{ "openapi": "3.1.0", "info": { "title": "Verbex Lab Tools API", "version": "0.2.0", "summary": "Deterministic wet-lab calculators and document builders.", "description": "Verbex Lab Tools are deterministic wet-lab calculators and document builders from Verbex, the voice lab notebook for iPhone and iPad. For a calculation, call the matching calculator (solution_prep, serial_dilution, pcr_master_mix, lnp_formulation, plate_map) directly; do not search first and do not search the web for the method. Use search and fetch only to find and read Verbex guides (protocols, notebooks, inventory, data integrity, bench math) and the 16 lab documentation templates; cite the url each result returns. Call a tool for every number a scientist will act on (masses, volumes, concentrations, dilution series) instead of calculating it yourself, and report the values exactly as returned, with units and the same significant figures (never add digits). Each result carries a self-check; describe results as checked by Verbex Lab Tools, never as validated or verified. Show the tool warnings and safety notes to the user. Results are calculation aids; the scientist verifies them against their own lab requirements. Inputs are used only to compute the response. Nothing is stored, no account is needed, and no AI model is called.\n\nThe same tools are available over MCP at https://www.verbalexperiment.com/mcp.", "contact": { "name": "Verbex support", "email": "support@verbalexperiment.com", "url": "https://www.verbalexperiment.com/support" }, "termsOfService": "https://www.verbalexperiment.com/privacy" }, "servers": [ { "url": "https://www.verbalexperiment.com" } ], "externalDocs": { "description": "Agent guide", "url": "https://www.verbalexperiment.com/llms.txt" }, "paths": { "/api/tools/molarity-calculator": { "post": { "operationId": "solution_prep", "summary": "Solution prep (molarity and C1V1)", "description": "Use when someone asks how much solid to weigh for a molar solution (how many grams for X mM in Y mL, making up a buffer or salt solution), or how much stock to dilute to a target concentration (C1V1). mode \"solid\": mass of solid to weigh from molecular weight, target concentration and final volume. mode \"stock\": C1V1 = C2V2 dilution from a stock, solving for stockVolume, stockConcentration, targetConcentration or finalVolume. Returns the primary result, a step summary, warnings and safety notes.\n\nFor people: https://www.verbalexperiment.com/tools/molarity-calculator", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/MolarityCalculatorInput" }, "example": { "mode": "stock", "solutionName": "100 mM Tris solution", "solveFor": "stockVolume", "stockConcentration": 1, "stockConcentrationUnit": "M", "targetConcentration": 100, "targetConcentrationUnit": "mM", "finalVolume": 100, "finalVolumeUnit": "mL", "stockVolumeUnit": "mL", "solvent": "water or buffer" } } } }, "responses": { "200": { "description": "Calculated result, with a notebook entry in Markdown.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/MolarityCalculatorOutput" } } } }, "400": { "description": "The body is not valid JSON." }, "422": { "description": "The inputs could not be used; validationErrors says why.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/MolarityCalculatorOutput" } } } } } } }, "/api/tools/serial-dilution-calculator": { "post": { "operationId": "serial_dilution", "summary": "Serial dilution planner", "description": "Use for any serial dilution (standard curves, titrations, dose series). Plans transfer and diluent volume per tube and the resulting concentration at each step, from a stock concentration, a constant dilution factor, the number of tubes and the final volume per tube.\n\nFor people: https://www.verbalexperiment.com/tools/serial-dilution-calculator", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SerialDilutionCalculatorInput" }, "example": { "seriesName": "10-fold dilution series", "stockConcentration": 1200, "concentrationUnit": "x", "dilutionFactor": 10, "steps": 3, "finalVolume": 100, "volumeUnit": "uL" } } } }, "responses": { "200": { "description": "Calculated result, with a notebook entry in Markdown.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SerialDilutionCalculatorOutput" } } } }, "400": { "description": "The body is not valid JSON." }, "422": { "description": "The inputs could not be used; validationErrors says why.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SerialDilutionCalculatorOutput" } } } } } } }, "/api/tools/pcr-master-mix-calculator": { "post": { "operationId": "pcr_master_mix", "summary": "PCR / qPCR master mix", "description": "Use when someone sets up a PCR or qPCR reaction mix for several wells. Calculates volume of each component per reaction and for the whole mix with excess, with water filling the remaining volume. Give each component a stock and final concentration (molar, ng/µL, x buffer, %), an amount per reaction (e.g. 1.25 U polymerase from 5 U/µL, 10 ng template from ng/µL), or a fixed volume. Template can be added per well separately. Do not list water; it is calculated.