Verbex Lab Tools

{
  "type": "object",
  "properties": {
    "lipids": {
      "type": "array",
      "items": {
        "type": "object",
        "required": [
          "name",
          "molPercent",
          "molecularWeight",
          "stockConcentration"
        ],
        "properties": {
          "name": {
            "type": "string",
            "description": "e.g. 'SM-102', 'DSPC', 'Cholesterol', 'DMG-PEG2000'."
          },
          "ionizable": {
            "type": "boolean",
            "default": false,
            "description": "True for the ionizable (cationic) lipid that sets the N/P ratio."
          },
          "stockUnit": {
            "enum": [
              "mg/mL",
              "mM"
            ],
            "type": "string",
            "default": "mg/mL"
          },
          "molPercent": {
            "type": "number",
            "maximum": 100,
            "exclusiveMinimum": 0
          },
          "molecularWeight": {
            "type": "number",
            "description": "g/mol, from the certificate of analysis (PEG-lipids are averages).",
            "exclusiveMinimum": 0
          },
          "aminesPerMolecule": {
            "type": "integer",
            "default": 1,
            "minimum": 1,
            "description": "Ionizable amines per molecule of the ionizable lipid."
          },
          "stockConcentration": {
            "type": "number",
            "description": "Concentration of the lipid stock in ethanol.",
            "exclusiveMinimum": 0
          }
        },
        "additionalProperties": false
      },
      "minItems": 2,
      "description": "Every lipid in the formulation; mol% must add up to 100 and exactly one is the ionizable lipid."
    },
    "npRatio": {
      "type": "number",
      "default": 6,
      "description": "Molar ratio of ionizable-lipid amines (N) to RNA phosphates (P).",
      "exclusiveMinimum": 0
    },
    "rnaMass": {
      "type": "number",
      "description": "Mass of RNA (mRNA, siRNA, sgRNA) to encapsulate.",
      "exclusiveMinimum": 0
    },
    "rnaMassUnit": {
      "enum": [
        "ug",
        "mg",
        "ng",
        "g"
      ],
      "type": "string",
      "default": "ug"
    },
    "rnaStockUnit": {
      "enum": [
        "mg/mL",
        "ug/uL",
        "ug/mL",
        "ng/uL"
      ],
      "type": "string",
      "default": "mg/mL"
    },
    "aqueousVolume": {
      "type": "number",
      "description": "Volume of the aqueous RNA phase.",
      "exclusiveMinimum": 0
    },
    "formulationName": {
      "type": "string"
    },
    "aqueousVolumeUnit": {
      "enum": [
        "uL",
        "mL",
        "L"
      ],
      "type": "string",
      "default": "uL"
    },
    "aqueousToEthanolRatio": {
      "type": "number",
      "default": 3,
      "description": "Volume ratio of aqueous (RNA) phase to ethanol (lipid) phase at mixing; 3 means 3:1.",
      "exclusiveMinimum": 0
    },
    "rnaStockConcentration": {
      "type": "number",
      "description": "Concentration of the RNA stock.",
      "exclusiveMinimum": 0
    },
    "nucleotideMolecularWeight": {
      "type": "number",
      "default": 330,
      "description": "Average mass per nucleotide used to estimate RNA phosphate (g/mol).",
      "exclusiveMinimum": 0
    }
  },
  "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.",
  "additionalProperties": true
}

{
  "type": "object",
  "properties": {
    "reactions": {
      "type": "integer",
      "maximum": 10000,
      "minimum": 1,
      "description": "Number of reactions (wells), including controls."
    },
    "components": {
      "type": "array",
      "items": {
        "type": "object",
        "required": [
          "name"
        ],
        "properties": {
          "name": {
            "type": "string",
            "description": "Component name, e.g. '2x SYBR Green mix', 'Forward primer', 'Taq polymerase'."
