Jean — Molecular Biology & Genomics

Reliability

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How to connect

Add it to any MCP client that supports remote servers.

{
  "mcpServers": {
    "jean-molecular-biology-genomics": {
      "type": "http",
      "url": "https://jeanslabs.vercel.app/mcp"
    }
  }
}

319 tools

• list_workflow_templates

  The built-in starter workflows — id, name, what each does and which tools it chains. Pass an `id` to get that template’s graph back, ready to hand to `run_workflow`. This server is stateless, so these are the shipped templates only, not anything a person has saved in their own…

• validate_workflow

  Would this workflow graph run? Returns the blocking errors — an unknown tool, a wire into a port that does not exist, a cycle — each naming the node and the port, without running anything.

• run_workflow

  Run a workflow graph: nodes naming tools, wires carrying one node’s output into another’s input, `$whenExpression` to make a step conditional, and `scatter` to run a step once per element of a list. Returns the run record — per-node status, outputs and errors, in topological…

• read_answer_window

  Read one window of an answer that came back cut to the size budget: the tool, the same arguments, the field its notice named, and which items or characters to return. The answer is derived again, so the window is the one that was cut.

• describe_tools

  The full description of each named tool: what it computes, its models and options, and what it refuses. The listing on this endpoint carries only each description’s opening.

• get_open_record

  Return the plasmid/sequence currently open in the editor. Emits it as a `record`, so it is the SOURCE node of a pipeline — wire its record into any downstream node's $subject.

• load_record

  Read a CHOSEN project document as a record — the pipeline's data-reader source, for running on a specific file instead of whatever happens to be open in the editor.

• list_library

  List the project's sequence documents (id, name, length, topology, kind).

• find_restriction_sites

  Cut positions of the given enzymes on the open plasmid (top/bottom cut, overhang, kind).

• find_star_sites

  Where the given enzymes could ALSO cut the open plasmid under non-standard conditions, from REBASE's own star-activity list and its one-base rule.

• check_methylation_block

  Whether the host's own methylation blocks the given enzymes ON THIS PLASMID, from REBASE's methylation-sensitivity tables localised onto your sites.

• digest_reaction_conditions

  The reaction a digest needs, from NEB's own data: the NEBuffer that serves every enzyme together (scored on the WORST enzyme's percent activity, a star-activity buffer disqualified at any percent), the incubation temperature(s), any cofactor that must be added (SAM or ATP), and…

• enzyme_cut_counts

  Per-enzyme cut counts on the open plasmid (the EcoRI² superscript-badge numbers).

• export_map_svg

  Render the open record's map to a publication SVG string, circular or linear — the same figure the Export panel draws, with the same knobs and the same defaults.

• run_gel_lane

  Resolve a gel lane (ladder / plasmid / digest / pcr) into [bp, form] bands for the open plasmid.

• draw_gel

  Run an agarose gel and photograph it: every lane's fragments migrated by the validated pydna model, drawn as a gel-doc image with the marker ladder's bp marks and each lane's name.

• primer_check

  Where a primer anneals on the open plasmid: 3'-anchored sites with identity % and the ✓/⚠/~/✗ verdict, graded at a bar you can move and that the answer states.

• design_oligo_plate_order

  Lay a set of oligos out as a supplier's PLATE order sheet: one worksheet per plate, in the well order the supplier's own order form fills, with the column shape its loading direction requires.

• build_genbank_submission

  Turn a record into the SUBMISSION SET NCBI's `table2asn` consumes: a `.fsa` whose defline carries the source modifiers, and a 5-column feature table (`.tbl`) beside it.

• build_ena_submission

  Turn a record into what ENA's Webin-CLI takes for an annotated sequence (`-context sequence`): an ENA flat file (`.embl`) and its manifest.

• screen_oligo_structure

  Fold a set of oligos and check them against each other: every oligo's hairpin, its self-dimer anywhere and its self-dimer at the 3' end, plus the cross-dimer with every other oligo in the set, at any position and at a 3' end.

• check_manufacturability

  Measure a sequence against what a NAMED synthesis vendor publishes it can make: length, average and windowed GC, homopolymer runs, tandem repeats, long repeats and hairpin-forming inverted repeats.

• design_gene_fragment_order

  Write the sheet IDT's gene-fragment PLATE upload takes for one or more designed fragments: one worksheet per 96-well plate, wells in the template's own order, and the template's four columns (well, name, sequence, 5' phosphorylation).

• classify_grammar_part

  Which Golden Braid / MoClo / Yeast ToolKit grammar, position and level the open plasmid represents (or null).

• align_read

  Pairwise-align ONE sequencing read against a reference and hand on the two gapped rows, so the read can be graded.

• trim_reads

  Trim sequencing adapters and low-quality ends off FASTQ reads before mapping, and report what was removed.

• fastq_qc

  FastQC's report on FASTQ reads, every module a default FastQC run reports: per-base quality boxes, per-tile quality (when the headers carry a tile), per-sequence quality, per-base sequence content, per-sequence GC against FastQC's theoretical normal, per-base N content, sequence…

• map_reads

  Map sequencing reads (FASTQ or FASTA) or assembled contigs onto a reference and return the alignment as SAM, the file a pileup viewer, a variant caller or `samtools` reads next.

• verify_read

  Grade a sequencing read against a reference (✓ verified / ⚠ near / ~ partial / ✗ divergent) from an alignment.

• read_sequencing_qc

  Read the QC files a sequencing provider returns alongside the reads: a per-base COVERAGE table, or a Plasmidsaurus summary (k-mer composition and the contamination estimate with its named source).

• domesticate_part

  Silently recode the internal Type-IIS sites inside a part's coding sequence so the part can be used in a Golden Gate assembly — same protein, no recognition site.

• design_fusion_site_primers

  Design the PCR primers that ADD Type-IIS fusion sites to a part: enzyme site, spacer and the four-base overhang you chose, on a Tm-matched annealing footprint.

• notebook_cross_refs

  Extract @plasmid / !action / &gel cross-references from a lab-notebook markdown body.

• history_protocol

  Render a construct's build history into a numbered bench-recipe protocol.

• scrub_restriction_sites

  Propose the minimal SILENT synonymous edits that remove forbidden restriction sites from a CDS (a design/write).

• fold_rna

  Minimum-free-energy secondary structure (dot-bracket + ΔG) of an RNA/DNA sequence (Turner-2004).

• pcr_amplify

  Amplify the subject template with a forward + reverse primer (pydna Anneal). Emits the first product as a NEW sequence record so downstream tools (digest, gel, map) operate on the amplicon, not the template — the tool→tool hand-off.

• design_mutagenesis_primers

  Design site-directed mutagenesis (SOE-PCR/QuikChange) primers for a point change on a CDS: the ranked inner mutagenic pairs, the constant outer pair, and the single spanning primer that replaces an outer when the site sits too near a CDS end.

• design_saturation_primers

  Design site-saturation mutagenesis (SSM) primers: one overlapping forward/reverse pair per site, each carrying a degenerate codon, sharing ONE reaction-level overlap and 3' temperature so every site amplifies in the same tube (both of Mutation Maker's solvers: fast approximation…

• design_multisite_primers

  Design QCLM (quick-change lightning multi-site) oligos: one primer per mutated site, all annealing in one reaction, with the codons drawn from an organism's usage table.

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