JSON Schemas

JSON inputs and schemas for DASi.

Default Cost Parameters

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{"_primer_min_span": -300,
 "_synthesis_left_span_range": [-500, 500],
 "_synthesis_step_size": 10,
 "global_material_modifier": 1.0,
 "global_time_cost": 10.0,
 "primer_cost": {"columns": ["name",
                             "min",
                             "max",
                             "base cost",
                             "cost per bp",
                             "time (days)"],
                 "data": [["IDTPrimer", 16.0, 60.0, 0.0, 0.15, 1.5],
                          ["IDTUltramer", 45.0, 200.0, 0.0, 0.4, 1.5]]},
 "primer_efficiency": {"columns": ["min", "max", "efficiency"],
                       "data": [[0, 10, 0.0],
                                [10, 15, 0.3],
                                [15, 20, 0.6],
                                [20, 30, 0.8],
                                [30, 40, 0.9],
                                [40, 45, 0.9],
                                [45, 50, 0.8],
                                [50, 100, 0.75],
                                [100, 120, 0.5],
                                [120, 150, 0.3],
                                [150, 250, 0.1],
                                [250, 300, 0.0]]},
 "primer_min_anneal": 16,
 "synthesis_cost": {"columns": ["min", "max", "base", "time"],
                    "data": [[0, 1, 0, 0],
                             [1, 100, "inf", "inf"],
                             [100, 500, 89.0, 3.0],
                             [500, 750, 129.0, 3.0],
                             [750, 1000, 149.0, 4.0],
                             [1000, 1250, 209.0, 7.0],
                             [1250, 1500, 249.0, 7.0],
                             [1500, 1750, 289.0, 7.0],
                             [1750, 2000, 329.0, 7.0],
                             [2000, 2250, 399.0, 7.0]]}}

Cost Parameter Schema

The JSON schema for the Cost Model input. Initialize the cost model using:

from dasi.cost import SpanCost
# open custom parameters
cost_model = SpanCost.open('my example.json')

