customizing_plans.md

Customizing Plans

JSON Files

There are 3 files that Menagerie takes as input.

aquarium_defaults.json is a file that contains configurations for Aquarium Operations that don't change very much, or have easily enumerable options. It contains a list of objects under the key operation_defaults:

{
  "operation_defaults": [
    {
      "name": "Challenge and Label",
      "input": {
        "Antibody": {
          "object_type": [
            {
              "name": "Antibody Stock"
            }
          ],
          "sample": [
            {
              "name": "Anti-c-myc-FITC"
            }
          ]
        },
        "Protease": {
          "object_type": [
            {
              "name": "Protease Stock"
            }
          ]
        },
        "Protease Concentration": {
          "value": [
            {
              "value": 250
            }
          ]
        },
        "Yeast Culture": {
          "object_type": [
            {
              "name": "Yeast Library Liquid Culture",
              "option_key": "library"
            },
            {
              "name": "Yeast 50ml culture",
              "option_key": "control"
            }
          ]
        }
      },
      "output": {
        "Labeled Yeast Library": {
          "object_type": [
            {
              "name": "Labeled Yeast Library Suspension",
              "option_key": "library"
            },
            {
              "name": "Labeled Yeast Strain Suspension",
              "option_key": "control"
            }
          ]
        }
      }
    }
  ]
}

params.json is similar to aquarium_defaults.json but it specifies defaults that are specific to your experiment but applied to all samples in the experiment. It is not currently supported.

plan.json specifies the Aquarium Samples and operational flow that uniquely comprise your experiment. It usually contains several parts called steps. The first step is sometimes the provision step:

{
  "id": 1,
  "name": "Provision Samples",
  "type": "provision",
  "operator": {
    "samples": [
      {
        "name": "DNA LIBRARY SAMPLE NAME",
        "sample_type": "DNA Library",
        "sample_key": "library"
      },
      {
        "name": "EBY100 + PETCONv3_baker",
        "sample_type": "Yeast Strain",
        "sample_key": "binding_negative"
      },
      {
        "name": "AMA1-best",
        "sample_type": "Yeast Strain",
        "sample_key": "fitc_binding_positive"
      },
      {
        "name": "Trypsin",
        "sample_type": "Protease",
        "sample_key": "trypsin"
      },
      {
        "name": "Chymotrypsin",
        "sample_type": "Protease",
        "sample_key": "chymotrypsin"
      },
      {
        "name": "Anti-c-myc-FITC",
        "sample_type": "Antibody",
        "sample_key": "anti_myc"
      }
    ]
  }
}

If provision step is present, then Menagerie will look for all of the samples listed in the Aquarium database. These can then be accessed in later steps using the sample_key attribute.

In subsequent steps, the operator contains an array of transformations. The source and destination entities are referred to by the sample_key:

{
  "id": 2,
  "name": "Round 1: low concentration",
  "type": "yeast_display_round",
  "operator": {
    "transformations": [
      {
        "destination": [
          {
            "sample_key": "library_expressing"
          }
        ],
        "source": [
          {
            "sample_key": "library"
          },
          {
            "concentration": 0,
            "sample_key": "trypsin"
          },
          {
            "sample_key": "anti_myc"
          }
        ]
      },
      {
        "destination": [
          {
            "sample_key": "library_chymotrypsin_1"
          }
        ],
        "source": [
          {
            "sample_key": "library"
          },
          {
            "concentration": 28,
            "sample_key": "chymotrypsin"
          },
          {
            "sample_key": "anti_myc"
          }
        ]
      },
      {
        "destination": [
          {
            "sample_key": "library_trypsin_1"
          }
        ],
        "source": [
          {
            "sample_key": "library"
          },
          {
            "concentration": 28,
            "sample_key": "trypsin"
          },
          {
            "sample_key": "anti_myc"
          }
        ]
      },
      {
        "destination": [
          {
            "sample_key": "autofluorescence_control"
          }
        ],
        "source": [
          {
            "sample_key": "binding_negative"
          },
          {
            "concentration": 0,
            "sample_key": "trypsin"
          },
          {
            "sample_key": "anti_myc"
          }
        ]
      }
    ]
  }
}