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DNA Sequences

 

DNA sequences are the bread and butter of the Benchling Molecular Biology suite. On Benchling, these are comprised of a string of nucleotides and collections of other attributes, such as annotations and primers.

 
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DNA Sequence Resource

 

id
string

ID of the DNA sequence

aliases
array

Array of aliases

annotations
array

Array of annotations objects on the sequence

archiveRecord
nested object

ArchiveRecord Resource if the DNA sequence is archived. This is null if the DNA sequence is not archived.

bases
string

Base pairs of the DNA sequence

createdAt
string

DateTime the DNA sequence was created

creator
nested object

UserSummary Resource of the user who created the DNA sequence

customFields
nested object

Custom fields set on the DNA sequence

dnaAlignmentIds
array

Ids of all alignments on the DNA sequence

entityRegistryId
string or null

Registry ID of the DNA sequence if registered

fields
nested object

See Fields Resource

folderId
string

ID of the folder that contains the DNA sequence

isCircular
boolean

If the sequence is circular or linear

length
integer

Number of base pairs in the sequence

modifiedAt
string

DateTime the DNA sequence was last modified

name
string

Name of the DNA sequence

primers
array

Primers that are created on the DNA sequence

registryId
string or null

Registry the DNA sequence is registered in

schema
nested object or null

Entity schema if set

schema.id
string

ID of the entity schema

schema.name
string

Name of the entity schema

translations
array

Array of translations objects on the sequence

webURL
string

URL of the DNA sequence

Annotation Resource

color
string

Hexadecimal color of the annotation

start
integer

Index where the annotation starts

end
integer

Index where the annotation stops

name
string

Name of the annotation

strand
integer

1 if forward, -1 if reverse, 0 if neither

type
string

User-defined text label for annotation

Primer Resource

bases
string

Bases of the primer

bindPosition
integer

Index where the primer binds

color
string

Hexadecimal color of the annotation

start
integer

Index where the primer starts

end
integer

Index where the primer ends

name
string

Name of the primer

overhangLength
integer

Number of bases in the primer overhang

strand
integer

1 if forward, -1 if reverse, 0 if neither

Translation Resource

start
integer

Index where the translation starts

end
integer

Index where the translation ends

strand
integer

1 if forward, -1 if reverse

aminoAcids
string

Amino acid sequence of the translation

regions
array of {"start", "end"} objects

Noncontiguous coding regions (e.g., exons). Sorted in 5' - 3' direction.

  "translations": [
    {
      "start": 3,
      "end": 89,
      "strand": 1,
      "aminoAcids": "QRICCNNKPEQEFVKILE",
      "regions": [
        {
          "start": 6,
          "end": 22,
        }
        {
          "start": 57,
          "end": 89,
        }
      ]
    }
  ],
 
{
  "aliases": [],
  "annotations": [
    {
      "color": "#FF9CCD",
      "end": 1855,
      "name": "bla gene",
      "start": 994,
      "strand": 1,
      "type": "gene"
    }
  ],
  "archiveRecord": {
    "reason": "Made in error"
  },
  "bases": "GTTTAGAGGATCTTTGTGAAGGAACCTT",
  "createdAt": "2017-04-18T05:54:36.388839+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {
    "ACCESSION": {
      "value": "urn.local...1328823972725.496"
    },
    "ORGANISM": {
      "value": "Cloning vector pNEBR-X1 other sequences; artificial sequences; vectors."
    }
  },
  "dnaAlignmentIds": ["seqanl_abc123", "seqanl_def456"],
  "entityRegistryId": null,
  "fields": {},
  "folderId": "lib_NStcGj3H",
  "id": "seq_RhYGVnHF",
  "isCircular": true,
  "length": 4286,
  "modifiedAt": "2017-04-18T05:54:36.971650+00:00",
  "name": "pNEBR",
  "primers": [
    {
      "bases": "TTTGCTCGTCTAAAA",
      "bindPosition": 20,
      "color": "#7EA7D8",
      "end": 35,
      "name": "another primer of interest",
      "overhangLength": 0,
      "start": 20,
      "strand": -1
    }
  ],
  "registryId": null,
  "schema": null,
  "translations": [
    {
      "start": 6,
      "end": 24,
      "strand": 1,
      "aminoAcids": "RIFVKE",
      "regions": [
        {
          "start": 6,
          "end": 24,
        }
      ]
    }
  ],
  "webURL": "https://benchling.com/benchling/f/NStcGj3H-benchling-lab/seq-RhYGVnHF-pnebr/edit"
}
 