# open default parameters
cost_model = SpanCost.open()

Cost Parameters Schema

This schema validate a json input for the DASi cost model

type

object

properties

  • global_time_cost

global time cost

the global cost of waiting 1 day

type

number

  • global_material_modifier

global material modifier

multiplies the effect of the material cost by this amount

type

number

examples

1

default

1

  • primer_min_anneal

minimum primer anneal

the minimum number of bases to consider for an annealing event

type

number

multipleOf

1.0

maximum

99

minimum

5

default

16

  • _primer_min_span

type

number

multipleOf

1.0

  • primer_efficiency

primer efficiency data frame

provides efficiency homology for gibson assembly

type

object

properties

  • data

type

array

items

type

array

items

type

number

multipleOf

1

type

number

multipleOf

1

type

number

maximum

1

additionalItems

False

  • columns

type

array

items

type

string

maxItems

3

minItems

3

uniqueItems

True

additionalProperties

False

  • primer_cost

type

object

properties

  • data

type

array

items

type

array

maxItems

6

minItems

6

  • columns

type

array

items

type

string

maxItems

6

minItems

6

uniqueItems

True

additionalProperties

False

  • synthesis_cost

type

object

properties

  • data

type

array

items

type

array

maxItems

4

minItems

4

  • columns

type

array

items

type

string

maxItems

4

minItems

4

uniqueItems

True

additionalProperties

False

  • _synthesis_step_size

type

number

multipleOf

1.0

  • _synthesis_left_span_range

type

array

items

type

number

multipleOf

1.0

type

number

multipleOf

1.0

additionalItems

False

additionalProperties

False

maxProperties

9

minProperties

9

Design Output Schema

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{
  "metadata": {
    "program": "dasi",
    "version": "0.2.1",
    "execution_trace": {
      "compile": {
        "__name__": "compile",
        "__spec__": "FullArgSpec(args=['self', 'post_process_kwargs'], varargs=None, varkw=None, defaults=(None,), kwonlyargs=[], kwonlydefaults=None, annotations={'post_process_kwargs': typing.Dict})",
        "start": "2021-02-23 12:12:46.881306",
        "end": "2021-02-23 12:12:47.075038",
        "args": {
          "post_process_kwargs": null
        },
        "algorithm": "standard optimization"
      },
      "optimize": {
        "__name__": "optimize",
