
- `solved` (string)
- `value` (number|null)

### `plan_rnaseq_experiment` (~897 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `count` (number)
- `counts` (array)
- `dispersion` (number)
- `dispersions` (array)
- `effect_mean` (number)
- `effect_sd` (number)
- `fdr` (number)
- `fold_change` (number)
- `m` (number)
- `m1` (number)
- `max_n` (number)
- `method` (string)
- `n` (number)
- `normalization_ratio` (number)
- `pi0` (array)
- `power` (number)
- `sigma` (number)
- `size_ratio` (number)
- `solve_for` (string)

Output parameters:

- `alpha` (number|null)
- `curve` (object|null)
- `method` (string|null)
- `n` (number|null)
- `perGene`
- `power` (number|null)
- `rCall` (string|null)
- `rows`
- `solved` (string|null)

### `simulate_rnaseq_power` (~850 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `call_by` (string)
- `changed_fraction` (number)
- `cutoff` (number)
- `depth_factors` (array)
- `dispersion` (number)
- `dispersion_pilot` (string)
- `dropped_strata` (array)
- `filter_by` (string)
- `genes` (number)
- `log_fold_change` (number)
- `log_mean` (number)
- `pilot` (string)
- `reads_per_sample` (number)
- `replicates` (array)
- `rounds` (number)
- `second_group` (array)
- `seed` (number)
- `strata` (array)
- `stratify_by` (string)
- `target` (string)
- `threshold` (number)

Output parameters:

- `power`
- `powerSE`
- `rScript` (string)
- `seqDepth`
- `strata`
- `stratifiedFDR`
- `stratifiedPower` (object|null)
- `summary`

### `rank_tradeoffs` (~614 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `crowding` (string)
- `filter` (string)
- `keep_duplicates` (boolean)
- `label` (string)
- `maximise` (string)
- `minimise` (string)
- `order` (string)
- `reference` (string)
- `table` (string, required)

Output parameters:

- `counts`
- `front`
- `fronts`
- `hypervolume` (number|null)
- `order` (string|null)
- `ranked`
- `reference`

### `solve_dilution` (~395 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `final_concentration` (number)
- `final_concentration_unit` (string)
- `final_volume` (number)
- `final_volume_unit` (string)
- `stock_concentration` (number)
- `stock_concentration_unit` (string)
- `stock_volume` (number)
- `stock_volume_unit` (string)

Output parameters:

- `diluent` (number|null)
- `fold` (number|null)
- `solved` (string)
- `unit` (string)
- `value` (number|null)

### `plan_serial_dilution` (~271 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `fold` (number)
- `steps` (number)
- `stock_concentration` (number, required)
- `stock_concentration_unit` (string)
- `tube_volume` (number, required)
- `tube_volume_unit` (string)

Output parameters:

- `diluent` (number|null)
- `final` (number|null)
- `transfer` (number|null)
- `tubes`

### `convert_mass_moles` (~355 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `amount` (number)
- `amount_unit` (string)
- `mass` (number)
- `mass_unit` (string)
- `molecular_weight` (number)
- `strands` (string)

Output parameters:

- `amount` (number|null)
- `copies` (number|null)
- `mass` (number|null)
- `molecularWeight` (number|null)

### `plan_master_mix` (~1360 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `components` (array)
- `include_dmso` (boolean)
- `include_q_solution` (boolean)
- `mg_final` (number)
- `overage` (number)
- `primer_final` (number)
- `primer_stock` (number)
- `reaction_volume` (number)
- `reactions` (number)
- `setup` (string)
- `template_volume` (number)

Output parameters:

- `dispensePerTube` (number|null)
- `mixTotal` (number|null)
- `multiplier` (number|null)
- `rows`

### `recombine` (~546 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `circular_only` (boolean)
- `fragments` (array)
- `greedy` (boolean)
- `guides` (array)
- `homology_bp` (number)
- `include_subject` (boolean)
- `multi_site_only` (boolean)
- `site1` (string)
- `site2` (string)
- `system` (string)

Output parameters:

- `discarded` (number)
- `productCount` (number)
- `products`
- `record` (object|null)
- `sites`

### `rank_strategies` (~491 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `digest_enzymes` (array)
- `enzyme` (string)
- `order_by` (string)
- `parts` (array)

Output parameters:

- `best` (string|null)
- `criteria`
- `feasible` (number)
- `notScored`
- `ranked`
- `refused`

### `ligate_fragments` (~492 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `allow_partial_overlap` (boolean)
- `blunt` (boolean)
- `circular_only` (boolean)
- `end_origins` (array)
- `end_treatments` (array)
- `enzymes` (array)
- `fill_in` (array)
- `fragment_indices` (array)
- `fragments` (array)
- `include_subject` (boolean)

Output parameters:

- `junctions`
- `layout`
- `nickedJunctions`
- `productCount` (number)
- `products`
- `record` (object|null)

### `restriction_ligate` (~466 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `blunt` (boolean)
- `circular_only` (boolean)
- `end_origins` (array)
- `end_treatments` (array)
- `enzymes` (array)
- `fragments` (array)
- `include_subject` (boolean)
- `sort_by_recognition_sites` (boolean)

Output parameters:

- `junctions`
- `layout`
- `nickedJunctions`
- `partiallyDigested`
- `productCount` (number)
- `products`
- `recognitionSites` (number)
- `record` (object|null)

### `ligation_independent_clone` (~319 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `arm_nt` (number)
- `circular_only` (boolean)
- `fragments` (array)
- `include_subject` (boolean)
- `method` (string)

Output parameters:

- `arm` (number)
- `armVerdict` (string)
- `productCount` (number)
- `products`
- `record` (object|null)
- `summary` (string)

### `fusion_pcr` (~215 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `fragments` (array)
- `include_subject` (boolean)
- `limit` (number)

Output parameters:

- `junctions`
- `productCount` (number)
- `productTm` (number)
- `products`
- `record` (object|null)
- `report` (string)

### `design_combinatorial_library` (~530 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `bins` (array, required)
- `chemistry` (string)
- `constants` (array)
- `max_members` (number)
- `min_homology_bp` (number)
- `rules` (array)
- `topology` (string)

Output parameters:

- `built` (number)
- `cartesian` (number)
- `members`
- `pruned`
- `reading` (string)
- `record` (object|null)

### `check_value` (~677 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `against` (number)
- `against_factor` (number)
- `against_offset` (number)
- `label` (string)
- `max` (number)
- `min` (number)
- `operator` (string)
- `record` (string)
- `report_only` (boolean)
- `set` (array)
- `text` (string)
- `threshold` (number)
- `value` (number, required)

Output parameters:

- `failed` (boolean)
- `message` (string)
- `passed` (boolean)
- `record` (object|null)
- `value`

### `filter_items` (~413 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `field` (string)
- `items` (array, required)
- `max` (number)
- `min` (number)
- `operator` (string)
- `set` (array)
- `text` (string)
- `value` (number)

Output parameters:

- `count` (number)
- `dropped` (number)
- `items`

### `get_selection` (~206 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `pad` (number)
- `reverse_complement` (boolean)

Output parameters:

- `end` (number)
- `length` (number)
- `record` (object|null)
- `sequence` (string)
- `start` (number)

### `pick_first` (~215 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `fallback` (string)
- `values` (array)

Output parameters:

- `index` (number)
- `ranCount` (number)
- `record` (object|null)
- `value`

### `check_rows` (~595 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `count` (number)
- `field` (string)
- `items` (array, required)
- `label` (string)
- `max` (number)
- `min` (number)
- `operator` (string)
- `record` (string)
- `report_only` (boolean)
- `require` (string)
- `set` (array)
- `text` (string)
- `value` (number)