{
  "color": "#FF9CCD",
  "end": 1855,
  "name": "bla gene",
  "start": 994,
  "strand": 1,
  "type": "gene"
}
 
{
  "bases": "TTTGCTCGTCTAAAA",
  "bindPosition": 20,
  "color": "#7EA7D8",
  "end": 35,
  "name": "another primer of interest",
  "overhangLength": 0,
  "start": 20,
  "strand": -1
}
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List DNA sequences

 
gethttps://benchling.com/api/v2/dna-sequences

Query Params

pageSize
string

Number of results to return. Defaults to 50, maximum of 100.

nextToken
string

Token for pagination

sort
string

Method by which to order search results. Valid sorts are modifiedAt (modified time, most recent first) and name (entity name, alphabetical). Optionally add :asc or :desc to specify ascending or descending order. Default is modifiedAt.

modifiedAt
string

Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those modified in the specified range. e.g. > 2017-04-30.

name
string

Name of a DNA Sequence. Restricts results to those with the specified name.

folderId
string

ID of a folder. Restricts results to those in the folder.

projectId
string

ID of a project. Restricts results to those in the project.

registryId
string

ID of a registry. Restricts results to those registered in this registry.

schemaId
string

ID of a schema. Restricts results to those of the specified schema.

schemaField.<name>
string

Schema field value. For Integer, Float, and Date type fields, supports the >=, and <= operators. If present, the schemaId param must also be present. Restricts results to those with a field of <name> whose value matches the filter specified in <value>.

archiveReason
string

Archive reason. Restricts DNA Sequences to those with the specified archive reason. Use “NOT_ARCHIVED” to filter for unarchived DNA Sequences.

Operators

Some query params support operators, which allow for more complex filtering logic. Operators are considered keywords, and any values that match an operator must be escaped with double quotes.

The following operators are supported:

  • >=, greater than or equal to (fields only)
  • <=, less than or equal to (fields only)
  • >, greater than (modified at only)

When using operators, they must be separated from the query value by a space, and the entire query string must be url-encoded.

See sample requests for examples of operator use.

Response

Returns a list of DNA Sequences.