\n\nFor people: https://www.verbalexperiment.com/tools/pcr-master-mix-calculator", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/PcrMasterMixCalculatorInput" }, "example": { "reactionName": "IL-6 qPCR, plate 2", "reactions": 46, "reactionVolume": 20, "reactionVolumeUnit": "uL", "excessPercent": 10, "templateVolume": 2, "components": [ { "name": "2x SYBR Green master mix", "stockConcentration": 2, "stockUnit": "x", "finalConcentration": 1, "finalUnit": "x" }, { "name": "Forward primer", "stockConcentration": 10, "stockUnit": "uM", "finalConcentration": 400, "finalUnit": "nM" }, { "name": "Reverse primer", "stockConcentration": 10, "stockUnit": "uM", "finalConcentration": 400, "finalUnit": "nM" } ] } } } }, "responses": { "200": { "description": "Calculated result, with a notebook entry in Markdown.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/PcrMasterMixCalculatorOutput" } } } }, "400": { "description": "The body is not valid JSON." }, "422": { "description": "The inputs could not be used; validationErrors says why.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/PcrMasterMixCalculatorOutput" } } } } } } }, "/api/tools/lnp-formulation-calculator": { "post": { "operationId": "lnp_formulation", "summary": "LNP formulation (lipid nanoparticles)", "description": "Plan a lipid nanoparticle (LNP) formulation for RNA: from RNA mass, N/P ratio and lipid mol% (e.g. ionizable lipid/DSPC/cholesterol/PEG-lipid 50/10/38.5/1.5), calculate moles, mass and stock volume of every lipid, the ethanol and aqueous phase volumes at the chosen mixing ratio (default 3:1), and final RNA concentration, ethanol fraction and lipid:RNA ratio. Molecular weights must come from the user or certificates of analysis.\n\nFor people: https://www.verbalexperiment.com/tools/lnp-formulation-calculator", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/LnpFormulationCalculatorInput" }, "example": { "formulationName": "SM-102 LNP, luciferase mRNA", "rnaMass": 100, "rnaMassUnit": "ug", "rnaStockConcentration": 1, "rnaStockUnit": "mg/mL", "npRatio": 6, "aqueousToEthanolRatio": 3, "aqueousVolume": 750, "aqueousVolumeUnit": "uL", "lipids": [ { "name": "SM-102", "molPercent": 50, "molecularWeight": 710.17, "stockConcentration": 25, "stockUnit": "mg/mL", "ionizable": true }, { "name": "DSPC", "molPercent": 10, "molecularWeight": 790.15, "stockConcentration": 10, "stockUnit": "mg/mL" }, { "name": "Cholesterol", "molPercent": 38.5, "molecularWeight": 386.65, "stockConcentration": 10, "stockUnit": "mg/mL" }, { "name": "DMG-PEG2000", "molPercent": 1.5, "molecularWeight": 2509.2, "stockConcentration": 10, "stockUnit": "mg/mL" } ] } } } }, "responses": { "200": { "description": "Calculated result, with a notebook entry in Markdown.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/LnpFormulationCalculatorOutput" } } } }, "400": { "description": "The body is not valid JSON." }, "422": { "description": "The inputs could not be used; validationErrors says why.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/LnpFormulationCalculatorOutput" } } } } } } }, "/api/tools/96-well-plate-map-builder": { "post": { "operationId": "plate_map", "summary": "Plate map (6- to 384-well)", "description": "Use when someone lays out a multiwell plate (ELISA, qPCR, cell or compound assays). Lays out a 6, 12, 24, 48, 96 or 384-well plate: standards, samples, controls and blanks with replicates, filled by row or column, optionally leaving edge wells empty and keeping replicate sets together. Returns a grid with a key and a well-by-well list.\n\nFor people: https://www.verbalexperiment.com/tools/96-well-plate-map-builder", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Tool96WellPlateMapBuilderInput" }, "example": { "plateName": "ELISA IL-6 plate 1", "format": 96, "standards": { "name": "Std", "points": 8, "replicates": 2 }, "samples": [ "Patient 01", "Patient 02", "Patient 03", "Patient 04", "Patient 05", "Patient 06", "Patient 07", "Patient 08", "Patient 09", "Patient 10" ], "replicates": 3, "controls": [ "Positive control" ], "controlReplicates": 2, "blanks": 2, "fillDirection": "column" } } } }, "responses": { "200": { "description": "Calculated result, with a notebook entry in Markdown.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Tool96WellPlateMapBuilderOutput" } } } }, "400": { "description": "The body is not valid JSON." }, "422": { "description": "The inputs could not be used; validationErrors says why.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/Tool96WellPlateMapBuilderOutput" } } } } } } }, "/api/tools/lab-protocol-template-builder": { "post": { "operationId": "protocol_template", "summary": "Lab protocol template", "description": "Build a structured lab protocol (purpose, materials, procedure, critical steps, acceptance criteria and more) for a protocol title, using a preset or custom sections. Returns Markdown and HTML ready to fill in or print.\n\nFor people: https://www.verbalexperiment.com/tools/lab-protocol-template-builder", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/LabProtocolTemplateBuilderInput" }, "example": { "protocolTitle": "ELISA protocol scaffold", "presetId": "elisa", "includeExecutionNotes": true, "includeVersionHistory": true, "sectionItems": [ { "id": "elisaPurpose", "source": "library" }, { "id": "elisaPlateLayout", "source": "library" }, { "id": "elisaStandardsControls", "source": "library" }, { "id": "elisaReagents", "source": "library" }, { "id": "elisaProcedure", "source": "library" }, { "id": "elisaAcceptanceCriteria", "source": "library" }, { "id": "versionHistory", "source": "library" } ] } } } }, "responses": { "200": { "description": "Calculated result, with a notebook entry in Markdown.