Output parameters:

- `failed` (boolean)
- `matched` (number)
- `message` (string)
- `offenders`
- `passed` (boolean)
- `record` (object|null)

### `summarize_rows` (~860 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `field` (string)
- `group_field` (string)
- `items` (array, required)
- `label` (string)
- `operation` (string)
- `percentile` (number)
- `second_field` (string)
- `trim` (number)

Output parameters:

- `count` (number)
- `groupCount` (number|null)
- `groups`
- `message` (string)
- `number` (number|null)
- `used` (number)
- `value`

### `multiplex_pcr` (~1209 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `conditions` (object)
- `cutoff_max_prim_prim_any_tm` (number)
- `cutoff_max_prim_prim_end_tm` (number)
- `cutoff_max_prod_len_diff` (number)
- `cutoff_max_tm_diff` (number)
- `cutoff_min_prod_len_diff` (number)
- `cutoff_prim_prim_any` (number)
- `cutoff_prim_prim_end1` (number)
- `cutoff_prim_prim_end2` (number)
- `cutoff_prim_prod_any` (number)
- `cutoff_prim_prod_end1` (number)
- `cutoffs_off` (array)
- `include_subject` (boolean)
- `limit` (number)
- `max_groups` (number)
- `max_per_group` (number)
- `max_size` (number)
- `min_size` (number)
- `pool` (boolean)
- `pool_preset` (string)
- `primers` (array)
- `templates` (array)

Output parameters:

- `ampliconCount` (number)
- `amplicons`
- `crossDimers`
- `diagnostics`
- `dimerMap` (object|null)
- `poolCount` (number)
- `pools`
- `primerStats`

### `read_structure` (~395 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `model` (number)
- `text` (string, required)

Output parameters:

- `atoms` (number)
- `bFactor`
- `cell`
- `chains`
- `dialect` (string)
- `disulfides` (number)
- `extent` (number)
- `format` (string)
- `formula` (string)
- `hasPolymer` (boolean)
- `hasResolution` (boolean)
- `helices` (number)
- `id` (string)
- `ligands`
- `method` (string)
- `models` (number)
- `modified`
- `residues` (number)
- `resolution` (number)
- `sequences`
- `strands` (number)
- `title` (string)
- `warnings`
- `waters` (number)

### `number_antibody` (~467 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `assignGermline` (boolean)
- `bitScoreThreshold` (number)
- `cdrDefinition` (string)
- `chainTypes` (array)
- `protein` (string, required)
- `scheme` (string)
- `species` (array)

Output parameters:

- `chainTypes`
- `domains`
- `hits`

### `antibody_liabilities` (~226 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cdrOnly` (boolean)
- `protein` (string, required)
- `rules` (array)

Output parameters:

- `cdrCount` (number)
- `count` (number)
- `liabilities`

### `humanize_antibody` (~378 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `backmutateVernier` (boolean)
- `cdrDefinition` (string)
- `domain` (number)
- `humanizeCdrs` (boolean)
- `iterations` (number)
- `protein` (string, required)

Output parameters:

- `humanized` (string)
- `identity` (number)
- `mutationCount` (number)
- `mutations`

### `graft_antibody_cdrs` (~426 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `backmutateVernier` (boolean)
- `cdrDefinition` (string)
- `domain` (number)
- `jGene` (string)
- `protein` (string, required)
- `rankByFrameworks` (boolean)
- `top` (number)
- `vGene` (string)

Output parameters:

- `candidates`
- `germline` (string)
- `grafted` (string)
- `identity` (number)

### `antibody_isotype` (~342 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `minIdentity` (number)
- `protein` (string, required)
- `species` (string)

Output parameters:

- `allele` (string)
- `domains`
- `gene` (string)
- `identity` (number)
- `species` (string)

### `antibody_molecule` (~319 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `format` (string)
- `heavy` (string, required)
- `light` (string, required)
- `pH` (number)

Output parameters:

- `absorbance`
- `chargeAtPH` (number)
- `extinction`
- `isoelectricPoint` (number)
- `molecularWeight` (number)

### `antibody_antigen_contacts` (~423 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `antibodyChain` (string)
- `antigenChains` (string)
- `interactingCutoff` (number)
- `model` (number)
- `text` (string, required)

Output parameters:

- `antibodyChains`
- `antigenChains`
- `byType`
- `contacts`
- `residues`

### `compare_antibodies` (~390 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `antibodies` (array)
- `chain` (string)
- `definition` (string)
- `include_subject` (boolean)
- `pH` (number)

Output parameters:

- `alignment` (string)
- `chains`
- `identical` (number)
- `mutations` (number)
- `positions`
- `refused`
- `regions`
- `rows`

### `antibody_canonical_classes` (~357 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `definition` (string)
- `protein` (string, required)
- `scheme` (string)
- `species` (array)

Output parameters:

- `classes`
- `domains`

### `antibody_position_frequencies` (~406 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `distribution` (string)
- `germline_species` (string)
- `protein` (string, required)
- `rare_below` (number)
- `species` (array)

Output parameters:

- `domains`
- `rare`

### `population_site_stats` (~346 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `group` (string)
- `groupBy` (string)
- `populations` (string)
- `vcf` (string, required)

Output parameters:

- `samples`
- `sites`
- `summary`

### `linkage_disequilibrium` (~606 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `end` (number)
- `estimator` (string)
- `group` (string)
- `groupBy` (string)
- `maxSites` (number)
- `minMac` (number)
- `populations` (string)
- `pruneSize` (number)
- `pruneStep` (number)
- `pruneThreshold` (number)
- `start` (number)
- `vcf` (string, required)

Output parameters:

- `pairs`
- `sites`
- `summary`

### `population_fst` (~457 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `blockLength` (number)
- `compare` (string)
- `estimator` (string)
- `groupBy` (string)
- `populations` (string, required)
- `vcf` (string, required)

Output parameters:

- `average`
- `matrix`
- `sites`

### `genotype_pca` (~574 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `groupBy` (string)
- `minMac` (number)
- `nComponents` (number)
- `populations` (string)
- `precision` (string)
- `prune` (boolean)
- `pruneSize` (number)
- `pruneStep` (number)
- `pruneThreshold` (number)
- `scaler` (string)
- `vcf` (string, required)

Output parameters:

- `coords`
- `explainedVariance`
- `explainedVarianceRatio`
- `sites`

### `population_ancestry` (~591 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `groupBy` (string)
- `holdOut` (boolean)
- `holdOutShare` (number)
- `iterations` (number)
- `kFrom` (number)
- `kTo` (number)
- `ploidy` (number)
- `populations` (string)
- `seed` (number)
- `tolerance` (number)
- `vcf` (string, required)

Output parameters:

- `ancestralGenotypeFrequencies`
- `ancestry`
- `bestK` (number|null)
- `runs`

### `differential_expression` (~2145 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `altHypothesis` (string)
- `avgTxLength` (string)
- `betaPrior` (boolean)
- `blind` (boolean)
- `contrast` (string)
- `cooksCutoff` (number)
- `cooksFilter` (boolean)
- `counts` (string, required)
- `design` (string)
- `filterByExpr` (boolean)
- `fitType` (string)
- `independentFiltering` (boolean)
- `lfcThreshold` (number)
- `method` (string)
- `minCount` (number)
- `minReplicatesForReplace` (number)
- `minTotalCount` (number)
- `minmu` (number)
- `name` (string)
- `pAdjustMethod` (string)
- `pcaGroup` (string)
- `pcaTop` (number)
- `reduced` (string)
- `reference` (string)
- `samples` (string, required)
- `sfType` (string)
- `shrink` (string)
- `test` (string)
- `transform` (string)
- `useT` (boolean)
- `weights` (string)