          },
          "finalUnit": {
            "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"
            ],
            "type": "string"
          },
          "stockUnit": {
            "enum": [
              "M",
              "mM",
              "uM",
              "nM",
              "pM",
              "g/L",
              "mg/mL",
              "ug/uL",
              "ug/mL",
              "ng/uL",
              "ng/mL",
              "U/uL",
              "U/mL",
              "x",
              "%"
            ],
            "type": "string",
            "description": "Stock unit: molar, mass per volume, U/µL for enzymes, x for fold buffers, % for percent."
          },
          "volumeUnit": {
            "enum": [
              "uL",
              "mL",
              "nL"
            ],
            "type": "string",
            "default": "uL"
          },
          "volumePerReaction": {
            "type": "number",
            "minimum": 0,
            "description": "Use instead of stock/final to add a fixed volume per reaction."
          },
          "finalConcentration": {
            "type": "number",
            "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.",
            "exclusiveMinimum": 0
          },
          "stockConcentration": {
            "type": "number",
            "description": "Concentration of the stock tube.",
            "exclusiveMinimum": 0
          }
        },
        "additionalProperties": false
      },
      "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."
    },
    "reactionName": {
      "type": "string",
      "description": "Name for the master mix, e.g. 'IL-6 qPCR plate 2'."
    },
    "excessPercent": {
      "type": "number",
      "default": 10,
      "maximum": 100,
      "minimum": 0,
      "description": "Extra master mix to cover pipetting loss, as a percent of the reactions."
    },
    "reactionVolume": {
      "type": "number",
      "description": "Total volume of one reaction, including template.",
      "exclusiveMinimum": 0
    },
    "templateVolume": {
      "type": "number",
      "default": 0,
      "minimum": 0,
      "description": "Template volume added to each well separately (not in the master mix)."
    },
    "reactionVolumeUnit": {
      "enum": [
        "uL",
        "mL",
        "nL"
      ],
      "type": "string",
      "default": "uL"
    },
    "templateVolumeUnit": {
      "enum": [
        "uL",
        "mL",
        "nL"
      ],
      "type": "string",
      "description": "Defaults to the reaction volume unit."
    }
  },
  "description": "Input contract for the Verbex PCR and qPCR master mix calculator. Water is calculated automatically to fill each reaction.",
  "additionalProperties": true
}

{
  "type": "object",
  "properties": {
    "blanks": {
      "type": "integer",
      "default": 0,
      "minimum": 0,
      "description": "Number of blank wells, placed last."
    },
    "format": {
      "enum": [
        6,
        12,
        24,
        48,
        96,
        384
      ],
      "type": "integer",
      "default": 96
    },
    "samples": {
      "type": "array",
      "items": {
        "type": "string"
      },
      "description": "Unique sample names, in placement order."
    },
    "controls": {
      "type": "array",
      "items": {
        "type": "string"
      },
      "description": "Control names (e.g. 'NTC', 'Positive control'), placed after samples."
    },
    "plateName": {
      "type": "string"
    },
    "standards": {
      "type": "object",
      "required": [
        "points"
      ],
      "properties": {
        "name": {
          "type": "string",
          "default": "Std",
          "description": "Short prefix, e.g. 'Std'."
        },
        "points": {
          "type": "integer",
          "maximum": 24,
          "minimum": 1
        },
        "replicates": {
          "type": "integer",
          "maximum": 24,
          "minimum": 1
        }
      },
      "description": "Optional standard curve, placed first.",
      "additionalProperties": false
    },
    "avoidEdges": {
      "type": "boolean",
      "default": false,
      "description": "Leave the outer wells empty to reduce edge effects."
    },
    "replicates": {
      "type": "integer",
      "default": 3,
      "maximum": 24,
      "minimum": 1,
      "description": "Replicates per sample."
    },
    "fillDirection": {
      "enum": [
        "row",
        "column"
      ],
      "type": "string",
      "default": "row",
      "description": "Fill across rows (A1, A2, …) or down columns (A1, B1, …)."
    },
    "controlReplicates": {
      "type": "integer",
      "maximum": 24,
      "minimum": 1,
      "description": "Defaults to the sample replicates."
    },
    "keepReplicatesTogether": {
      "type": "boolean",
      "default": true,
      "description": "Start a new row or column instead of splitting a replicate set."
    }
  },
  "description": "Input contract for the Verbex plate map builder: lays out samples, standards, controls and blanks with replicates on 6- to 384-well plates.",
  "additionalProperties": true
}

{
  "type": "object",
  "allOf": [
    {
      "if": {
        "required": [
          "mode"
        ],
        "properties": {
          "mode": {
            "const": "solid"
          }
        }
      },
      "then": {
        "required": [
          "targetConcentration",
          "targetConcentrationUnit",
          "finalVolume",
          "finalVolumeUnit",
          "molecularWeight"
        ]
      }
    },
    {
      "if": {
        "required": [
          "mode"
        ],
        "properties": {
          "mode": {
            "const": "stock"
          }
        }
      },
      "then": {
        "oneOf": [
          {
            "required": [
              "stockVolume",
              "targetConcentration",
              "finalVolume"
            ],
            "properties": {
              "solveFor": {
                "const": "stockConcentration"
              }
            }
          },
          {
            "required": [
              "stockConcentration",
              "targetConcentration",
              "finalVolume"
            ],
            "properties": {
              "solveFor": {
                "const": "stockVolume"
              }
            }
          },
          {
            "required": [
              "stockConcentration",
              "stockVolume",
              "finalVolume"
            ],
            "properties": {
              "solveFor": {
                "const": "targetConcentration"
              }
            }
          },
          {
            "required": [
              "stockConcentration",
              "stockVolume",
              "targetConcentration"
            ],
            "properties": {
              "solveFor": {
                "const": "finalVolume"
              }
            }
          }
        ],
        "required": [
          "solveFor",
          "stockConcentrationUnit",
          "stockVolumeUnit",
          "targetConcentrationUnit",
          "finalVolumeUnit"
        ]
      }
    }
  ],
  "properties": {
    "mode": {
      "enum": [
        "solid",
        "stock"
      ],
      "type": "string",
      "description": "Use solid to calculate mass from molecular weight, or stock for C1V1 dilution."
    },
    "solvent": {
      "type": "string",
      "description": "Solvent or diluent to include in the preparation note."
    },
    "solveFor": {
      "enum": [
        "stockVolume",
        "stockConcentration",
        "targetConcentration",
        "finalVolume"
      ],
      "type": "string",
      "description": "For stock mode, choose which C1V1 variable to solve."
    },
    "finalVolume": {
      "type": "number",
      "description": "V2 final preparation volume.",
      "exclusiveMinimum": 0
    },
    "stockVolume": {
      "type": "number",
      "description": "V1 stock volume.",
      "exclusiveMinimum": 0
    },
    "solutionName": {
      "type": "string",
      "description": "Name for the solution being prepared."
    },
    "finalVolumeUnit": {
      "enum": [
        "L",
        "mL",
        "uL"
      ],
      "type": "string"
    },
    "molecularWeight": {
      "type": "number",
      "description": "Molecular weight in g/mol. Required when mode is solid.",
      "exclusiveMinimum": 0
    },
    "stockVolumeUnit": {
      "enum": [
        "L",
        "mL",
        "uL"
      ],
      "type": "string"
    },
    "stockConcentration": {
      "type": "number",
      "description": "C1 starting stock concentration.",
      "exclusiveMinimum": 0
    },
    "targetConcentration": {
      "type": "number",
      "description": "C2 final or desired target concentration.",
      "exclusiveMinimum": 0
    },
    "stockConcentrationUnit": {
      "enum": [
        "M",
        "mM",
        "uM",
        "nM"
      ],
      "type": "string"
    },
    "targetConcentrationUnit": {
      "enum": [
        "M",
        "mM",
        "uM",
        "nM"
      ],
      "type": "string"
    }
  },
  "description": "Input contract for the Verbex molarity and solution preparation endpoint.",
  "additionalProperties": true
}