# Return sequences with schema ID ts_54KEGtRf (the ID of the plasmid schema)
# and with a Resistance of Kan
curl https://benchling.com/api/v2/dna-sequences \
?pageSize=2&schemaId=ts_54KEGtRf&schemaField.Resistance=Kan \
 -u sk_YOUR_SECRET_KEY:
# Return sequences with schema ID ts_54KEGtRf (the ID of the plasmid schema)
# and with a length equal to or under 1000
curl https://benchling.com/api/v2/dna-sequences \
?pageSize=2&schemaId=ts_54KEGtRf&schemaField.Length=%3E%3D%201000 \
 -u sk_YOUR_SECRET_KEY:
# Return sequences with the schema ID ts_54KEGtRf (the ID of the plasmid schema) 
# and a Gene of Interest field that contains a link to the sequence with ID seq_oiFW238G
curl https://benchling.com/api/v2/dna-sequences \
?pageSize=2&schemaId=ts_54KEGtRf&schemaField.Gene%20%of%20Interest=seq_oiFW238G \
 -u sk_YOUR_SECRET_KEY:
# Return sequences modified after 2012-12-27T04:32:12.512764,
# limited to 2 results per page
curl https://benchling.com/api/v2/dna-sequences \
?pageSize=2&modifiedAt=%3E%202012-12-27T04%3A32%3A12.512764 \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/dna-sequences \
?pageSize=2&archiveReason=NOT_ARCHIVED%20OR%20Expended \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
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{
  "dnaSequences": [
    {
      "aliases": [
        "myAlias"
      ],
      "annotations": [],
      "archiveRecord": null,
      "bases": "GATTACA",
      "createdAt": "2017-04-20T18:11:56.283088+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {
        "custom": {
          "value": "field"
        }
      },
      "entityRegistryId": null,
      "fields": {
        "Long Text": {
          "isMulti": false,
          "textValue": "long text lon text",
          "type": "long_text",
          "value": "long text lon text"
        },
        "Resistance Gene": {
          "isMulti": true,
          "textValue": null,
          "type": "dropdown",
          "value": []
        },
        "Gene of Interest": {
          "isMulti": true,
          "textValue": null,
          "type": "sequence_link",
          "value": ["seq_oiFW238G"]
        },
        "Length": {
          "isMulti": false,
          "textValue": "500",
          "type": "integer",
          "value": 500
        },
      },
      "folderId": "lib_qbRUVQIj",
      "id": "seq_asQya4lk",
      "isCircular": false,
      "length": 7,
      "modifiedAt": "2017-04-20T19:02:02.789550+00:00",
      "name": "My Sequence",
      "primers": [],
      "registryId": null,
      "schema": {
        "id": "ts_54KEGtRf",
        "name": "Plasmid"
      },
      "translations": [],
      "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/seq-asQya4lk-my-sequence/edit"
    },
    {
      "aliases": [],
      "annotations": [],
      "archiveRecord": null,
      "bases": "ATCGATCCA",
      "createdAt": "2017-04-18T05:54:56.247545+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {},
      "entityRegistryId": "pBN037",
      "fields": {
        "Long Text": {
          "isMulti": false,
          "textValue": null,
          "type": "long_text",
          "value": null
        },
        "Resistance Gene": {
          "isMulti": true,
          "textValue": null,
          "type": "dropdown",
          "value": []
        },
        "Gene of Interest": {
          "isMulti": true,
          "textValue": null,
          "type": "sequence_link",
          "value": []
        }
        "Length": {
          "isMulti": false,
          "textValue": "600",
          "type": "integer",
          "value": 600
        },
      },
      "folderId": "lib_R8KcsjhW",
      "id": "seq_YnxMrdLo",
      "isCircular": false,
      "length": 9,
      "modifiedAt": "2017-04-18T19:58:44.275971+00:00",
      "name": "pBN037",
      "primers": [],
      "registryId": "src_NetYd96a",
      "schema": {
        "id": "ts_54KEGtRf",
        "name": "Plasmid"
      },
      "translations": [],
      "webURL": "https://benchling.com/benchling/f/R8KcsjhW-academic-registry/seq-YnxMrdLo-pbn037/edit"
    }
  ]
}
 
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Get a DNA sequence

 
gethttps://benchling.com/api/v2/dna-sequences/dna_sequence_id

Path Params

dna_sequence_id
string
required

ID of the DNA sequence

Response

Returns a DNA Sequence resource.

curl https://benchling.com/api/v2/dna-sequences/seq_asQya4lk \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
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{
  "aliases": [
    "myAlias"
  ],
  "annotations": [],
  "archiveRecord": null,
  "bases": "GATTACA",
  "createdAt": "2017-04-20T18:11:56.283088+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "authors": [
    {
      "handle": "lpasteur",
      "id": "ent_jdKampO5",
      "name": "Louis Pasteur"
    }
  ],
  "customFields": {
    "Submitter": {
      "value": "Rachel"
    }
  },
  "entityRegistryId": null,
  "fields": {
    "Long Text": {
      "isMulti": false,
      "textValue": "long text lon text",
      "type": "long_text",
      "value": "long text lon text"
    },
    "Resistance Gene": {
      "isMulti": true,
      "textValue": null,
      "type": "dropdown",
      "value": []
    },
    "Sequence Link": {
      "isMulti": true,
      "textValue": null,
      "type": "sequence_link",
      "value": []
    }
  },
  "folderId": "lib_qbRUVQIj",
  "id": "seq_asQya4lk",
  "isCircular": false,
  "length": 7,
  "modifiedAt": "2017-04-20T19:02:02.789550+00:00",
  "name": "My Sequence",
  "primers": [],
  "registryId": null,
  "schema": {
    "id": "ts_54KEGtRf",
    "name": "Plasmid"
  },
  "translations": [
    {
      "start": 0,
      "end": 3,
      "strand": 1,
      "aminoAcids": "D",
      "regions": [
        {
          "start": 0,
          "end": 3,
        }
      ]
    }
  ],
  "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/seq-asQya4lk-my-sequence/edit"
}
 