Output parameters:

- `dispersionPlot` (object|null)
- `downGenes` (string)
- `genes`
- `maPlot` (object|null)
- `meanCounts` (string)
- `rankedList` (string)
- `sampleDistances`
- `samplePca` (object|null)
- `significantGenes` (string)
- `summary`
- `testedGenes` (string)
- `upGenes` (string)
- `volcano` (object|null)

### `gene_set_overrepresentation` (~584 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `forceUniverse` (boolean)
- `geneSets` (string, required)
- `genes` (string, required)
- `maxGSSize` (number)
- `minGSSize` (number)
- `pAdjustMethod` (string)
- `pvalueCutoff` (number)
- `qvalueCutoff` (number)
- `universe` (string)
- `weights` (string)

Output parameters:

- `enriched`
- `summary`
- `terms`

### `gene_set_enrichment` (~1041 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `adaptive` (boolean)
- `engine` (string)
- `eps` (number)
- `exponent` (number)
- `geneSets` (string, required)
- `maxGSSize` (number)
- `maxPerm` (number)
- `method` (string)
- `minGSSize` (number)
- `minPerm` (number)
- `nPermSimple` (number)
- `nperm` (number)
- `pAdjustMethod` (string)
- `permutations` (number)
- `pvalThreshold` (number)
- `pvalueCutoff` (number)
- `ranked` (string, required)
- `sampleSize` (number)
- `scoreType` (string)
- `seed` (number)

Output parameters:

- `enriched`
- `runningScore` (object|null)
- `summary`
- `terms`

### `gene_set_camera` (~941 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `allowNegCor` (boolean)
- `contrast` (string)
- `counts` (string)
- `design` (string)
- `directional` (boolean)
- `estimateCorrelation` (boolean)
- `fdrCutoff` (number)
- `filterByExpr` (boolean)
- `geneSets` (string, required)
- `interGeneCor` (number)
- `minCount` (number)
- `minTotalCount` (number)
- `name` (string)
- `ranked` (string)
- `reference` (string)
- `samples` (string)
- `statistic` (string)
- `useRanks` (boolean)

Output parameters:

- `enriched`
- `summary`
- `terms`

### `discover_site_avoidance` (~698 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `correction` (string)
- `enzymes` (array)
- `include_subject` (boolean)
- `min_site_length` (number)
- `null_model` (string)
- `positions` (boolean)
- `seed` (number)
- `sequences` (array)
- `shuffle_k` (number)
- `shuffles` (number)

Output parameters:

- `avoided`
- `avoidedCount` (number)
- `correction` (string)
- `enriched`
- `enrichedCount` (number)
- `nullModel` (string)
- `sweep`
- `tests`

### `discover_codon_outliers` (~1045 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `alt_init` (boolean)
- `correction` (string)
- `file_codes` (array)
- `genetic_code` (number)
- `min_codons` (number)
- `pool_files` (boolean)
- `sequences` (array)

Output parameters:

- `genes`
- `outlierCount` (number)
- `outliers`
- `result`
- `skipped`

### `discover_tree_incongruence` (~608 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `correction` (string)
- `loci` (array, required)
- `permutations` (number)
- `seed` (number)

Output parameters:

- `called`
- `global`
- `loci`
- `nullModel` (string)
- `result`

### `discover_reference_concordance` (~374 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cq_table` (string, required)
- `permutations` (number)
- `seed` (number)

Output parameters:

- `conditions`
- `genes`
- `nullModel` (string)
- `p` (number|null)
- `result`
- `w` (number|null)

### `discover_target_validation` (~485 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `gene` (string, required)
- `kappa` (number)
- `tables` (array, required)

Output parameters:

- `combined` (number|null)
- `jointP` (number|null)
- `nullModel` (string)
- `rejected` (boolean)
- `result`
- `tests`

### `discover_flag_rates` (~603 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `correction` (string)
- `flags` (array)
- `include_subject` (boolean)
- `seed` (number)
- `sequences` (array)
- `shuffle_k` (number)
- `shuffles` (number)

Output parameters:

- `hitCount` (number)
- `hits`
- `nullModel` (string)
- `rates`
- `sweep`
- `tests`

### `discover_gene_tree_discordance` (~704 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alignments` (array, required)
- `alpha` (number)
- `correction` (string)
- `gamma_categories` (number)
- `replicates` (number)
- `seed` (number)
- `sh_form` (string)
- `species_tree` (string, required)

Output parameters:

- `alternatives`
- `discordant` (number)
- `genes`
- `rejected` (number)
- `sweep`

### `check_assay_decay` (~515 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `assay` (string)
- `include_subject` (boolean)
- `primers` (array)
- `probes` (array)
- `sequences` (array, required)
- `three_prime_window` (number)

Output parameters:

- `oligos`
- `result`
- `sites`
- `threePrime` (number)
- `worst`
- `worstRate` (number)

### `audit_cds_annotations` (~300 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `genbank` (array, required)

Output parameters:

- `flagged`
- `flags`
- `readThrough`
- `result`

### `validate_gene_trait` (~603 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `categories` (array, required)
- `expression_test` (string)
- `gene` (string, required)
- `kappa` (number)
- `tissues` (array)
- `trait_genes` (array)

Output parameters:

- `e` (number)
- `nullRate`
- `result`
- `supported` (boolean)
- `tests`

### `discover_reference_stability` (~515 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `correction` (string)
- `genes` (array, required)
- `neighbours` (number)
- `pseudocount` (number)
- `tissues` (array)

Output parameters:

- `candidates`
- `rankers`
- `result`
- `stable`
- `unstable`

### `discover_annotation_contradictions` (~671 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `correction` (string)
- `decoding` (string)
- `feature` (string)
- `predictor` (string)

Output parameters:

- `contradicted`
- `count` (number)
- `result`
- `selfCheck`

### `rank_next_tests` (~584 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `beliefs` (object)
- `beta` (number)
- `ledger` (object)
- `mode` (string)
- `n` (number)
- `noise_sd` (number)
- `prior_sd` (number)
- `target_bits` (number)
- `tests` (array)
- `trials` (number)

Output parameters:

- `beliefs`
- `best` (string)
- `bits` (number|null)
- `byCost`
- `gain`
- `note` (string)
- `ranked`
- `result`
- `samplesForTarget` (number|null)

### `describe_discovery_corpus` (~191 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `sequences` (array)

Output parameters:

- `files`
- `records`

### `run_discovery_programme` (~1572 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `budget_seconds` (number)
- `hypotheses` (array)
- `kappa` (number)
- `ledger` (object)
- `organism` (string)
- `posterior_beliefs` (array)
- `run` (object)
- `sequences` (array)

Output parameters:

- `decisions`
- `followUp`
- `ledger`
- `report`
- `result`
- `run`
- `supportedCount` (number)

### `research_run_status` (~242 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `run` (object, required)
- `sequences` (array)

Output parameters:

- `decisions`
- `drift`
- `pending`
- `status`

### `list_research_runs` (~250 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `runs` (array)

Output parameters:

- `count` (number)
- `refused`
- `runs`

### `resume_research_run` (~345 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `budget_seconds` (number)
- `run` (object, required)
- `sequences` (array)

Output parameters:

- `decisions`
- `report`
- `resumed`
- `run`

### `cancel_research_run` (~264 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `hypotheses` (array)
- `reason` (string)
- `run` (object, required)

Output parameters:

- `cancelled`
- `run`
- `status`

### `plan_next_tools` (~421 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `after` (string)
- `independent_only` (boolean)
- `max_steps` (number)
- `output_types` (array)
- `read_only` (boolean)
- `target_type` (string)