        "__spec__": "FullArgSpec(args=['self', 'n_paths'], varargs=None, varkw=None, defaults=(3,), kwonlyargs=[], kwonlydefaults=None, annotations={'return': typing.Dict[str, dasi.design.design_result.DesignResult]})",
        "start": "2021-02-23 12:12:47.075159",
        "end": "2021-02-23 12:12:47.091454",
        "args": {
          "n_paths": 1
        },
        "algorithm": "standard optimization"
      }
    }
  },
  "designs": {
    "0b9d1c89-0289-4bbc-b650-613e678918d7": {
      "compiled": true,
      "run": true,
      "success": false,
      "assemblies": [],
      "record": {
        "name": "<unknown name>",
        "length": 9438,
        "id": "<unknown id>",
        "is_circular": true
      },
      "sequence": {
        "bases": "TACTTTGTAGAATACATCACTGAACGAGGTAGTCTCGTTGAATCGCTGCGATGGTCGACAGATTACGCTCGATAGCGGTGGGCAAGCGGAAAGGAGTCATACCACGTCAATTAAAGATGCTACCTGCGAACTGTGGTACCATGATAGATCAGTTCCGTCTTCATTGGTTAGTCGACGTGGAAAACGCTTCTAAGGACGCTACGAGAATAGATCCAACTCGGTGGCAAGACCTCGCGGATACTCCACAAATCTACTGACACGGCCTGCTTGTGTACCGCTGATGAACGTCGTGTTGCTAACTGACTACCGGTACCTGTAGACTGTTTGTGCGACCTAGCCTGTGAAAGGCCTTAGGCGAGACTACAGTACTACCCGCCTTGGAGGAGAGCCGGGGCAGGTGTTCCCACGCCCATACGAAAAGATACACAATTCCAAGTGACGTGCTTGAGAAGAGAACACAGCATGCTACAGGGATTACACGCTAAATCATCCTTACATTCTGGAGCTTTGAGTCAATCTCTGAACTGCCGGCCGCTCCATCCTGTAGTGCAACCGTCCAGAATGAATGGGTTCTCTCAAGGGAATCCAGCTATTCCAGTTTCCTTTCCTGCGTGATCATAATAGCAGTTGACCTATATGCCTTCTACGTGCCATGTCACCCCGAGGAATTTTGAAGTAGATCTACGGGCAACAGAGACCAGGAGATGGATTGAATACGAATTGAAAACAATTAATAGGTTGCTCTGAAATTCACAAGAAGGAGGTGAATGCCTCATCACGCGCCTATAATCCTAGTACAGTTCCGTCCACAGGTAAGCTTTATTTACGACTCGAGGGTCACTGACCACAAAACCACAAGCTACTGAGGTTCTGCCAGGAAGGTGGTGGCCGCCTCTGCAATCGTCCAGCGTCTCCGTCCTCATTCATGTAACATACTCTGGTGGCGCTTCCAAATGATACAATCCAGGTTGGATGGTGTTAGTTATCAACACCAGGGCAATCTGCCCTATAACGACTTTCTCATGAACCTGCAATGCTTCCTCACTCCATGGGCAACCTTGCTTAAATCATACAGACGAGCGTTATCTATTCATACAGAAATGTCCAAGGGGGGACGCCGCAGAACGATGTATGTAAGGGTTTAATACCGGCAATTATGCTAAGTCGGCCAGGCGACGGAGTGGATTACGTCACTCGTCTCCGATAAGCTCTGGGTAGAGCCAATGACCATTGTTGTGAGAGTCATCTTGCCCTGGAGCAGCAACCCGCAGACATTCATAGTTAACAGCCGCCTGGATTGGATCCGTCAGGTAGAATGGAAGCCGTCAACAAGCTAGGCCCATCATCCCATATCAGGATCCAAGGATATGCGATCCGGGTCCAGACCTGTGCTACCACATCCTATTCTATGCAGCTTTCGTTTAAGAAACAAGCCTAAGACGGTTGCATGAATAGTTGTGGTAAGCTATCCTAGGGTTAGTCTCAGCCCGATGAGGATATCGGGCCTAGTTCATGGATGTGTACACGCGTCACCTTGAGCGGATCTGGTATATGGGAAAGACCTTCCAAGAGGTGAATCACTCCCTGTATTGGCTTCAGGCCCATGTAAAACTCGCGGTAACCACATATGGACAGCAGTTCGAAGTTGTCTGAATTACCATGTAAGAGACTGGGACACACCAAAGGAAGGGAGCCTCCCCCCAATTGCACGCTGTTATGGTAATACCTTCTAGTAGCCTGTTGTGTAGGGCTTTGAAGGCTTGTCTTCTACTGACGAGGGTTGAAGGAAATTGTGAGATTTCATCGACCGGCGCCCCATTTGATTGCAATTGGAAACCCCGACAGCCACAATTGACCATAGTCACTACCTGCCCCGCGAGAGCTTATCGGTGATATTCGTTTACTAAGGTTTTACGGAGTGTCACCAAGTTTCACTTCCAACTTCCTATCCATATTCTTAACGATGCTACAAATACCTAGCCAACGCCCTTAAGGGGTTATTGACGCGTCGTAATAACGTCTTGTAGAGGGCACCATTGGAGCTTGTGTAGAGTGGGCCACTGAAACCTCGAGCTACCCAGAAAATACGATCCTGGACGTACCAAACTTCGCTCGTATACTCCTGGAATATCTTGGCATTTTCCCGCATAATACAGTATCTAGGATTCGTACGTAGGGCCACCAGCTTACTGCCTTTGGTCGCCACACAAGACCCAAGCCGAAACGGCGTTTCCAATATTCGTACTACCACTGGCGCCATTGGACATCGTATGGGTGTCTTTCGCTCGCACCATAACGCACGCAGTTTACTAGATCTCATCGCCTCCACGAGTAGCTTGGGTGTTTGGACATTGGCGTGGCGTGTACTGGGATGGCAAAAAAACTAGTTTGTGTTGTCGACCGAGGCAGTACTAAATGCCTGTCATAGAGGTTTGAACATCATTACAGGAAACCTCCCCTTGTGGAACGAACGCCTGCCATTCGGTGATGAGTAGAGGATGTGAGGCGTGTTCTCTAGTATGCTTAGGATGTATATTCCTCCCCACGCCTCCTCGTCTGGCAATTGCAGTTACTCCTACTACCGGGTCTCCGTTGAATTCGGAAGACCTGGTGGACTCGCGCGATTTTGAAAATGAAACCTTGAGGAGTTTTTAAACATAGCCCTTCGCCCCACTTAAACGGTACAATACCCTGGGGGCAACTTCGACAACGTTGTACATCACGGAGACTGAAGAACACTATTGGGTACCCATATATACGAGAGCCACATTATGGGCGGTTCGAAGCCAATTATCTTAGAATAGTCTGACTAGGTCCGGCACTTTCCCAGAAAGCACCAATTTTGGTGAGCTGCACAATTCCACACGTGGTAATAGCATATGGGGGCTCTTTGATACGAAAGAACTATGTGAAACCTAACTATTGTTGCTGACTGATGTCCTAACGAGGACTAGGATTTAGGCCTCATACGCAGTTTGTTCTGGAAGCGTGGAAAATATCGTACAACACATAAGCTCACCTAAATCTACTACAGTGACTTGTCCACGAAAATATGGAGGTGAGTGTCATCGTTAACTTAAAAGGGCACAACGGTCGGCGTGAGCTGCGGACTGATTTGGCGACAACTGGGCGCATGCTCTTCTAAAAACGGTGGACACCGCCTCTATAGAGCACTCCTAATGCTTGAAACTCGGCGGCCTGTGAGCAGCAACGGGATTTGGTCATTACAACTTACCCAAGGCCCCATCCGTCTAAGTGTTAAAGCTTTTAGGAAGCTATCTATTCTAGATTTACAGCGATCCAGCTACAGGACTATCTTCGCTTGGAACATACTACTGGGGAACTTGCTGCCAAAAAAATAGGCTCCTCTTATTAAGCCAATTTGCAATTGGAGACATGGGCACTGTCAGTTTTGCAGTTACGTAGTCAGCGGCCTTTACACTACAACCACGTGGGTTCATTTTCAGGGCCACCACCCAGCCTTGAACAGCGCAGAGGGGAGTTCTGATTAACTCTTTCAAGCTTCCTTTATGGGAGCCTTTAAAGGATTCTTTTTCCCTGGGCCATTAATTCAAACGCCATGTGCTCAACCTTGCTACTAACAGCTTCCTTGACCGTGTGGAGTTGCCAATGGGCTTCGCACTATGTTGCTAACAGCAGCCGTAACCGACGTGTACTCAATTTGTTTCCTGATAGCAACGTTAGCTCGTCCATTAGGATTTTAAGCCTCCATCCTCACCAGGGAGGGTCCGTCGCGAGGGCGCAATTGTCTATGGGATTGGACTGTCTTCCTGCATACCTGAGTCGTCAGGAGCCTGATTATATAGGTGGAGATACGGAGAGTGAGCCAAATTCTCACATTGGGGGACGCGTTGAGTAATGCTGGGCTCGTATCTCGTAGACAGACACGCTCCTTTATCCGTTGTATCGTTCTGGAGTGAGCGAAGCGATTGATCCACCTCCTGCCCATTACCGAGTTATGACACCTACAGTGGTTTCTCAGTGATGCCATTGGACTAAGTGGTTGCTCCTTTTCTCCTGAATGTCCGCTGGAGGCCTATCCTGGCGGATCAGTTGAAGGTCAATCGTTTACTTCGCGTTGTGCCAGGAGTCCGTGACCGTCGGAAATTTGTTCATACATGTGCTGCGCTCGCGTTAAAAAGACGGCGTGTTTCCAGAGTGGCTACACCGCTTCGAACTAGGCTAGATTACCGCGGTGCTCGGGCAAAAAGCTTCATTTTTTCCCCGAGACTCATCCCGGATCGCGAAAACCATGCGAGAATCACAAAGTGGAAGTAAATTGCTGGTTTCGTCGAACGCCATATCGACCCCGCTTTGGACAAAGCCACATGCCTAGACACGGCGACATACCGAATTATAGGACGAAGTACAATTCTGACCCGTTTGAGTCCTCAAAGAAAGTGCCCTATTGACAAAAAAGCAATTGCGACATAGGCCGCTATTGTCGGTGGAACAGTCTAAGTGCTCCAGCCTTTACTACTTGGCAGCGGGGCTACTGCCCTGCCCACAATTATCAGAAGGCTTGTACCCTAGATGAGGAAGGGTATAAGGGTATCAGCCATACGCGTACTCCGATGGTCTCTAAAGTTTTTATACCCCCGTTAATATATTCAAAGACACACCCAAAGAGGGAATACCGCATTCGGGGAGCTCCGCCCGCATATATGAGAGTTCGGCCGAACCTAATAGGTCATAGTCGAAACTGGTGACTATAAGTTGGTACATGACGGGCAATTATCTACGAATAGCTAAGCAGCGGTCAATAAACGGCCGACGCCCCCAGCCCATCGTTTTGAAAGAGGGGGAATATTGAGCTGGATCCGGTGTCACTTATTCCACCAACCATTATGGTAAATTATAGGCTGCATGCATACAAAGTACCTATGGCCCTTTAGAAAACTTGGGATCTCTCACTCCTTGCTCGTACTTTCGCACGGTAGGGCCACAGGATCGTAAATAGTGCTTTGAGGCTCTGTCCATCCTTGATGGCCCTGCGTGGGCCAGATCAGGATGAGGAGTTTGACAAATTGTGTGGCCAATCGTTAAGCACTATTAGTCGCTGGTGCGAGAGGTGCTGCTCGTTTACGCAGGAGTTTCAGCCGTGTATCGGACCTGCAGGCGGCGACTGGTGAATCTTCCCACGGGAGATGCTGAGATGGATGTCTTAACACCAGAGATGACTCCTCCGATGTAACCTATTATTGAGTCTAATTGCTCAATTGTAGCGTTATTCAATAAGACGAATTATTACATCCGCTTAATCTGTTAGACCCCCGGGCAGCTACAGCTGTTCCGACATAGTCTTAACTCAGTATACGACTGTTGGCGGATGGATCATAGGAGTTCATTAGAGATACCAGTACGACTGTACTGGGAAAGGCTTGTCCTGTCAGTCATATCGAGGCGTGTCGACAATCGGTACGTGAACATGATCCACCGAACGGATGCGTCATCGAGAACGATCTGAATGCAATCACCTTACTCTAGGATGGTGATTCAAGACATGTTTTCTTCAGACCGACCCCACGGCGTACATTCGACTCCTGGATTTTGACGATGGTAAGAGCTCTTCTGTAGAACCTATCACTTGACCGTGAGACCAGGTGAGATGCAAGTTTAGTCACCGACTCTGCTGTGAGGAGTTGTAAGCGCCGGCTTCGACGTCGTGCATTGGTGAGACATGTTGCGTAAAACGCTTGTAATAATGCTCTATAAACCTAAGAACTTATCCCGGGTCACCCACTTCAATTCGATGGGCTGCACCTACGCATTTCGAAAAGAGCCGAATAGGCAGGAGGATGGAATGACGGAATTAGACGCTTTCCTATATATTTTTATCCTCTTGGCCATTATTGCCTCTGTGGCGTGCTTAATCGCCAACCCCCGTAGTATAGACTTTTTCCCACGCCATGAGACTCGCAGTTGAACACGGTGTGCGGCAAATTTCCGCGAAGTTTTGGGGCGAACCCGAATAGAACCAAGACAGTGAGCTGTACGATTTATGACGCAGCTTGGTTCGAAGCCTCCAGTCCTCTATAGGGTTCGCAGGGATACCGACTACGGCTGAGGTTATAGAAGCAGCTAGCAACTCTGAACCGCCCACATTTTTAGAAACACCGTCTGCAAGTCTCGATGGATAATAGAGGTGTGATTACATACTTAGGTATCCGACAATACACCTGTAGATTAGTAGTTATCCCGCAGTAAATGTCGCCCGGACGCATGTGAACACGCCAGACCGAGGAGTTCCTACTCGGCAGTTCGGGGTACTTATCACTAATCGCGCAGGACCAGGCCGGGCTGCCGTCTTCCATTAGTGACTATTCCGCAAAAAACTGAACTCTTCTAAGACCTGTGCTTGTTATTCCGCTCTTGCCCCCTGGTATTAAACCTTGTGTGAGCTGTTGCCCGGACGAGGAGCAGACTTTGTTTACTGTTTGCAGTAGGAGAGCGCTCTCTGAGAGACAACCGCGGAGCTACGTCCGGGTGTCGCCGTCCGGCCGATCGAAGCTGTGTCTGTCGGGACCTGTCATTTAAATCTCTGACAGCTACCACGTATGCAGAGACAAGTTCAGCCGTATGCGGGACAAACAGCCAGGAAAATCCTGCCGCTGACAACACGGGTCTGCATCATCAGGAACTCCGTGTATTTTTTCTGATGGTCTACTAAACTACGCAGGTTATTGGACAACGCGTCGGCACCTCGGTGGTACTCGGCTGGGGCGGAAGGACTTGACCGATATGTCACGCTTGAGGGGCTCAGGTTGCGCCCACAGTGTTTAAAGCTGGTTATATAAGGTGTTCGTGCTTCCTGCAGGTGTGAATCTGCACGAAGATCGTTGGACCCTCCTAAAACGGAATCTACTCACGGTCCAAAAGCCGAAACATCCAATCCAGTAGACGTGCCCCCACGAACTTCACCGGTAATACCGACATCGCCGGTCTTCGGAAGAAGCACAGCTTCACATGTGTGGACCCAAATTCTGGAACTCGACGGTCTCTGTGGCGTGTCATGACCTATCGCGCAATACATCCTTCTCAAAATCTAGAGCCGTAAGTAGAACAGAACTGTGGATACTTTAGTGCCAATAATAGTATCCTATGAACTTGACAGGTTCAACAAAAGCAGTTAAAGCCTGTGCCGATTCGGGAGAGCACCGAAAGAATGAGAGTGGAACCAAGCCTTGTCCTGGGCCTTTGCCGTAAGTGCCGGCCAGAGAACGCCCGTAACCCAAACGACTACCACAAATGTCGAGGTGCAGGGCGTCTATGATAGGTGACATAACAGTGAGATCATACAGACAAAGCGGAACCGCCAACGCTCCATTACTACTTTCAGTGCTACCTGCATTCGCACTGTCGACTCCGTTGGTAGGGGAAGCGGAATCGTGGGAACTACCCCAGTACTTTACAAGGCACAAGCTCTTCTGAGTACACCACTGTACGTGATGGTTCGCTGTGCACATCTCGAGCCAAGCGAACATTCACTCGGTGACACCCTAAGGCGTTTTAGCATTGCCGTTGCCACGTTCCTCTAATTTCTGCCGTTCCCGTGCAGATCCAACTCCCACCGTAGGGGGCGTTCAGATCTGCGCCGTAGTCAAATATAGCTTATCTTTGGTGGACCAAACCCTGCCCCTTGCTTATGAGGATCCTCGATGTTTAATGAACGTAGGCGGTCACGGGGGGGGGAGGAGACATGCGGCCCGAGTTAAATCGCCACCCACAGGGGCGATCTCTTCTGAGCTAGGTATTGTCATGGCTGGAGTGTAACACATATAAGACTGTAAGGAAGTATCGGAGCACAACCTATACTGAGTGGTCAAATAGAGGCATTCGTTCGCATTGCTGTACAGGCAGTCGATGTACCCGGGCTTCAGTTCTGTACGATCTTGGGATACAAAACGGTAGTCTTCCCGCGCTTATTAGAGGCCCATTACCTACCTCTCTAACACGGCTATGCACTCATGCGTACGCACGAGAGTAGATTCTTGAGTCGTGGCAGTACATCAAGGTGGCGGGCGAGTTTCATCCCTCGCTCCCAACTTTTCGGGGACAACATTTCGCCAAAAAAGTATCCGCCCAAATCTCGACAGACGTTCAAAAGTCAGATCCTTCAATGTGGTTTTTCCGAGCTATGGCTAGATAAGCCCCTAAAAGTCGCAGTTCCACTTCGCAGGTAACCGAACGTGTGTATTAATCCGGAATCATTGATTTGTTTCCTAATGGAGGTAATGCTGCAACATCAGTCAAACTCCCTGATGCCTCGGGCCAGTAGAGCCGCGCGGGATACCGTAGCAAGTCTACACGTCCCGCTCACGAGGGGTCCAGATGGCTATGACATGTCCTTCTTCAAATTGGTCATCACACGCCGTTGCGAAGTAACCGCTGAGTCCTCCGTTCCTTGAAAGGTCCCTCTCGGGTCACTTACGGACAACCACTGGACATAACGTATTCAGCCTCATGTGCACCGCTTGGCATCTTTCGGCTTTCATAACCTTATCCCTTCTGCTCGTGTGGCTCTTCTGATTTCCTACTTAAAAGGAATCATTCAGATCGAACACACGTACGTCTGGGAAGGGGATTCTAAGGAGGACTGTCAGTACAACTGTACCATTCAACGAGCGAGAGATTCTCATGACTTATTGTGCTCGTAGCACCTTGTCGTAACACTTCCATGCTACGCAAAACTGTCCTAGTCAGCTACACCAGAATCGATAGTGATTAACTAACAAGGGAAGGTAAGCCGTGGGCGTCGAGACTTTAACTGCTAAAGCGCGGTAAGTCACAACCTGGTATGGTGATCAACCCCACTTCAAAGCTCCTCTATCAAAAGGATGTGACTACTGGGTATAGCCTCAGGCTGCCTCTACTTTCGTCTTGCGGGGTGCGATTAGCAACACTTGGTAAGACTTCGATCATGAGCCTTGGCTACGACGCTACCAACACGCGTGTCGGTCCCTTTACCTCGGCAAGGGGACCTCAGGTGGCTAATTTTGAAATGACAATTAACTAGCCGTCGTACAGCAAAGCCTGTACGTGTACAGTCGGGAAAAGCTCTACGGGCCGCATCCGTAGTTTACCGGTCGATGGAGCCTTAGCACATACGCTGGGAGACGGATCAATAGAGGGTAAACGCACATTTAGGACGCCAGAACCTAATGAAATCCGATTAACAAAGTCCCGCACTACATAGACCGAAATGTCCGAATTTTCTCTTCCGGCGAAATGCGGCCCTATTGCTGGTAGATACTGTTTGTGCGTAGCGATTAATCATAGTTGAGAGTAACGCATCTAAGCGGCGGTTTTGCGATCTCGGTACACGTCGTTCGCGATCGTAGGCACGCAAATCTTCGGACCATCCAATTCACTCCGAGACAGGGCGTTGGGTCCTGGTCCGCATACGCTCTGTTCACA",
        "length": 9438,
        "name": "<unknown name>",
        "id": "<unknown id>",
        "annotations": [
          {
            "start": 78,
            "end": 403,