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/LabProtocolTemplateBuilderOutput" } } } }, "400": { "description": "The body is not valid JSON." }, "422": { "description": "The inputs could not be used; validationErrors says why.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/LabProtocolTemplateBuilderOutput" } } } } } } }, "/api/tools/eln-template-builder": { "post": { "operationId": "eln_template", "summary": "Electronic lab notebook entry template", "description": "Build an electronic lab notebook (ELN) entry template for an experiment: objective, materials, procedure, observations and conclusion sections from a preset or custom list, optionally with timestamp fields and voice-capture prompts. Returns Markdown and HTML.\n\nFor people: https://www.verbalexperiment.com/tools/eln-template-builder", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ElnTemplateBuilderInput" }, "example": { "experimentTitle": "Cell culture passage record", "presetId": "cellCulture", "includeTimestamps": true, "includeVoicePrompts": true, "sectionItems": [ { "id": "objective", "source": "library" }, { "id": "materials", "source": "library" }, { "id": "procedure", "source": "library" }, { "id": "observations", "source": "library" }, { "id": "deviations", "source": "library" }, { "id": "custom-cell-health", "source": "custom", "title": "Cell Health Notes" }, { "id": "review", "source": "library" } ] } } } }, "responses": { "200": { "description": "Calculated result, with a notebook entry in Markdown.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ElnTemplateBuilderOutput" } } } }, "400": { "description": "The body is not valid JSON." }, "422": { "description": "The inputs could not be used; validationErrors says why.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ElnTemplateBuilderOutput" } } } } } } }, "/api/tools/reagent-label-scanner": { "post": { "operationId": "parse_reagent_label", "summary": "Reagent label parser", "description": "Turn text read from a reagent bottle or kit label (OCR or typed) into structured fields such as product name, catalog number, lot, expiry, concentration and storage. Parses the provided text only; send the label text, not an image.\n\nFor people: https://www.verbalexperiment.com/tools/reagent-label-scanner", "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ReagentLabelScannerInput" }, "example": { "ocrText": "Cellartis\nPower Primary HEP Medium\nY20020\nLot AOX0016S\nExp OCT. 2025\nStore at -20C\n250 mL", "sourceImageName": "cellartis-hep-medium-label.jpg", "ocrConfidence": 92 } } } }, "responses": { "200": { "description": "Calculated result, with a notebook entry in Markdown.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ReagentLabelScannerOutput" } } } }, "400": { "description": "The body is not valid JSON." }, "422": { "description": "The inputs could not be used; validationErrors says why.", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/ReagentLabelScannerOutput" } } } } } } } }, "components": { "schemas": { "MolarityCalculatorInput": { "title": "Molarity and Solution Prep Calculator Input", "description": "Input contract for the Verbex molarity and solution preparation endpoint.", "type": "object", "additionalProperties": false, "properties": { "mode": { "type": "string", "enum": [ "solid", "stock" ], "description": "Use solid to calculate mass from molecular weight, or stock for C1V1 dilution." }, "solutionName": { "type": "string", "description": "Name for the solution being prepared." }, "solvent": { "type": "string", "description": "Solvent or diluent to include in the preparation note." }, "molecularWeight": { "type": "number", "exclusiveMinimum": 0, "description": "Molecular weight in g/mol. Required when mode is solid." }, "targetConcentration": { "type": "number", "exclusiveMinimum": 0, "description": "C2 final or desired target concentration." }, "targetConcentrationUnit": { "type": "string", "enum": [ "M", "mM", "uM", "nM" ] }, "finalVolume": { "type": "number", "exclusiveMinimum": 0, "description": "V2 final preparation volume." }, "finalVolumeUnit": { "type": "string", "enum": [ "L", "mL", "uL" ] }, "solveFor": { "type": "string", "enum": [ "stockVolume", "stockConcentration", "targetConcentration", "finalVolume" ], "description": "For stock mode, choose which C1V1 variable to solve." }, "stockConcentration": { "type": "number", "exclusiveMinimum": 0, "description": "C1 starting stock concentration." }, "stockConcentrationUnit": { "type": "string", "enum": [ "M", "mM", "uM", "nM" ] }, "stockVolume": { "type": "number", "exclusiveMinimum": 0, "description": "V1 stock volume." }, "stockVolumeUnit": { "type": "string", "enum": [ "L", "mL", "uL" ] } }, "required": [ "mode" ], "allOf": [ { "if": { "properties": { "mode": { "const": "solid" } }, "required": [ "mode" ] }, "then": { "required": [ "targetConcentration", "targetConcentrationUnit", "finalVolume", "finalVolumeUnit", "molecularWeight" ] } }, { "if": { "properties": { "mode": { "const": "stock" } }, "required": [ "mode" ] }, "then": { "required": [ "solveFor", "stockConcentrationUnit", "stockVolumeUnit", "targetConcentrationUnit", "finalVolumeUnit" ], "oneOf": [ { "properties": { "solveFor": { "const": "stockConcentration" } }, "required": [ "stockVolume", "targetConcentration", "finalVolume" ] }, { "properties": { "solveFor": { "const": "stockVolume" } }, "required": [ "stockConcentration", "targetConcentration", "finalVolume" ] }, { "properties": { "solveFor": { "const": "targetConcentration" } }, "required": [ "stockConcentration", "stockVolume", "finalVolume" ] }, { "properties": { "solveFor": { "const": "finalVolume" } }, "required": [ "stockConcentration", "stockVolume", "targetConcentration" ] } ] } } ] }, "MolarityCalculatorOutput": { "title": "Molarity and Solution Prep Calculator Output", "description": "Response contract for the Verbex molarity and solution preparation endpoint.", "type": "object", "additionalProperties": false, "properties": { "notebookEntry": { "type": [ "string", "null" ], "description": "Short notebook-ready Markdown entry: inputs, results to 4 significant figures and an independent Check line. Null when the request is invalid." }, "ok": { "type": "boolean" }, "tool": { "const": "molarity-calculator" }, "toolVersion": { "type": "string" }, "schemaVersion": { "type": "string" }, "generatedAt": { "type": "string", "format": "date-time" }, "result": { "type": "object", "description": "Structured calculation object also returned as outputs.json.", "additionalProperties": true }, "outputs": { "type": "object", "additionalProperties": false, "properties": { "json": { "type": "object", "additionalProperties": true }, "markdown": { "type": "string", "description": "ELN-ready Markdown note." }, "html": { "type": "string", "description": "Formatted HTML note for rich-text editors." } }, "required": [ "json", "markdown", "html" ] }, "validationErrors": { "type": "array", "items": { "type": "string" } }, "warnings": { "type": "array", "items": { "type": "string" } }, "safetyNotes": { "type": "array", "items": { "type": "string" } }, "links": { "type": "object", "additionalProperties": false, "properties": { "human": { "type": "string", "format": "uri" }, "manifest": { "type": "string", "format": "uri" }, "inputSchema": { "type": "string", "format": "uri" }, "outputSchema": { "type": "string", "format": "uri" }, "exampleRequest": { "type": "string", "format": "uri" }, "exampleResponse": { "type": "string", "format": "uri" } }, "required": [ "human", "manifest", "inputSchema", "outputSchema" ] }, "privacy": { "type": "object", "additionalProperties": false, "properties": { "accountRequired": { "type": "boolean" }, "storesInput": { "type": "boolean" }, "cloudAiUsed": { "type": "boolean" }, "note": { "type": "string" } }, "required": [ "accountRequired", "storesInput", "cloudAiUsed", "note" ] } }, "required": [ "ok", "tool", "toolVersion", "schemaVersion", "generatedAt", "result", "outputs", "validationErrors", "warnings", "safetyNotes", "links", "privacy" ] }, "SerialDilutionCalculatorInput": { "title": "Serial Dilution Protocol Planner Input", "description": "Input contract for the Verbex serial dilution calculator endpoint.", "type": "object", "additionalProperties": false, "properties": { "seriesName": { "type": "string", "description": "Name for the dilution series." }, "stockConcentration": { "type": "number", "exclusiveMinimum": 0, "description": "Starting stock concentration before the first dilution." }, "concentrationUnit": { "type": "string", "enum": [ "M", "mM", "uM", "nM", "pM", "mg/mL", "ug/mL", "ng/uL", "ng/mL", "x" ], "description": "Unit for stock and calculated final concentrations." }, "dilutionFactor": { "type": "number", "exclusiveMinimum": 1, "description": "Constant dilution factor applied at each dilution step." }, "steps": { "type": "integer", "minimum": 1, "maximum": 12, "description": "Number of dilution tubes to generate." }, "finalVolume": { "type": "number", "exclusiveMinimum": 0, "description": "Final volume in each tube." }, "volumeUnit": { "type": "string", "enum": [ "uL", "mL" ], "description": "Volume unit for transfer, diluent, and final tube volumes." } }, "required": [ "stockConcentration", "concentrationUnit", "dilutionFactor", "steps", "finalVolume", "volumeUnit" ] }, "SerialDilutionCalculatorOutput": { "title": "Serial Dilution Protocol Planner Output", "description": "Response contract for the Verbex serial dilution calculator endpoint.", "type": "object", "additionalProperties": false, "properties": { "notebookEntry": { "type": [ "string", "null" ], "description": "Short notebook-ready Markdown entry: inputs, results to 4 significant figures and an independent Check line. Null when the request is invalid." }, "ok": { "type": "boolean" }, "tool": { "const": "serial-dilution-calculator" }, "toolVersion": { "type": "string" }, "schemaVersion": { "type": "string" }, "generatedAt": { "type": "string", "format": "date-time" }, "result": { "type": "object", "description": "Structured dilution object also returned as outputs.json.", "additionalProperties": true }, "outputs": { "type": "object", "additionalProperties": false, "properties": { "json": { "type": "object", "additionalProperties": true }, "markdown": { "type": "string", "description": "ELN-ready Markdown dilution plan." }, "html": { "type": "string", "description": "Formatted HTML dilution plan for rich-text editors." }, "csv": { "type": "string", "description": "CSV dilution table." } }, "required": [ "json", "markdown", "html", "csv" ] }, "validationErrors": { "type": "array", "items": { "type": "string" } }, "warnings": { "type": "array", "items": { "type": "string" } }, "safetyNotes": { "type": "array", "items": { "type": "string" } }, "links": { "type": "object", "additionalProperties": false, "properties": { "human": { "type": "string", "format": "uri" }, "manifest": { "type": "string", "format": "uri" }, "inputSchema": { "type": "string", "format": "uri" }, "outputSchema": { "type": "string", "format": "uri" }, "exampleRequest": { "type": "string", "format": "uri" }, "exampleResponse": { "type": "string", "format": "uri" } }, "required": [ "human", "manifest", "inputSchema", "outputSchema" ] }, "privacy": { "type": "object", "additionalProperties": false, "properties": { "accountRequired": { "type": "boolean" }, "storesInput": { "type": "boolean" }, "cloudAiUsed": { "type": "boolean" }, "note": { "type": "string" } }, "required": [ "accountRequired", "storesInput", "cloudAiUsed", "note" ] } }, "required": [ "ok", "tool", "toolVersion", "schemaVersion", "generatedAt", "result", "outputs", "validationErrors", "warnings", "safetyNotes", "links", "privacy" ] }, "PcrMasterMixCalculatorInput": { "title": "PCR Master Mix Calculator Input", "description": "Input contract for the Verbex PCR and qPCR master mix calculator. Water is calculated automatically to fill each reaction.", "type": "object", "additionalProperties": false, "properties": { "reactionName": { "type": "string", "description": "Name for the master mix, e.g. 'IL-6 qPCR plate 2'." }, "reactions": { "type": "integer", "minimum": 1, "maximum": 10000, "description": "Number of reactions (wells), including controls." }, "reactionVolume": { "type": "number", "exclusiveMinimum": 0, "description": "Total volume of one reaction, including template." }, "reactionVolumeUnit": { "type": "string", "enum": [ "uL", "mL", "nL" ], "default": "uL" }, "excessPercent": { "type": "number", "minimum": 0, "maximum": 100, "default": 10, "description": "Extra master mix to cover pipetting loss, as a percent of the reactions." }, "templateVolume": { "type": "number", "minimum": 0, "default": 0, "description": "Template volume added to each well separately (not in the master mix)." }, "templateVolumeUnit": { "type": "string", "enum": [ "uL", "mL", "nL" ], "description": "Defaults to the reaction volume unit." }, "components": { "type": "array", "minItems": 1, "description": "Master mix components except water (water fills the remaining volume). Give each either a stock and final concentration (or amount per reaction), or a fixed volume per reaction.", "items": { "type": "object", "additionalProperties": false, "required": [ "name" ], "properties": { "name": { "type": "string", "description": "Component name, e.g. '2x SYBR Green mix', 'Forward primer', 'Taq polymerase'." }, "stockConcentration": { "type": "number", "exclusiveMinimum": 0, "description": "Concentration of the stock tube." }, "stockUnit": { "type": "string", "enum": [ "M", "mM", "uM", "nM", "pM", "g/L", "mg/mL", "ug/uL", "ug/mL", "ng/uL", "ng/mL", "U/uL", "U/mL", "x", "%" ], "description": "Stock unit: molar, mass per volume, U/µL for enzymes, x for fold buffers, % for percent." }, "finalConcentration": { "type": "number", "exclusiveMinimum": 0, "description": "Final concentration in the reaction (same kind of unit as the stock), or an amount per reaction (U, ng, pmol) when the stock is a concentration." }, "finalUnit": { "type": "string", "enum": [ "M", "mM", "uM", "nM", "pM", "g/L", "mg/mL", "ug/uL", "ug/mL", "ng/uL", "ng/mL", "U/uL", "U/mL", "x", "%", "mol", "mmol", "umol", "nmol", "pmol", "g", "mg", "ug", "ng", "pg", "U" ] }, "volumePerReaction": { "type": "number", "minimum": 0, "description": "Use instead of stock/final to add a fixed volume per reaction." }, "volumeUnit": { "type": "string", "enum": [ "uL", "mL", "nL" ], "default": "uL" } } } } }, "required": [ "reactions", "reactionVolume", "components" ] }, "PcrMasterMixCalculatorOutput": { "title": "PCR Master Mix Calculator Output", "description": "Response envelope shared by Verbex Lab Tools endpoints. outputs.markdown is a notebook-ready entry with a built-in check.", "type": "object", "required": [ "ok", "tool", "toolVersion", "schemaVersion", "result", "outputs", "validationErrors", "warnings", "safetyNotes", "links", "privacy" ], "properties": { "notebookEntry": { "type": [ "string", "null" ], "description": "Short notebook-ready Markdown entry: inputs, results to 4 significant figures and an independent Check line. Null when the request is invalid." }, "ok": { "type": "boolean" }, "tool": { "const": "pcr-master-mix-calculator" }, "toolVersion": { "type": "string" }, "schemaVersion": { "type": "string" }, "generatedAt": { "type": "string", "format": "date-time" }, "result": { "type": "object" }, "outputs": { "type": "object", "properties": { "json": { "type": "object" }, "markdown": { "type": "string" } } }, "validationErrors": { "type": "array", "items": { "type": "string" } }, "warnings": { "type": "array", "items": { "type": "string" } }, "safetyNotes": { "type": "array", "items": { "type": "string" } }, "links": { "type": "object" }, "privacy": { "type": "object" } } }, "LnpFormulationCalculatorInput": { "title": "LNP Formulation Calculator Input", "description": "Input contract for the Verbex lipid nanoparticle (LNP) formulation calculator: lipid amounts from RNA mass, N/P ratio and lipid mol%, and the ethanol and aqueous phase volumes for mixing.", "type": "object", "additionalProperties": false, "properties": { "formulationName": { "type": "string" }, "rnaMass": { "type": "number", "exclusiveMinimum": 0, "description": "Mass of RNA (mRNA, siRNA, sgRNA) to encapsulate." }, "rnaMassUnit": { "type": "string", "enum": [ "ug", "mg", "ng", "g" ], "default": "ug" }, "rnaStockConcentration": { "type": "number", "exclusiveMinimum": 0, "description": "Concentration of the RNA