Output parameters:

- `count` (number)
- `message` (string)
- `outputs`
- `paths`
- `tools`
- `untyped`

### `enzyme_collection` (~250 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `name` (string)

Output parameters:

- `available`
- `census`
- `collection` (string)
- `count` (number)
- `cutting`
- `enzymes`
- `singleCutters`
- `unresolved`

### `list_experiments` (~248 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `collection` (string)
- `limit` (number)
- `search` (string)
- `tag` (string)

Output parameters:

- `collections`
- `count` (number)
- `entries`
- `total` (number)

### `record_experiment` (~394 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `body_md` (string, required)
- `collection` (string)
- `entry_id` (string)
- `tags` (array)
- `title` (string)

Output parameters:

- `bodyChars` (number)
- `collection` (string)
- `created` (boolean)
- `crossRefs`
- `entry_id` (string)
- `tags`
- `title` (string)
- `unresolved`

### `add_notebook_figure` (~346 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `caption` (string)
- `drawing` (string)
- `entry_id` (string)
- `tab` (string)

Output parameters:

- `caption` (string)
- `entry_id` (string)
- `figure` (number)

### `save_enzyme_collection` (~322 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `activate` (boolean)
- `enzymes` (array, required)
- `name` (string, required)
- `replace` (boolean)

Output parameters:

- `active` (boolean)
- `collection` (string)
- `count` (number)
- `created` (boolean)
- `enzymes`

### `remember_lab_preference` (~666 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `clear` (array)
- `expression_host` (string)
- `polymerase` (string)
- `polymerase_product` (string)
- `primer_gc_max` (number)
- `primer_gc_min` (number)
- `primer_length_max` (number)
- `primer_length_min` (number)

Output parameters:

- `changed`
- `preferences`
- `reading` (string)

### `check_color_balance` (~271 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `barcodes` (array, required)
- `instrument` (string)

Output parameters:

- `acrossChemistries`
- `channelPlot` (object|null)
- `cycles`
- `ok` (boolean)
- `tier` (string)
- `violations`

### `design_free_codes` (~488 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `barcodes` (array)
- `length` (number)
- `limit` (number)
- `max_errors` (number)
- `max_gc` (number)
- `max_homopolymer` (number)
- `mode` (string)
- `reserved` (array)

Output parameters:

- `barcodes`
- `count` (number)
- `dropped`

### `assemble_index_oligos` (~408 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `adapter_3` (string)
- `adapter_5` (string)
- `barcodes` (array, required)
- `format` (string)
- `primer` (string)
- `reverse_complement_tag` (boolean)
- `spacer` (string)

Output parameters:

- `count` (number)
- `longest` (number)
- `oligos`
- `warnings`

### `check_index_pool` (~902 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `i5_cycles` (number)
- `i7_cycles` (number)
- `instrument` (string)
- `kit` (string)
- `library_prep` (string)
- `metric` (string)
- `pool` (string)
- `required_distance` (number)

Output parameters:

- `checks`
- `closestPairs`
- `failures` (number)
- `guarantee`
- `hopping`
- `reads`
- `samples` (number)
- `skipped`
- `verdict` (string)

### `melting_temperature` (~781 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `conditions` (object)
- `dmso_method` (string)
- `model` (string)
- `oligo` (string, required)

Output parameters:

- `baseTm` (number)
- `caveat` (string)
- `gc` (number)
- `lockedBases` (number)
- `model` (string)
- `steps`
- `thermodynamics`
- `tm` (number)

### `back_translate` (~549 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `append_stop` (boolean)
- `host` (string)
- `protein` (string, required)
- `seed` (number)
- `strategy` (string)
- `table` (string)

Output parameters:

- `cautions`
- `conclusion` (string)
- `dna` (string)
- `gc` (number)
- `provenance`
- `residues`
- `undefinedResidues`
- `unweightedResidues`

### `apply_feature_file` (~395 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `coordinates_only` (boolean)
- `file` (string)
- `sequence` (string)

Output parameters:

- `added` (number)
- `basis` (string)
- `duplicate` (number)
- `outOfRange`
- `record` (object|null)

### `auto_annotate` (~755 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `accepted_only` (boolean)
- `alternatives` (number)
- `gateway` (boolean)
- `genetic_code` (number)
- `greedy_gateway` (boolean)
- `hide_fragments` (boolean)
- `libraries` (array)
- `lox_p` (boolean)
- `max_expect` (number)
- `min_coverage` (number)
- `min_identity` (number)
- `min_pi_per_match` (number)
- `mode` (string)
- `policy` (string)

Output parameters:

- `featureCount` (number)
- `features`
- `perSource`
- `record` (object|null)

### `mask_sequence` (~478 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `context` (array)
- `hicut` (number)
- `level` (number)
- `locut` (number)
- `masker` (string)
- `sequence` (string)
- `unit_size` (number)
- `window` (number)

Output parameters:

- `hardMasked` (string)
- `intervals`
- `masked` (string)
- `maskedFraction` (number)
- `provenance`

### `screen_contamination` (~1449 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `build` (string)
- `dust` (boolean)
- `gap_extend` (number)
- `gap_open` (number)
- `internal_moderate` (number)
- `internal_strong` (number)
- `internal_weak` (number)
- `min_score` (number)
- `penalty` (number)
- `reward` (number)
- `sequence` (string)
- `suspect_origin_max` (number)
- `terminal_distance` (number)
- `terminal_moderate` (number)
- `terminal_strong` (number)
- `terminal_weak` (number)
- `ungapped_cutoff` (number)
- `word_size` (number)
- `x_drop_gapped` (number)
- `x_drop_gapped_final` (number)
- `x_drop_ungapped` (number)

Output parameters:

- `cleanSequence` (string)
- `contaminatedPct` (number)
- `maskedSequence` (string)
- `matches`
- `segments`
- `worst` (string)

### `codon_optimality` (~394 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `host` (string)
- `sequence` (string)
- `table` (string)
- `threshold` (number)

Output parameters:

- `fop` (number)
- `nonOptimal` (number)
- `optimalCodons` (number)
- `report`
- `scored` (number)

### `codon_table_fetch` (~603 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `coverage` (string)
- `mode` (string)
- `organism` (string, required)
- `save_as` (string)
- `source` (string)

Output parameters:

- `cds` (number|null)
- `codons` (number|null)
- `gc3` (number|null)
- `organism` (string)
- `report`
- `table`

### `ebi_align` (~817 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `email` (string)
- `include_subject` (boolean)
- `parameters` (string)
- `sequences` (array)
- `service` (string)
- `stype` (string)

Output parameters:

- `alignment`
- `hits`
- `identity`
- `jobId` (string)
- `local`
- `newick` (string)
- `pairwise`
- `patterns`
- `profileHits`
- `raw` (string)
- `repeats`
- `rows`
- `topology`

### `blast_search` (~565 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `databases` (array)
- `email` (string)
- `feature` (string)
- `parameters` (string)
- `program` (string)
- `region` (string)
- `sequence` (string)

Output parameters:

- `hitCount` (number)
- `hits`
- `jobId` (string)
- `provenance`
- `sequences` (string)
- `tabular` (string)
- `topCoverage` (number)
- `topExpect` (number|null)
- `topHit`
- `topIdentity` (number)