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BulkGet DNA sequences

 
gethttps://benchling.com/api/v2/dna-sequences:bulk-get

Query Params

dnaSequenceIds
string

Comma separated list of DNA sequence IDs

Response

Returns a list of DNA Sequence resources.

curl https://benchling.com/api/v2/dna-sequences:bulk-get?dnaSequenceIds=seq_asQya4lk,seq_YnxMrdLo \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
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{
  "dnaSequences": [
    {
      "aliases": [
        "myAlias"
      ],
      "annotations": [],
      "archiveRecord": null,
      "bases": "GATTACA",
      "createdAt": "2017-04-20T18:11:56.283088+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {
        "custom": {
          "value": "field"
        }
      },
      "entityRegistryId": null,
      "fields": {
        "Long Text": {
          "isMulti": false,
          "textValue": "long text lon text",
          "type": "long_text",
          "value": "long text lon text"
        },
        "Resistance Gene": {
          "isMulti": true,
          "textValue": null,
          "type": "dropdown",
          "value": []
        },
        "Sequence Link": {
          "isMulti": true,
          "textValue": null,
          "type": "sequence_link",
          "value": []
        }
      },
      "folderId": "lib_qbRUVQIj",
      "id": "seq_asQya4lk",
      "isCircular": false,
      "length": 7,
      "modifiedAt": "2017-04-20T19:02:02.789550+00:00",
      "name": "My Sequence",
      "primers": [],
      "registryId": null,
      "schema": {
        "id": "ts_54KEGtRf",
        "name": "Plasmid"
      },
      "translations": [],
      "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/seq-asQya4lk-my-sequence/edit"
    },
    {
      "aliases": [],
      "annotations": [],
      "archiveRecord": null,
      "bases": "ATCGATCCA",
      "createdAt": "2017-04-18T05:54:56.247545+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {},
      "entityRegistryId": "pBN037",
      "fields": {
        "Long Text": {
          "isMulti": false,
          "textValue": null,
          "type": "long_text",
          "value": null
        },
        "Resistance Gene": {
          "isMulti": true,
          "textValue": null,
          "type": "dropdown",
          "value": []
        },
        "Sequence Link": {
          "isMulti": true,
          "textValue": null,
          "type": "sequence_link",
          "value": []
        }
      },
      "folderId": "lib_R8KcsjhW",
      "id": "seq_YnxMrdLo",
      "isCircular": false,
      "length": 9,
      "modifiedAt": "2017-04-18T19:58:44.275971+00:00",
      "name": "pBN037",
      "primers": [],
      "registryId": "src_NetYd96a",
      "schema": {
        "id": "ts_54KEGtRf",
        "name": "Plasmid"
      },
      "translations": [],
      "webURL": "https://benchling.com/benchling/f/R8KcsjhW-academic-registry/seq-YnxMrdLo-pbn037/edit"
    }
  ]
}
 
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Create a DNA sequence

 
posthttps://benchling.com/api/v2/dna-sequences

Body Params

aliases
array of strings

Aliases to add to the DNA sequence

annotations
array

Annotations to create on the DNA sequence

bases
string
required

Base pairs for the DNA sequence

customFields
object

Custom fields to add to the DNA sequence

customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

fields
object

Fields to set on the DNA sequence. Must correspond with the schema's field definitions.