            "strand": -1,
            "color": "#71da69",
            "name": "433c",
            "type": "misc_feature"
          },
          {
            "start": 403,
            "end": 1359,
            "strand": -1,
            "color": "#1a0920",
            "name": "c321",
            "type": "misc_feature"
          },
          {
            "start": 1806,
            "end": 1919,
            "strand": -1,
            "color": "#d7ab91",
            "name": "12b6db9a-8990-41e1-937d-9fe561943606",
            "type": "misc_feature"
          },
          {
            "start": 1919,
            "end": 2080,
            "strand": -1,
            "color": "#52582a",
            "name": "27dcc7eb-7a84-4373-bd91-6451327416e9",
            "type": "misc_feature"
          },
          {
            "start": 2102,
            "end": 2842,
            "strand": -1,
            "color": "#59f0d6",
            "name": "3e4e",
            "type": "misc_feature"
          },
          {
            "start": 3463,
            "end": 4352,
            "strand": -1,
            "color": "#432175",
            "name": "ffef",
            "type": "misc_feature"
          },
          {
            "start": 4352,
            "end": 4772,
            "strand": -1,
            "color": "#d566ac",
            "name": "c422",
            "type": "misc_feature"
          },
          {
            "start": 6194,
            "end": 6667,
            "strand": -1,
            "color": "#53788b",
            "name": "a2c28aec-9fbb-474a-99b6-15cdde9dcfd4",
            "type": "misc_feature"
          },
          {
            "start": 6841,
            "end": 7126,
            "strand": 1,
            "color": "#185e98",
            "name": "4bbc",
            "type": "misc_feature"
          },
          {
            "start": 7126,
            "end": 7685,
            "strand": 1,
            "color": "#6ff31e",
            "name": "df2c",
            "type": "misc_feature"
          },
          {
            "start": 7685,
            "end": 8512,
            "strand": 1,
            "color": "#11bf79",
            "name": "89df",
            "type": "misc_feature"
          },
          {
            "start": 8512,
            "end": 8660,
            "strand": 1,
            "color": "#7a0e05",
            "name": "c96d",
            "type": "misc_feature"
          }
        ],
        "customFields": {
          "topology": "circular"
        },
        "isCircular": true
      }
    }
  },
  "molecules": [],
  "reactions": []
}

