manifest.json

{
  "version": "0.6.0",
  "format": "python",
  "license": "MIT",
  "description": "Protocols for everyone, by Ben Miles",
  "protocols": [
    {
      "name": "SpreadNPick",
      "description": "Generates a run to spread a volume of bacteria, then pick colonies after incubation. Accepts 6 bacteria samples maximum, and max number of colonies picked per sample is 8.",
      "command_string": "python -m miles_public_protocols.spread_n_pick",
      "inputs": {
        "media": {
          "type": "string",
          "description": "Growth media for the liquid culture"
        },
        "solid_culture_plate": {
          "type": "container",
          "description": "Choose the container to plate the bacteria into"
        },
        "samples": {
          "type": "aliquot+",
          "description": "Bacteria to plate, maximum is 6"
        },
        "sample_volume": {
          "type": "volume",
          "description": "Volume of bacteria to plate, recommended 1-5 µL."
        },
        "media_volume": {
          "type": "volume",
          "description": "Recommended 1500µL of media, sample + media + antibiotic cannot exceed 2000µL"
        },
        "antibiotic_id": {
          "type": "string",
          "description": "Resource ID of desired antibiotic."
        },
        "antibiotic_volume": {
          "type": "volume",
          "description": "Volume of antibiotic, media and sample must not exceed 2000µL"
        },
        "carbon_source": {
          "type": "aliquot+",
          "description": "Optional carbon source supplement, when using minimal media."
        },
        "carbon_source_volume": {
          "type": "volume",
          "description": "Volume of carbon source solution, media and sample must not exceed 2000µL"
        },
        "plate_growth_time": {
          "type": "time",
          "description": "Length of time the plated bacteria should grow"
        },
        "liq_growth_time": {
          "type": "time",
          "description": "Length of time the picked colonies should grow for in liquid culture"
        },
        "minimum_picked_colonies": {
          "type": "integer",
          "description": "Minimum number of colonies that should be picked from the solid culture. Must be less than 8."
        }
      },
      "preview": {
        "refs": {
          "bacteria": {
            "type": "micro-2.0",
            "store": "cold_4"
          },
          "arabinose": {
            "type": "micro-2.0",
            "store": "cold_4"
          }
        },
        "parameters": {
          "media": "sup-M9",
          "media_volume": "1500:microliter",
          "samples": ["bacteria/0", "bacteria/0","bacteria/0"],
          "sample_volume": "1:microliter",
          "antibiotic_id": "rs17p6t8ty2ny4",
          "antibiotic_volume": "25:microliter",
          "carbon_source": ["arabinose/0"],
          "carbon_source_volume": "25:microliter",
          "plate_growth_time": "16:hour",
          "liq_growth_time": "16:hour",
          "minimum_picked_colonies": 2
        }
      }
    },
    {
      "name": "SerialDilutePlus",
      "description": "Does serial dilutions",
      "command_string": "python -m miles_public_protocols.serial_dilute_plus",
      "inputs": {
        "diluent": {
          "type": "string",
          "description": "What you want your sample to be diluted in"
        },
        "samples":{
          "type": "group+",
          "description": "Aliquots you wise to dilute",
          "inputs": {
            "sample":{
              "type": "aliquot",
              "description": "Aliquot to be diluted"
            },
            "dilution_factor":{
              "type": "integer",
              "description": "Dilution factor, 10 will be a 10X dilution each time."
            }
          }
        },
        "storage_condition": {
          "type": "string",
          "description": "where you want your dilutions to be stored after the dilutions."
        }
      },
      "preview": {
        "refs": {
          "bacteria": {
            "type": "micro-2.0",
            "store": "cold_4"
          }
        },
        "parameters": {
          "diluent": "sup-M9",
          "samples": [
            {
              "sample": "bacteria/0",
              "dilution_factor": 10
            }
          ],
          "storage_condition": "cold_4"
        }
      }
    },
    {
      "name": "GlycerolStorage",
      "description": "Does glycerol bacterial stock solutions for -80 storage",
      "command_string": "python -m miles_public_protocols.glycerol_storage",
      "inputs": {
        "samples":{
          "type": "group+",
          "description": "Bacterial liquid cultures you want to store long term.",
          "inputs": {
            "sample":{
              "type": "aliquot",
              "description": "Aliquot to be diluted and stored. Usually 500uL of overnight culture."
            },
            "label":{
              "type": "string",
              "description":"label for your sample"
            }
          }
        }
      },
      "preview": {
        "refs": {
          "bacteria": {
            "type": "micro-2.0",
            "store": "cold_4"
          }
        },
        "parameters": {
          "samples": [
            {
              "sample": "bacteria/0",
              "label": "ben sample 1"
            },
            {
              "sample": "bacteria/0",
              "label": "ben sample 2"
            },
            {
              "sample": "bacteria/0",
              "label": "ben sample 3"
            },
            {
              "sample": "bacteria/0",
              "label": "ben sample 4"
            }
          ]
        }
      }
    }
  ]
}