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

folderId
string
required

ID of the folder containing the DNA sequence

isCircular
boolean
required

Whether the DNA sequence is circular or linear

name
string
required

Name of the DNA sequence

schemaId
string

ID of the DNA sequence's schema

translations
array

Translations to create on the DNA sequence

Response

Returns a DNA Sequence Resource for the created sequence.

curl -XPOST https://benchling.com/api/v2/dna-sequences \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "aliases": ["myAlias"],
    "annotations": [],
    "bases": "GATTACA",
    "customFields": {
      "Submitter": {
      	"value": "Rachel"
      }
    },
    "fields": {
    	"Sequence Link": {
      	"value": ["seq_YwuI0zC2", "seq_JK1ktG3S"]
      }
    },
    "folderId": "lib_NStcGj3H",
    "isCircular": false,
    "name": "pBN9999",
    "schemaId": "ts_54KEGtRf"
    "translations": [
      {
        "start": 0,
        "end": 3,
        "strand": 1
      }
    ],
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
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{
  "aliases": ["myAlias"],
  "annotations": [],
  "archiveRecord": null,
  "bases": "GATTACA",
  "createdAt": "2017-04-25T03:22:34.097153+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {
    "Submitter": {
      "value": "Rachel"
    }
  },
  "entityRegistryId": null,
  "fields": {
    "Long Text": {
      "isMulti": false,
      "textValue": null,
      "type": "long_text",
      "value": null
    },
    "Resistance Gene": {
      "isMulti": true,
      "textValue": null,
      "type": "dropdown",
      "value": []
    },
    "Sequence Link": {
      "isMulti": true,
      "textValue": "Sequence 1, Sequence 2",
      "type": "sequence_link",
      "value": ["seq_YwuI0zC2", "seq_JK1ktG3S"]
    }
  },
  "folderId": "lib_NStcGj3H",
  "id": "seq_DhVZ2qld",
  "isCircular": false,
  "length": 7,
  "modifiedAt": "2017-04-25T03:22:34.291249+00:00",
  "name": "pBN9999",
  "primers": [],
  "registryId": null,
  "schema": {
    "id": "ts_54KEGtRf",
    "name": "Plasmid"
  },
  "translations": [
    {
      "start": 0,
      "end": 3,
      "strand": 1,
      "aminoAcids": "D",
      "regions": [
        {
          "start": 0,
          "end": 3
        }
      ]
    }
  ],
  "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/seq-DhVZ2qld-pbn9999/edit"
}
 
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Bulk create DNA sequences

 
posthttps://benchling.com/api/v2/dna-sequences:bulk-create

Body Params

dnaSequences
object
dnaSequences.aliases
array of strings

Aliases to add to the DNA sequence

dnaSequences.annotations
array

Annotations to create on the DNA sequence

dnaSequences.bases
string
required

Base pairs for the DNA sequence

dnaSequences.customFields
object

Custom fields to add to the DNA sequence

dnaSequences.customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

dnaSequences.fields
object

Fields to set on the DNA sequence. Must correspond with the schema's field definitions.

dnaSequences.fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

dnaSequences.folderId
string
required

ID of the folder containing the DNA sequence

dnaSequences.isCircular
boolean
required

Whether the DNA sequence is circular or linear

dnaSequences.name
string
required

Name of the DNA sequence

dnaSequences.schemaId
string

ID of the DNA sequence's schema

dnaSequences.translations
array

Translations to create on the DNA sequence

Response

This endpoint launches a long-running task and returns the Task ID of the launched task.