DASi design output

This schema validates a json output for the DASi design

type

object

properties

  • metadata

type

object

properties

  • program

program name

type

string

  • version

semantic version of the program

type

string

  • execution_trace

execution trace that generated this output

type

object

  • molecules

type

array

items

#/definitions/molecule

  • reactions

type

array

items

#/definitions/reaction

  • designs

#/definitions/design_status

definitions

  • sequence

This schema validates a JSON that represents a DNA/RNA sequence

type

object

properties

  • bases

Bases of the sequence as a string with no white spaces.

type

string

  • length

Optional length of the sequence

type

integer

  • name

Optional name of the sequence

type

string

  • id

Optional id of the sequence

type

string

  • isCircular

Whether the topology of the sequence is circular (or linear if false)

type

boolean

  • annotations

List of (optional) sequence annotations

type

array

items

#/definitions/sequenceAnnotation

  • customFields

Optional list of custom fields on the sequence.

type

object

examples

location

benchtop

LIMS_ID

UWBF_31251

  • sequenceAnnotation

Sequence annotation

type

object

properties

  • start

inclusive start of the annotation

type

integer

  • end

exclusive end of the annotation

type

integer

  • color

color of the annotation

type

string

  • type

type of annotation

type

string

  • base

type

object

properties

  • __name__

name of the object

type

string

  • __index__

indesx of the object

type

integer

  • __type__

type of object

type

string

enum

reaction, molecule

examples

molecule

reaction

  • used_in_assemblies

#/definitions/_used_in_assemblies

  • molecule

allOf

#/definitions/base

type

object

properties

  • sequence

#/definitions/sequence

  • __meta__

type

object

  • reaction

allOf

#/definitions/base

type

object

properties

  • used_in_assemblies

#/definitions/_used_in_assemblies

  • inputs

list of molecules this reaction uses as inputs (by molecule index)

type

array

items

type

integer

  • outputs

list of molecules this reaction uses as outputs (by molecule index)

type

array

items

type

integer

  • _used_in_assemblies

type

array

items

type

object

properties

  • design_key

type

string

  • assembly

type

integer

  • design_status

Summary of the design results

type

object

patternProperties

  • ^.*$

#/definitions/design_result_status

  • design_result_status

type

object

properties

  • compiled

if true, then the compilation step has been run

type

boolean

  • run

if true, then the optimization step has been run

type

boolean

  • success

if true, then this design has at least one assembly

type

boolean

  • assemblies

summary of assemblies for this design

type

array

items

#/definitions/assembly_status

  • assembly_status

type

object

properties

  • cost

Cost summary for this assembly

type

object

  • final_assembly_reaction

The index of the final assembly reaction

type

array

items

type

integer

  • summary

type

array

items

type

object

properties

  • reaction_index

type

integer

  • metadata

type

object

  • outputs

Summarized list of reactions that produce molecules used in the assembly.

type

array

items

type

object

properties

  • start

The start index (inclusive) of where the output molecule maps to the design

type

integer

  • end

The end index (exclusive) of where the output molecule maps to the design

type

integer

  • type

The type name of the reaction.

type

string