stock." }, "rnaStockUnit": { "type": "string", "enum": [ "mg/mL", "ug/uL", "ug/mL", "ng/uL" ], "default": "mg/mL" }, "npRatio": { "type": "number", "exclusiveMinimum": 0, "default": 6, "description": "Molar ratio of ionizable-lipid amines (N) to RNA phosphates (P)." }, "nucleotideMolecularWeight": { "type": "number", "exclusiveMinimum": 0, "default": 330, "description": "Average mass per nucleotide used to estimate RNA phosphate (g/mol)." }, "aqueousToEthanolRatio": { "type": "number", "exclusiveMinimum": 0, "default": 3, "description": "Volume ratio of aqueous (RNA) phase to ethanol (lipid) phase at mixing; 3 means 3:1." }, "aqueousVolume": { "type": "number", "exclusiveMinimum": 0, "description": "Volume of the aqueous RNA phase." }, "aqueousVolumeUnit": { "type": "string", "enum": [ "uL", "mL", "L" ], "default": "uL" }, "lipids": { "type": "array", "minItems": 2, "description": "Every lipid in the formulation; mol% must add up to 100 and exactly one is the ionizable lipid.", "items": { "type": "object", "additionalProperties": false, "required": [ "name", "molPercent", "molecularWeight", "stockConcentration" ], "properties": { "name": { "type": "string", "description": "e.g. 'SM-102', 'DSPC', 'Cholesterol', 'DMG-PEG2000'." }, "molPercent": { "type": "number", "exclusiveMinimum": 0, "maximum": 100 }, "molecularWeight": { "type": "number", "exclusiveMinimum": 0, "description": "g/mol, from the certificate of analysis (PEG-lipids are averages)." }, "stockConcentration": { "type": "number", "exclusiveMinimum": 0, "description": "Concentration of the lipid stock in ethanol." }, "stockUnit": { "type": "string", "enum": [ "mg/mL", "mM" ], "default": "mg/mL" }, "ionizable": { "type": "boolean", "default": false, "description": "True for the ionizable (cationic) lipid that sets the N/P ratio." }, "aminesPerMolecule": { "type": "integer", "minimum": 1, "default": 1, "description": "Ionizable amines per molecule of the ionizable lipid." } } } } }, "required": [ "rnaMass", "rnaStockConcentration", "aqueousVolume", "lipids" ] }, "LnpFormulationCalculatorOutput": { "title": "LNP Formulation Calculator Output", "description": "Response envelope shared by Verbex Lab Tools endpoints. outputs.markdown is a notebook-ready entry with a built-in check.", "type": "object", "required": [ "ok", "tool", "toolVersion", "schemaVersion", "result", "outputs", "validationErrors", "warnings", "safetyNotes", "links", "privacy" ], "properties": { "notebookEntry": { "type": [ "string", "null" ], "description": "Short notebook-ready Markdown entry: inputs, results to 4 significant figures and an independent Check line. Null when the request is invalid." }, "ok": { "type": "boolean" }, "tool": { "const": "lnp-formulation-calculator" }, "toolVersion": { "type": "string" }, "schemaVersion": { "type": "string" }, "generatedAt": { "type": "string", "format": "date-time" }, "result": { "type": "object" }, "outputs": { "type": "object", "properties": { "json": { "type": "object" }, "markdown": { "type": "string" } } }, "validationErrors": { "type": "array", "items": { "type": "string" } }, "warnings": { "type": "array", "items": { "type": "string" } }, "safetyNotes": { "type": "array", "items": { "type": "string" } }, "links": { "type": "object" }, "privacy": { "type": "object" } } }, "Tool96WellPlateMapBuilderInput": { "title": "Plate Map Builder Input", "description": "Input contract for the Verbex plate map builder: lays out samples, standards, controls and blanks with replicates on 6- to 384-well plates.", "type": "object", "additionalProperties": false, "properties": { "plateName": { "type": "string" }, "format": { "type": "integer", "enum": [ 6, 12, 24, 48, 96, 384 ], "default": 96 }, "samples": { "type": "array", "items": { "type": "string" }, "description": "Unique sample names, in placement order." }, "replicates": { "type": "integer", "minimum": 1, "maximum": 24, "default": 3, "description": "Replicates per sample." }, "standards": { "type": "object", "additionalProperties": false, "required": [ "points" ], "description": "Optional standard curve, placed first.", "properties": { "name": { "type": "string", "default": "Std", "description": "Short prefix, e.g. 'Std'." }, "points": { "type": "integer", "minimum": 1, "maximum": 24 }, "replicates": { "type": "integer", "minimum": 1, "maximum": 24 } } }, "controls": { "type": "array", "items": { "type": "string" }, "description": "Control names (e.g. 'NTC', 'Positive control'), placed after samples." }, "controlReplicates": { "type": "integer", "minimum": 1, "maximum": 24, "description": "Defaults to the sample replicates." }, "blanks": { "type": "integer", "minimum": 0, "default": 0, "description": "Number of blank wells, placed last." }, "fillDirection": { "type": "string", "enum": [ "row", "column" ], "default": "row", "description": "Fill across rows (A1, A2, …) or down columns (A1, B1, …)." }, "avoidEdges": { "type": "boolean", "default": false, "description": "Leave the outer wells empty to reduce edge effects." }, "keepReplicatesTogether": { "type": "boolean", "default": true, "description": "Start a new row or column instead of splitting a replicate set." } } }, "Tool96WellPlateMapBuilderOutput": { "title": "Plate Map Builder Output", "description": "Response envelope shared by Verbex Lab Tools endpoints. outputs.markdown is a notebook-ready entry with a built-in check.", "type": "object", "required": [ "ok", "tool", "toolVersion", "schemaVersion", "result", "outputs", "validationErrors", "warnings", "safetyNotes", "links", "privacy" ], "properties": { "notebookEntry": { "type": [ "string", "null" ], "description": "Short notebook-ready Markdown entry: inputs, results to 4 significant figures and an independent Check line. Null when the request is invalid." }, "ok": { "type": "boolean" }, "tool": { "const": "96-well-plate-map-builder" }, "toolVersion": { "type": "string" }, "schemaVersion": { "type": "string" }, "generatedAt": { "type": "string", "format": "date-time" }, "result": { "type": "object" }, "outputs": { "type": "object", "properties": { "json": { "type": "object" }, "markdown": { "type": "string" } } }, "validationErrors": { "type": "array", "items": { "type": "string" } }, "warnings": { "type": "array", "items": { "type": "string" } }, "safetyNotes": { "type": "array", "items": { "type": "string" } }, "links": { "type": "object" }, "privacy": { "type": "object" } } }, "LabProtocolTemplateBuilderSectionItems": { "type": "array", "description": "Ordered protocol sections to include. Library sections use source=library and an existing id. Custom sections use source=custom with a title.", "items": { "type": "object", "additionalProperties": false, "properties": { "id": { "type": "string" }, "source": { "type": "string", "enum": [ "library", "custom" ] }, "title": { "type": "string" }, "description": { "type": "string" } }, "required": [ "id", "source" ] } }, "LabProtocolTemplateBuilderInput": { "title": "Lab Protocol Template Builder Input", "description": "Input contract for the Verbex lab protocol template builder endpoint.", "type": "object", "additionalProperties": false, "properties": { "protocolTitle": { "type": "string", "description": "Title for the protocol scaffold." }, "presetId": { "type": "string", "enum": [ "general", "elisa", "westernBlot", "qpcr", "cellCulture" ], "description": "Protocol scaffold preset to use." }, "preset": { "type": "string", "enum": [ "general", "elisa", "westernBlot", "qpcr", "cellCulture" ], "description": "Alias for presetId." }, "includeExecutionNotes": { "type": "boolean", "description": "Whether to include ELN execution notes for running the protocol." }, "includeVersionHistory": { "type": "boolean", "description": "Whether to include protocol version history when present in sectionItems." }, "sectionItems": { "$ref": "#/components/schemas/LabProtocolTemplateBuilderSectionItems" }, "sections": { "$ref": "#/components/schemas/LabProtocolTemplateBuilderSectionItems", "description": "Alias for sectionItems." } } }, "LabProtocolTemplateBuilderOutput": { "title": "Lab Protocol Template Builder Output", "description": "Response contract for the Verbex lab protocol template builder endpoint.", "type": "object", "additionalProperties": false, "properties": { "notebookEntry": { "type": [ "string", "null" ], "description": "Short notebook-ready Markdown entry: inputs, results to 4 significant figures and an independent Check line. Null when the request is invalid." }, "ok": { "type": "boolean" }, "tool": { "const": "lab-protocol-template-builder" }, "toolVersion": { "type": "string" }, "schemaVersion": { "type": "string" }, "generatedAt": { "type": "string", "format": "date-time" }, "result": { "type": "object", "additionalProperties": true, "properties": { "tool": { "const": "lab-protocol-template-builder" }, "protocolTitle": { "type": "string" }, "sections": { "type": "array", "items": { "type": "object", "additionalProperties": true } }, "safetyNotes": { "type": "array", "items": { "type": "string" } } } }, "outputs": { "type": "object", "additionalProperties": false, "properties": { "json": { "type": "object", "additionalProperties": true }, "markdown": { "type": "string" }, "html": { "type": "string" } }, "required": [ "json", "markdown", "html" ] }, "validationErrors": { "type": "array", "items": { "type": "string" } }, "warnings": { "type": "array", "items": { "type": "string" } }, "safetyNotes": { "type": "array", "items": { "type": "string" } }, "links": { "type": "object", "additionalProperties": true }, "privacy": { "type": "object", "additionalProperties": false, "properties": { "accountRequired": { "type": "boolean" }, "storesInput": { "type": "boolean" }, "cloudAiUsed": { "type": "boolean" }, "note": { "type": "string" } }, "required": [ "accountRequired", "storesInput", "cloudAiUsed", "note" ] } }, "required": [ "ok", "tool", "toolVersion", "schemaVersion", "generatedAt", "result", "outputs", "validationErrors", "warnings", "safetyNotes", "links", "privacy" ] }, "ElnTemplateBuilderSectionItems": { "type": "array", "description": "Ordered ELN sections to include. Library sections use source=library and an existing id. Custom sections use source=custom with a title.", "items": { "type": "object", "additionalProperties": false, "properties": { "id": { "type": "string" }, "source": { "type": "string", "enum": [ "library", "custom" ] }, "title": { "type": "string" }, "description": { "type": "string" } }, "required": [ "id", "source" ] } }, "ElnTemplateBuilderInput": { "title": "ELN Template Builder Input", "description": "Input contract for the Verbex ELN template builder endpoint.", "type": "object", "additionalProperties": false, "properties": { "experimentTitle": { "type": "string", "description": "Title for the ELN entry template." }, "presetId": { "type": "string", "enum": [ "general", "cellCulture", "molecularBiology", "chemistry" ], "description": "ELN