The task response contains the full list of DNA Sequence resources that were created.

curl -XPOST https://benchling.com/api/v2/dna-sequences:bulk-create \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
  "dnaSequences": [
    {
      "folderId": "lib_zHxiDoPT",
      "name": "pBR322",
      "bases": "GATTACAGATTACAGATTACA",
      "isCircular": true,
      "annotations": [
        {
          "name": "Backbone",
          "start": 3,
          "end": 10,
          "strand": 1
        }
      ],
      "translations": [
        {
          "start": 2,
          "end": 5,
          "strand": -1
        }
      ]
    }
  ]
}'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
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{
  "dnaSequences": [
    {
      "schema": null,
      "primers": [],
      "folderId": "lib_zHxiDoPT",
      "archiveRecord": null,
      "name": "pBR322",
      "creator": {
        "handle": "L.Pasteur",
        "id": "ent_SXi104eI",
        "name": "Louis Pasteur"
      },
      "url": "/l-pasteur/f/zHxiDoPT-myod-functionality/seq-gso8KcKl-pbr322/edit",
      "fields": {},
      "webURL": "https://benchling.com/l-pasteur/f/zHxiDoPT-myod-functionality/seq-gso8KcKl-pbr322/edit",
      "translations": [
        {
          "regions": [
            {
              "start": 2,
              "end": 5
            }
          ],
          "start": 2,
          "end": 5,
          "strand": -1,
          "aminoAcids": "*"
        }
      ],
      "id": "seq_gso8KcKl",
      "length": 21,
      "bases": "GATTACAGATTACAGATTACA",
      "modifiedAt": "2018-05-24T16:21:01.669249+00:00",
      "isCircular": true,
      "registryId": null,
      "customFields": {},
      "entityRegistryId": null,
      "annotations": [
        {
          "end": 10,
          "name": "Backbone",
          "color": "#FF9CCD",
          "start": 3,
          "type": "",
          "strand": 1
        }
      ],
      "createdAt": "2018-05-24T16:21:01.408054+00:00",
      "aliases": []
    }
  ]
}
{
  "taskId": "aada9c8d-160f-439e-956f-3e804b942647"
}
 
Suggest Edits

Update a DNA sequence

 
patchhttps://benchling.com/api/v2/dna-sequences/dna_sequence_id

Path Params

dna_sequence_id
string
required

Body Params

aliases
array of strings

Aliases to set for the sequence. Replaces the existing aliases.

annotations
array

Annotations to create on the DNA sequence (will replace any existing annotations). Required if another change would affect existing annotations (e.g. bases are changed and annotations exist)

bases
string

Overwrite the existing sequence, including annotations, translations and primers. Specify the new annotations, translations, and primers through their respective fields.

customFields
object

Custom fields to set on the sequence. Creates new fields if field name does not match an existing custom field.

customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

entityRegistryId
string

Registry ID to set for the DNA sequence (only works for sequences that are already registered)

fields
object

Schema fields to set on the sequence

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

folderId
string

ID of the folder containing the sequence

isCircular
boolean

Whether the sequence is circular or linear

name
string

Name of the sequence

primers
array of strings
required

Currently, only deleting all primers is supported (empty array). Required if another change would affect existing primers (e.g. bases are changed and primers exist)

schemaId
string

ID of the sequence's schema

translations
array

Translations to create on the DNA sequence (will replace any existing translations). Required if another change would affect existing translations (e.g. bases are changed and translations exist)

Response

Returns the Sequence Resource of the updated sequence.

curl -XPATCH https://benchling.com/api/v2/dna-sequences/seq_DhVZ2qld \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "aliases": ["myNewAlias"],
    "annotations": [
        {"name": "ann1", "start": 1, "end": 4, "strand": 1},
        {"name": "ann2", "start": 2, "end": 5, "strand": -1, "color": "#B4ABAC", "type": "gene"}
    ],
    "customFields": {},
    "entityRegistryId": "new_registry_id",
		"fields": {
    	"Sequence Link": {
      	"value": ["seq_YwuI0zC2", "seq_JK1ktG3S"]
      }
    },
    "folderId": "lib_cFG1WoHc",
    "isCircular": false,
    "name": "My New Name",
    "primers": [],
    "schemaId": "ts_54KEGtRf",
    "translations": [{"start": 1, "end": 4, "strand": 1}],
  }'
A binary file was returned