### `design_primer_pairs` (~1160 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `conditions` (object)
- `excluded` (array)
- `existing_forward` (string)
- `existing_reverse` (string)
- `fwd_tail` (string)
- `gc_max` (number)
- `gc_min` (number)
- `mispriming_library` (string)
- `n_pairs` (number)
- `primer_length_max` (number)
- `primer_length_min` (number)
- `product_size_max` (number)
- `product_size_min` (number)
- `region_end` (number)
- `region_start` (number)
- `rev_tail` (string)
- `target_end` (number)
- `target_start` (number)
- `target_tm` (number)
- `task` (string)
- `tm_window_max` (number)
- `tm_window_min` (number)
- `weight_cross_dimer` (number)
- `weight_cross_end` (number)
- `weight_di_repeat` (number)
- `weight_end3` (number)
- `weight_gc` (number)
- `weight_gc_clamp` (number)
- `weight_hairpin` (number)
- `weight_length` (number)
- `weight_mispriming` (number)
- `weight_poly_x` (number)
- `weight_self_dimer` (number)
- `weight_self_end` (number)
- `weight_specificity` (number)
- `weight_tm` (number)
- `weight_tm_pair` (number)

Output parameters:

- `forward` (string)
- `pairCount` (number)
- `pairs`
- `productLen` (number)
- `reverse` (string)
- `shortfall` (string)
- `ta` (number)

### `find_primer_snps` (~557 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `assembly` (string, required)
- `forward` (string)
- `pairs` (array)
- `position` (string, required)
- `reverse` (string)
- `snp_set` (string)
- `template` (string)
- `window_end` (number)
- `window_start` (number)

Output parameters:

- `excluded`
- `flagged` (number)
- `primers`
- `snps`

### `check_primer_specificity` (~518 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `database` (string)
- `email` (string)
- `forward` (string)
- `pairs` (string)
- `reverse` (string)
- `template` (string)
- `top_n` (number)

Output parameters:

- `forward` (string)
- `identical`
- `ranked`
- `reverse` (string)
- `specificCount` (number)

### `blast_project_sequences` (~351 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `feature` (string)
- `maxExpect` (number)
- `program` (string)
- `region` (string)
- `sequence` (string)

Output parameters:

- `hitCount` (number)
- `hits`
- `provenance`
- `sequences` (string)
- `tabular` (string)
- `topCoverage` (number)
- `topExpect` (number|null)
- `topHit`
- `topIdentity` (number)

### `find_assemblies` (~322 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `assembly` (string)
- `organism` (string, required)
- `replicons` (boolean)

Output parameters:

- `accession` (string)
- `assemblies`
- `assembly` (string)
- `length` (number)
- `organism` (string)
- `replicons`

### `search_records` (~349 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `limit` (number)
- `query` (string, required)
- `sources` (array)

Output parameters:

- `accession` (string)
- `accessions` (string)
- `hitCount` (number)
- `hits`
- `source` (string)
- `unavailable`

### `fetch_record` (~363 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `accession` (string, required)
- `db` (string)
- `format` (string)
- `record_index` (number)
- `source` (string)

Output parameters:

- `circular` (boolean)
- `featureCount` (number)
- `length` (number)
- `name` (string)
- `provenance`
- `record` (object|null)

### `list_samples` (~318 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `kind` (string)
- `limit` (number)
- `query` (string)

Output parameters:

- `ids`
- `samples`
- `total` (number)

### `match_part_by_sequence` (~286 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cap` (number)
- `name` (string)
- `sequence` (string, required)

Output parameters:

- `coverage`
- `description` (string)
- `licence` (string)
- `matched` (boolean)
- `matches`
- `page` (string)
- `part` (string)
- `role` (string)
- `strand` (string)
- `title` (string)

### `query_database` (~1042 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `authority` (string, required)
- `limit` (number)
- `query` (string, required)

Output parameters:

- `authority` (string)
- `count` (number)
- `endpoints`
- `envelope`
- `results`
- `retrievedAt` (string)

### `fetch_article` (~214 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `id` (string, required)

Output parameters:

- `endpoints`
- `license`
- `markdown` (string)
- `pmcid` (string)
- `retrievedAt` (string)
- `title` (string)

### `find_accessions` (~218 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `text` (string, required)

Output parameters:

- `accessions`
- `found`
- `namespaces`
- `summary` (string)
- `unresolved`

### `fetch_clinvar_vcf` (~275 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `assembly` (string)
- `chrom` (string, required)
- `end` (number, required)
- `max_records` (number)
- `start` (number, required)

Output parameters:

- `endpoints`
- `fileDate` (string)
- `records` (number)
- `summary` (string)
- `truncated` (boolean)
- `vcf` (string)

### `compare_reads_to_reference` (~413 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `end_phred` (number)
- `genetic_code` (number)
- `min_phred` (number)
- `quality_filter` (boolean)
- `reads` (array)

Output parameters:

- `accepted` (number)
- `alignmentFigure` (string|null)
- `cautions`
- `conclusion` (string)
- `consensus` (string)
- `coveragePct` (number)
- `derivation`
- `gaps`
- `identityPct` (number)
- `perRead`
- `record` (object)
- `variants`

### `alignment_agreement` (~533 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alignment` (string)
- `gene_track` (string)
- `locus` (string)
- `reference` (string)
- `variants` (boolean)

Output parameters:

- `cautions`
- `compared` (number)
- `conclusion` (string)
- `genes`
- `mismatched` (number)
- `noCall` (number)
- `pathogenic` (number)
- `rate` (number)
- `reads` (number)
- `variants`
- `window` (string)

### `alignment_window` (~393 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alignment` (string)
- `hide_duplicates` (boolean)
- `hide_secondary` (boolean)
- `hide_supplementary` (boolean)
- `locus` (string)
- `max_reads` (number)
- `min_mapq` (number)

Output parameters:

- `coverage`
- `depthPlot` (object|null)
- `depth_max` (number)
- `depth_mean` (number)
- `hidden` (number)
- `insert_size`
- `read_count` (number)
- `reads`
- `sampled` (boolean)
- `window` (string)

### `describe_project` (~206 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `title` (string)

Output parameters:

- `files` (number)
- `text` (string)
- `unread`

### `list_traces` (~166 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)

Output parameters:

- `count` (number)
- `ids`
- `names`

### `get_construction_history` (~308 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string)
- `limit` (number)
- `molecule` (string)
- `query` (string)

Output parameters:

- `cautions`
- `conclusion` (string)
- `depth` (number)
- `derivation`
- `enzymes`
- `graph`
- `inputs` (number)
- `matched` (number)
- `origin` (string)
- `process_flow`
- `protocol` (string)
- `source` (string)
- `steps`
- `total` (number)

### `compare_constructions` (~270 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `against` (string, required)
- `document` (string)
- `key` (string)

Output parameters:

- `rows`
- `shared` (number)
- `similarity` (number)

### `export_construction_record` (~501 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string)
- `format` (string)
- `sbol_syntax` (string)

Output parameters:

- `available`
- `caution` (string)
- `filename` (string)
- `format` (string)
- `source` (string)
- `syntax` (string)
- `text` (string)

### `size_fragments` (~3383 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `adenylation_threshold` (number)
- `allele_tolerance` (number)
- `document` (string)
- `include_ladder_channel` (boolean)
- `kit` (string)
- `kit_file` (string)
- `ladder_dye` (number)
- `ladder_run` (string)
- `lane_standard` (string)
- `max_size` (number)
- `method` (string)
- `min_peak_spacing` (number)
- `min_size` (number)
- `pullup_threshold` (number)
- `require_resolvable` (boolean)
- `stutter_threshold` (number)
- `threshold` (number)

Output parameters:

- `accuracy`
- `alleles`
- `genotype`
- `ladder_calibration`
- `lane_standard_fit`
- `peakCount` (number)
- `peaks`
- `run`
- `sizeStandard`
- `sizes`