template preset to use." }, "preset": { "type": "string", "enum": [ "general", "cellCulture", "molecularBiology", "chemistry" ], "description": "Alias for presetId." }, "includeTimestamps": { "type": "boolean", "description": "Whether to include record metadata fields." }, "includeVoicePrompts": { "type": "boolean", "description": "Whether to include Verbex-style section voice prompts." }, "sectionItems": { "$ref": "#/components/schemas/ElnTemplateBuilderSectionItems" }, "sections": { "$ref": "#/components/schemas/ElnTemplateBuilderSectionItems", "description": "Alias for sectionItems." } } }, "ElnTemplateBuilderOutput": { "title": "ELN Template Builder Output", "description": "Response contract for the Verbex ELN template builder endpoint.", "type": "object", "additionalProperties": false, "properties": { "notebookEntry": { "type": [ "string", "null" ], "description": "Short notebook-ready Markdown entry: inputs, results to 4 significant figures and an independent Check line. Null when the request is invalid." }, "ok": { "type": "boolean" }, "tool": { "const": "eln-template-builder" }, "toolVersion": { "type": "string" }, "schemaVersion": { "type": "string" }, "generatedAt": { "type": "string", "format": "date-time" }, "result": { "type": "object", "additionalProperties": true, "properties": { "tool": { "const": "eln-template-builder" }, "experimentTitle": { "type": "string" }, "sections": { "type": "array", "items": { "type": "object", "additionalProperties": true } }, "safetyNotes": { "type": "array", "items": { "type": "string" } } } }, "outputs": { "type": "object", "additionalProperties": false, "properties": { "json": { "type": "object", "additionalProperties": true }, "markdown": { "type": "string" }, "html": { "type": "string" } }, "required": [ "json", "markdown", "html" ] }, "validationErrors": { "type": "array", "items": { "type": "string" } }, "warnings": { "type": "array", "items": { "type": "string" } }, "safetyNotes": { "type": "array", "items": { "type": "string" } }, "links": { "type": "object", "additionalProperties": true }, "privacy": { "type": "object", "additionalProperties": false, "properties": { "accountRequired": { "type": "boolean" }, "storesInput": { "type": "boolean" }, "cloudAiUsed": { "type": "boolean" }, "note": { "type": "string" } }, "required": [ "accountRequired", "storesInput", "cloudAiUsed", "note" ] } }, "required": [ "ok", "tool", "toolVersion", "schemaVersion", "generatedAt", "result", "outputs", "validationErrors", "warnings", "safetyNotes", "links", "privacy" ] }, "ReagentLabelScannerInput": { "title": "Reagent Label Scanner Input", "type": "object", "additionalProperties": false, "properties": { "ocrText": { "type": "string", "description": "OCR text extracted from a reagent label image. The browser tool performs OCR locally; this endpoint parses provided text only." }, "sourceImageName": { "type": "string", "description": "Optional source image file name or identifier for review context." }, "ocrConfidence": { "type": [ "number", "null" ], "minimum": 0, "maximum": 100, "description": "Optional OCR confidence percentage from the OCR engine." } }, "required": [ "ocrText" ] }, "ReagentLabelScannerOutput": { "title": "Reagent Label Scanner Output", "type": "object", "additionalProperties": true, "properties": { "notebookEntry": { "type": [ "string", "null" ], "description": "Short notebook-ready Markdown entry: inputs, results to 4 significant figures and an independent Check line. Null when the request is invalid." }, "ok": { "type": "boolean" }, "tool": { "const": "reagent-label-scanner" }, "toolVersion": { "type": "string" }, "schemaVersion": { "type": "string" }, "generatedAt": { "type": "string" }, "result": { "type": "object", "properties": { "tool": { "const": "reagent-label-scanner" }, "version": { "type": "string" }, "sourceImageName": { "type": "string" }, "ocrConfidence": { "type": [ "number", "null" ] }, "rawText": { "type": "string" }, "fieldRows": { "type": "array", "items": { "type": "object", "properties": { "key": { "type": "string" }, "label": { "type": "string" }, "value": { "type": "string" }, "confidence": { "type": "string" }, "needsReview": { "type": "boolean" }, "sourceText": { "type": "string" } }, "required": [ "key", "label", "value", "confidence", "needsReview" ] } }, "tableColumns": { "type": "array", "items": { "type": "string" } }, "tableRows": { "type": "array", "items": { "type": "object" } }, "validationErrors": { "type": "array", "items": { "type": "string" } }, "reviewFlags": { "type": "array", "items": { "type": "string" } }, "warnings": { "type": "array", "items": { "type": "string" } }, "safetyNotes": { "type": "array", "items": { "type": "string" } } }, "required": [ "tool", "version", "fieldRows", "tableColumns", "tableRows", "validationErrors", "reviewFlags", "warnings", "safetyNotes" ] }, "outputs": { "type": "object", "properties": { "json": { "type": "object" }, "markdown": { "type": "string" }, "html": { "type": "string" }, "csv": { "type": "string" } }, "required": [ "json", "markdown", "html", "csv" ] }, "validationErrors": { "type": "array", "items": { "type": "string" } }, "warnings": { "type": "array", "items": { "type": "string" } }, "safetyNotes": { "type": "array", "items": { "type": "string" } } }, "required": [ "ok", "tool", "toolVersion", "schemaVersion", "generatedAt", "result", "outputs", "validationErrors", "warnings", "safetyNotes" ] } } } }