### `load_trace` (~350 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string)
- `min_quality` (number)
- `reverse_complement` (boolean)
- `trim` (boolean)

Output parameters:

- `ambiguous` (number)
- `expectedAccuracy` (number)
- `length` (number)
- `meanQuality` (number)
- `qualities`
- `qualityPlot` (object|null)
- `readQuality` (number)
- `record` (object|null)
- `sequence` (string)
- `trace`

### `trace_raw_signal` (~256 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string)

Output parameters:

- `baseline`
- `baselineSpread` (number)
- `droppedFromFront` (number)
- `peakRawValue` (number)
- `rawScans` (number)

### `draw_trace` (~468 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `bases` (number)
- `bases_row` (boolean)
- `document` (string)
- `from` (number)
- `palette` (string)
- `quality` (boolean)
- `trace_height` (number)
- `width` (number)

Output parameters:

- `firstBase` (number)
- `hasQuality` (boolean)
- `height` (number)
- `lastBase` (number)
- `meanQuality` (number)
- `read` (string)
- `sequence` (string)
- `svg` (string|null)
- `width` (number)

### `trim_trace` (~342 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string)
- `method` (string)
- `min_q` (number)
- `win_size` (number)

Output parameters:

- `firstBaseKept` (number)
- `keptBases` (number)
- `lastBaseKept` (number)
- `meanQualityDiscarded` (number)
- `meanQualityKept` (number)
- `methodUsed` (string)
- `reading` (string)
- `sequence` (string)

### `consensus_from_traces` (~684 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `algorithm` (string)
- `document` (string)
- `forward_primer` (string)
- `min_conf` (number)
- `primer_match` (number)
- `quality_trim` (boolean)
- `reverse_complement_second` (boolean)
- `reverse_primer` (string)
- `second_document` (string)
- `trim_end_gaps` (boolean)
- `trim_min_good` (number)
- `trim_primers` (boolean)
- `trim_window` (number)

Output parameters:

- `ambiguousPositions` (number)
- `consensus` (string)
- `length` (number)
- `reading` (string)
- `readsUsed` (number)
- `trimmedFromEnds` (number)

### `verify_construct` (~465 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `band_margin` (number)
- `confident_coverage` (number)
- `design` (string, required)
- `gap_extend` (number)
- `gap_open` (number)
- `match` (number)
- `min_coverage` (number)
- `min_result_fraction` (number)
- `mismatch` (number)
- `result` (string, required)
- `word_size` (number)

Output parameters:

- `affectedFeatures`
- `differenceCount` (number)
- `differences`
- `identity` (number)
- `largeEvents`
- `report`
- `uncalledPositions` (number)
- `worstConsequence` (string)

### `crispr_quantify_edits` (~422 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `base_editing` (boolean)
- `control` (string, required)
- `donor` (string)
- `edited` (string, required)
- `guides` (array, required)
- `indel_max_size` (number)

Output parameters:

- `baseEdits`
- `checks`
- `contributions`
- `hdrPct` (number)
- `iceD` (number)
- `iceScore` (number)
- `inseparable`
- `knockoutScore` (number)
- `perGuide`
- `rSquared` (number)
- `report`
- `spectrum`

### `tide_quantify_indels` (~603 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `control` (string, required)
- `edited` (string, required)
- `guide` (string, required)
- `max_shift` (number)
- `p_threshold` (number)
- `seq_end` (number)
- `seq_start` (number)
- `window_end` (number)
- `window_start` (number)

Output parameters:

- `aberrantSignal`
- `breaksite` (number)
- `efficiency` (number)
- `indels`
- `insertionBases`
- `rSquared` (number)
- `report`
- `significantIndels`

### `quantify_base_editing` (~662 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string)
- `guide` (string, required)
- `guide_end` (number)
- `guide_is_reverse_complement` (boolean)
- `guide_start` (number)
- `p_value_cutoff` (number)
- `trim3` (number)
- `trim5` (number)

Output parameters:

- `calls`
- `edited` (boolean)
- `guideStart` (number)
- `report`
- `topChange` (string)
- `topPercent` (number)
- `topPosition` (number)

### `detect_trace_indel` (~400 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `breakpoint_scan` (number)
- `document` (string)
- `quality_value_reading` (string)
- `table` (string)

Output parameters:

- `found` (boolean)
- `longAllele` (string)
- `qualityJump` (number)
- `report`
- `shortAllele` (string)
- `sizeInBases` (number)
- `startsAtBase` (number)

### `recompute_trace_quality` (~271 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string)
- `table` (string)

Output parameters:

- `bases` (number)
- `instrumentBases` (number)
- `meanQuality` (number)

### `call_bases_from_trace` (~269 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string)
- `table` (string)

Output parameters:

- `bases` (number)
- `instrumentBases` (number)
- `meanQuality` (number)

### `call_mixed_bases_from_trace` (~426 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string)
- `min_ratio` (number)
- `mode` (string)
- `table` (string)

Output parameters:

- `bases` (number)
- `instrumentBases` (number)
- `meanQuality` (number)
- `mixedBases` (number)

### `adopt_trace_calls` (~411 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `min_ratio` (number)
- `mode` (string)
- `table` (string)

Output parameters:

- `bases` (number)
- `basesBefore` (number)
- `everythingPlaced` (boolean)
- `sequence` (string)

### `restore_trace_file_calls` (~185 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)

Output parameters:

- `bases` (number)
- `sequence` (string)

### `export_trace` (~445 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `document` (string)
- `format` (string)
- `trim` (string)
- `use_internal_name` (boolean)

Output parameters:

- `bases` (number)
- `carriedQuality` (boolean)
- `fileBases` (number)
- `filename` (string)
- `firstBaseKept` (number)
- `lastBaseKept` (number)
- `reading` (string)
- `sequence` (string)
- `text` (string)
- `trimUsed` (string)

### `scan_protein_domains` (~742 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `applications` (string)
- `email` (string)
- `goTerms` (boolean)
- `integratedOnly` (boolean)
- `maxEvalue` (number)
- `pathways` (boolean)
- `protein` (string, required)
- `representativeOnly` (boolean)
- `sortBy` (string)
- `visibleLibraries` (string)

Output parameters:

- `count` (number)
- `domains` (string)
- `jobId` (string)
- `matches`
- `provenance`

### `rps_blast_cdd` (~636 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `compbasedadj` (number)
- `db` (string)
- `dmode` (string)
- `dna` (string)
- `evalue` (number)
- `filter` (boolean)
- `maxhit` (number)
- `protein` (string)
- `smode` (string)

Output parameters:

- `cdsid` (string)
- `count` (number)
- `hits`

### `rps_blast_smart` (~313 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `evalue` (number)
- `max_target_seqs` (number)
- `protein` (string, required)
- `source` (string)

Output parameters:

- `count` (number)
- `domains`

### `rpstblastn_smart` (~393 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `comp_based_stats` (number)
- `evalue` (number)
- `genetic_code` (number)
- `max_target_seqs` (number)
- `sequence` (string)
- `source` (string)

Output parameters:

- `count` (number)
- `domains`

### `delta_blast_smart` (~399 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `domain_inclusion_evalue` (number)
- `evalue` (number)
- `max_target_seqs` (number)
- `protein` (string, required)
- `source` (string)
- `subjects` (string)
- `threshold` (number)

Output parameters:

- `count` (number)
- `domains`
- `profile`
- `proteins`

### `find_linear_motifs` (~852 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `compartments` (string)
- `domains` (string)
- `expectCutoff` (number)
- `families` (string)
- `filterInDomains` (boolean)
- `protein` (string, required)
- `species` (string)
- `structuralContext` (string)

Output parameters:

- `accounting`
- `count` (number)
- `hits`
- `provenance`

### `lookup_residue_sites` (~232 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `accession` (string, required)

Output parameters:

- `residueCount` (number)
- `signatures`

### `run_gel_plate` (~826 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `agarose_percent` (number)
- `form` (string)
- `ladder` (string)
- `lane_names` (array)
- `lanes` (array, required)
- `mobility_model` (string)
- `render_mode` (string)

Output parameters:

- `bands`
- `calibratedBy` (string)
- `cautions`
- `conclusion` (string)
- `derivation`
- `unmeasurable`

### `build_assembly_report` (~381 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `assembly_name` (string)
- `enzyme` (string)
- `errors` (array)
- `products` (array)
- `warnings` (array)

Output parameters:

- `constructCount` (number)
- `errorsCsv` (string)
- `partsUsed`
- `report`
- `stats`
- `summaryCsv` (string)
- `summaryText` (string)
- `warningsCsv` (string)

### `resolve_gene_sets` (~383 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `authority` (string)
- `genes` (string)
- `organism` (string, required)

Output parameters:

- `geneSets` (string)
- `provenance`

### `crispr_score_deephf` (~472 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `model` (string)
- `protospacers` (array, required)

Output parameters:

- `best` (string)
- `efficiencies`
- `model` (string)
- `scored` (number)
- `scores`

### `crispr_score_deepspcas9` (~412 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `contexts` (array, required)

Output parameters:

- `best` (string)
- `indelPercents`
- `scored` (number)
- `scores`

### `score_variant_effect` (~634 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `model` (string)
- `offset_idx` (number)
- `protein` (string, required)
- `strategy` (string)
- `variants` (array, required)

Output parameters:

- `caption` (string)
- `leastDamaging` (string)
- `model` (string)
- `mostDamaging` (string)
- `passes` (number)
- `ranked`
- `scores`
- `strategy` (string)
- `variantCount` (number)

### `copy_number_read` (~641 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `bins` (number)
- `chromosome` (number)
- `compare` (string)
- `data_set` (string)
- `end` (number)
- `file` (string)
- `start` (number)

Output parameters:

- `chromosomes`
- `compared`
- `data_sets`
- `index_source` (string)
- `lanes` (string|null)
- `provenance`
- `summary` (string)
- `tracks`

### `copy_number_segment` (~1761 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `cbs_eta` (number)
- `cbs_seed` (number)
- `cbs_trim` (number)
- `cbs_undo_prune` (number)
- `cbs_undo_sd` (number)
- `cbs_undo_splits` (string)
- `chromosome` (number)
- `data_set` (string)
- `file` (string)
- `graph` (string)
- `hmm_model` (string)
- `methods` (string)
- `pcf_gamma` (number)
- `pcf_kmin` (number)
- `pcf_method` (string)
- `pcf_normalize` (boolean)
- `pelt_minseglen` (number)
- `pelt_penalty` (string)
- `pelt_penalty_value` (number)
- `pelt_standardize` (boolean)

Output parameters:

- `agreement`
- `derivation`
- `segments`
- `summary` (string)

### `copy_number_findings` (~381 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `data_set` (string)
- `file` (string)
- `min_bases` (number)
- `min_markers` (number)

Output parameters:

- `bed` (string)
- `chromosomes`
- `findings`
- `source` (string)
- `summary` (string)

### `annotate_region` (~439 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `build` (string, required)
- `chromosome` (string, required)
- `dosage` (string)
- `end` (number, required)
- `start` (number, required)
- `tracks` (string)

Output parameters:

- `coding`
- `dgv`
- `genes`
- `segdups`
- `summary` (string)

### `browse_region` (~558 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `assembly` (string, required)
- `gene` (string)
- `gene_track` (string)
- `locus` (string)
- `nuclease` (string)

Output parameters:

- `protein`
- `refusals`
- `sites`
- `summary` (string)
- `window` (string)

### `copy_number_regions` (~660 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `build` (string)
- `data_set` (string)
- `file` (string)
- `min_bases` (number)
- `min_markers` (number)
- `regions` (string)

Output parameters:

- `provenance`
- `regions`
- `summary` (string)
- `unplaced`

### `copy_number_somatic` (~264 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `detected_only` (boolean)
- `file` (string)

Output parameters:

- `calls`
- `detected`
- `provenance`
- `summary` (string)

### `copy_number_allele_split` (~308 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `estimated_only` (boolean)
- `file` (string)

Output parameters:

- `metrics`
- `provenance`
- `segments`
- `summary` (string)

### `copy_number_loh` (~430 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alpha` (number)
- `error_rate` (number)
- `file` (string)
- `min_genomic_span` (number)

Output parameters:

- `accounting`
- `provenance`
- `runs`
- `summary` (string)
- `window`

### `copy_number_compare` (~502 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `compare` (string, required)
- `compare_data_set` (string)
- `data_set` (string)
- `file` (string)
- `min_bases` (number)
- `min_markers` (number)

Output parameters:

- `compared`
- `only_in_compare`
- `only_in_file`
- `provenance`
- `shared`
- `summary` (string)
- `unmatched_chromosomes`

### `copy_number_mosaicism` (~609 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `chromosome` (number)
- `data_set` (string)
- `file` (string)
- `graph` (string)
- `mosaic_bandwidth` (number)
- `mosaic_confidence_window` (number)

Output parameters:

- `called`
- `provenance`
- `segments`
- `summary` (string)

### `plan_thermocycler_program` (~854 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `amplicon_bp` (number, required)
- `anneal_c` (number, required)
- `cycles` (number)
- `enzyme` (string)
- `gc_percent` (number, required)
- `polymerase` (string)
- `steps` (string)
- `touchdown` (boolean)
- `touchdown_cycles` (number)
- `touchdown_delta_c` (number)

Output parameters:

- `denatureC` (number)
- `denatureSec` (number)
- `extensionSec` (number)
- `findings`
- `fromDatasheet`
- `program` (string)
- `totalCycles` (number)

### `read_variant_calls` (~693 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `contig` (string)
- `end` (number)
- `file` (string)
- `include_missing_qual` (boolean)
- `info_key` (string)
- `info_value` (string)
- `limit` (number)
- `min_qual` (number)
- `pass_only` (boolean)
- `sample` (string)
- `start` (number)
- `types` (array)

Output parameters:

- `filters_applied`
- `matched` (number)
- `read` (number)
- `samples`
- `scope` (string)
- `summary` (string)
- `variants`

### `variant_call_summary` (~322 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `contig` (string)
- `file` (string)
- `pass_only` (boolean)

Output parameters:

- `counts`
- `filters`
- `indelPlot` (object|null)
- `indel_lengths`
- `not_counted`
- `per_contig`
- `per_sample`
- `qual`
- `substitutionMap` (object|null)
- `substitutions`
- `summary` (string)
- `tstv`

### `variant_consequences` (~478 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `file` (string)
- `limit` (number)
- `min_impact` (string)
- `offset` (number)
- `reference` (string)
- `up_down_stream_bp` (number)

Output parameters:

- `annotated` (number)
- `annotations`
- `by_term`
- `calls`
- `not_annotated` (number)
- `summary` (string)

### `apply_variant_call` (~368 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alt_index` (number)
- `contig` (string, required)
- `file` (string)
- `offset` (number)
- `pos` (number, required)
- `sequence` (string, required)

Output parameters:

- `applied`
- `delta` (number)
- `edited_end` (number)
- `edited_start` (number)
- `sequence` (string)
- `summary` (string)

### `list_databases` (~158 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `domain` (string)

Output parameters:

- `count` (number)
- `sources`

### `lookup_gene` (~220 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `limit` (number)
- `query` (string, required)
- `source` (string, required)

Output parameters:

- `count` (number|null)
- `envelope`
- `provenance`
- `records`

### `lookup_variant` (~296 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `limit` (number)
- `query` (string, required)
- `source` (string, required)

Output parameters:

- `count` (number|null)
- `envelope`
- `provenance`
- `records`

### `lookup_protein` (~280 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `limit` (number)
- `query` (string, required)
- `source` (string, required)

Output parameters:

- `count` (number|null)
- `envelope`
- `provenance`
- `records`

### `lookup_compound` (~206 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `limit` (number)
- `query` (string, required)
- `source` (string, required)

Output parameters:

- `count` (number|null)
- `envelope`
- `provenance`
- `records`

### `lookup_clinical` (~204 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `limit` (number)
- `query` (string, required)
- `source` (string, required)

Output parameters:

- `count` (number|null)
- `envelope`
- `provenance`
- `records`

### `search_literature` (~213 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `limit` (number)
- `query` (string, required)
- `source` (string, required)

Output parameters:

- `count` (number|null)
- `envelope`
- `provenance`
- `records`

### `lookup_omics` (~209 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `limit` (number)
- `query` (string, required)
- `source` (string, required)

Output parameters:

- `count` (number|null)
- `envelope`
- `provenance`
- `records`

### `lookup_ontology` (~230 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `limit` (number)
- `query` (string, required)
- `source` (string, required)

Output parameters:

- `count` (number|null)
- `envelope`
- `provenance`
- `records`

### `assess_small_molecule` (~444 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alert_sets` (array)
- `molecule` (string, required)
- `rules` (array)

Output parameters:

- `alerts`
- `atom_contributions`
- `bioavailability_radar`
- `boiled_egg`
- `canonical_smiles` (string)
- `descriptors`
- `formula`
- `np_likeness`
- `qed`
- `rules`
- `scaffold`
- `solubility`
- `structure` (string|null)
- `summary` (string)
- `synthetic_accessibility`

### `compare_molecules` (~366 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `fingerprint` (string)
- `molecule` (string, required)
- `other` (string, required)
- `tversky_a` (number)
- `tversky_b` (number)

Output parameters:

- `count_similarity`
- `metrics`
- `summary` (string)
- `tanimoto_by_fingerprint`

### `enumerate_protonation_states` (~302 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `max_variants` (number)
- `molecule` (string, required)
- `ph_max` (number)
- `ph_min` (number)
- `precision` (number)

Output parameters:

- `capped` (boolean)
- `sites`
- `states`
- `summary` (string)

### `search_molecule_library` (~194 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `molecules` (array, required)
- `smarts` (string, required)

Output parameters:

- `hits`
- `summary` (string)
- `unread`

### `screen_molecule_library` (~708 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `alert_sets` (array)
- `bins` (number)
- `molecules` (array, required)
- `property` (string)
- `rules` (array)
- `split_rule` (string)

Output parameters:

- `distribution`
- `rows`
- `summary` (string)

### `canonical_tautomer` (~256 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `max_tautomers` (number)
- `max_transforms` (number)
- `molecule` (string, required)

Output parameters:

- `canonical` (string)
- `summary` (string)
- `tautomers`

### `enumerate_reaction` (~296 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `max_combinations` (number)
- `reactants` (array, required)
- `smarts` (string)
- `template` (string)

Output parameters:

- `capped` (boolean)
- `products`
- `summary` (string)

### `write_structure_library` (~309 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `format` (string)
- `molecules` (array, required)
- `names` (array)
- `with_properties` (boolean)

Output parameters:

- `summary` (string)
- `text` (string)
- `unread`

### `cluster_molecules` (~326 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `clusters` (number)
- `method` (string)
- `molecules` (array, required)
- `picks` (number)
- `reordering` (boolean)
- `seed` (number)
- `threshold` (number)

Output parameters:

- `groups`
- `picks`
- `summary` (string)
- `unread`

### `map_chemical_space` (~221 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `molecules` (array, required)
- `space` (string)

Output parameters:

- `explained`
- `points`
- `summary` (string)

### `scaffold_network` (~247 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `molecules` (array, required)
- `rules` (string)

Output parameters:

- `edges`
- `nodes`
- `summary` (string)

### `decompose_r_groups` (~193 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `core` (string, required)
- `molecules` (array, required)

Output parameters:

- `rows`
- `summary` (string)
- `unmatched`

### `matched_molecular_pairs` (~202 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `max_size` (number)
- `molecules` (array, required)

Output parameters:

- `summary` (string)
- `transformations`

### `activity_cliffs` (~244 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `activities` (array, required)
- `molecules` (array, required)
- `scale` (string)

Output parameters:

- `pairs`
- `summary` (string)

### `generate_conformers` (~355 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `count` (number)
- `energy_tolerance` (number)
- `force_field` (string)
- `gradient_tolerance` (number)
- `max_iterations` (number)
- `max_torsion_sets` (number)
- `minimise` (boolean)
- `molecule` (string, required)
- `seed` (number)
- `sixty_degree_steps` (boolean)
- `strategy` (string)

Output parameters:

- `conformers`
- `file_energy`
- `summary` (string)

### `map_reaction_atoms` (~237 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `reaction` (string, required)

Output parameters:

- `confidence` (number)
- `mapped` (string)

### `build_addgene_deposit` (~296 tokens)

Input parameters:

- `_files` (array)
- `_subject` (object)
- `answers` (object)
- `genbank` (string, required)

Output parameters:

- `columns`
- `file`
- `problems`
- `reading` (string)
- `written` (number)

## Diagnostics

Captured diagnostic sections: TLS, DNSSEC, Authorisation, Transports. The full working is on the page: https://verifymcp.io/servers/genmnz-jean/jeanslabs#diagnostics

## Score history

- 2026-11-05: 72
- 2026-11-04: 71
- 2026-11-03: 71
- 2026-11-02: 70
- 2026-11-01: 70
- 2026-10-31: 69
- 2026-10-30: 69
- 2026-10-29: 68
- 2026-10-28: 68
- 2026-10-27: 67
- 2026-10-26: 67
- 2026-10-25: 67
- 2026-10-24: 66
- 2026-10-23: 66
- 2026-10-22: 65
- 2026-10-21: 65
- 2026-10-20: 64

## Common questions

### What is the Jean — Molecular Biology & Genomics MCP server?

Jean — Molecular Biology & Genomics is an MCP server listed in the public MCP registry as io.github.genmnz/jean. Validated molecular biology tools: cloning, primers, CRISPR, Sanger, alignment, qPCR, phylogenetics. This page covers its hosted endpoint (https://jeanslabs.vercel.app/mcp).

### Is the Jean — Molecular Biology & Genomics MCP server safe to use?

Jean — Molecular Biology & Genomics scores 72 out of 100 on VerifyMCP. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### Does the Jean — Molecular Biology & Genomics MCP server require authentication?

No. We connected to Jean — Molecular Biology & Genomics without credentials and it answered, so anything it exposes is reachable by anyone who knows the address.

### Is the Jean — Molecular Biology & Genomics MCP server still maintained?

Jean — Molecular Biology & Genomics is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

## Links

- Remote endpoint: https://jeanslabs.vercel.app/mcp
- Website: https://jeanslabs.vercel.app/docs/api/mcp
- Changelog RSS feed: https://verifymcp.io/servers/genmnz-jean/jeanslabs.xml
- Changelog JSON feed: https://verifymcp.io/servers/genmnz-jean/jeanslabs.json
- HTML version of this page: https://verifymcp.io/servers/genmnz-jean/jeanslabs