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{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "aliases": ["myNewAlias"],
  "annotations": [
    {"name": "ann1", "start": 1, "end": 4, "strand": 1, "color": "#FF9CCD", "type": ""},
    {"name": "ann2", "start": 2, "end": 5, "strand": -1, "color": "#B4ABAC", "type": "gene"}
  ],
  "archiveRecord": null,
  "bases": "CCATAG",
  "createdAt": "2017-04-25T03:22:34.097153+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {
    "Submitter": {
      "value": "Rachel"
    }
  },
  "entityRegistryId": null,
  "fields": {
    "Long Text": {
      "isMulti": false,
      "textValue": null,
      "type": "long_text",
      "value": null
    },
    "Resistance Gene": {
      "isMulti": true,
      "textValue": null,
      "type": "dropdown",
      "value": []
    },
    "Sequence Link": {
      "isMulti": true,
      "textValue": "Sequence 1, Sequence 2",
      "type": "sequence_link",
      "value": ["seq_YwuI0zC2", "seq_JK1ktG3S"]
    }
  },
  "folderId": "lib_cFG1WoHc",
  "id": "seq_DhVZ2qld",
  "isCircular": false,
  "length": 6,
  "modifiedAt": "2017-04-25T03:29:34.291249+00:00",
  "name": "pBN9999",
  "primers": [],
  "registryId": null,
  "schema": {
    "id": "ts_54KEGtRf",
    "name": "Plasmid"
  },
  "translations": [{
    "aminoAcids": "H",
    "end": 4,
    "regions": [
      {
        "end": 4,
        "start": 1
      }
    ],
    "start": 1,
    "strand": 1
    }],
  "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/seq-DhVZ2qld-pbn9999/edit"
}
 
Suggest Edits

Autofill DNA sequence parts

 
posthttps://benchling.com/api/v2/dna-sequences:autofill-parts

Body Params

dnaSequenceIds
array of strings

Array of DNA sequence IDs

Response

This endpoint launches a long-running task and returns the Task ID of the launched task.

When successful, the task has an empty response.

curl -XPOST https://benchling.com/api/v2/dna-sequences:autofill-parts \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "dnaSequenceIds": ["seq_pJjmug6L"]
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "taskId": "23f47c9a-4e30-48ff-a5a1-bdc6a69eddf3"
}
 
Suggest Edits

Archive DNA sequences

Archives DNA sequences and any batches of the DNA sequence.

 
posthttps://benchling.com/api/v2/dna-sequences:archive

Body Params

dnaSequenceIds
array of strings
required

Array of DNA sequence IDs

reason
string
required

Reason that DNA sequences are being archived. One of ["Made in error", "Retired", "Expended", "Shipped", "Contaminated", "Expired", "Missing", "Other"].

Response

IDs of all items that were archived, grouped by resource type. This includes the IDs of DNA sequences along with any IDs of batches that were archived.

curl -XPOST https://benchling.com/api/v2/dna-sequences:archive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "dnaSequenceIds": ["seq_pJjmug6L"],
    "reason": "Expended"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "dnaSequenceIds": ["seq_pJjmug6L"],
  "batchIds": ["bat_SkxnWL1n"]
}
 
Suggest Edits

Unarchive DNA sequences

Unarchives DNA sequences and any batches that were archived along with them.

 
posthttps://benchling.com/api/v2/dna-sequences:unarchive

Body Params

dnaSequenceIds
array of strings
required

Array of DNA sequence IDs

Response

IDs of all items that were unarchived, grouped by resource type. This includes the IDs of DNA sequences along with any IDs of batches that were unarchived.

curl -XPOST https://benchling.com/api/v2/dna-sequences:unarchive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "dnaSequenceIds": ["seq_pJjmug6L"]
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "dnaSequenceIds": ["seq_pJjmug6L"],
  "batchIds": ["bat_SkxnWL1n"]
}
 
Suggest Edits

Oligos

 

Oligos are short linear DNA sequences that can be attached as primers to full DNA sequences. Just like other entities, they support schemas, tags, and aliases.

 
Suggest Edits

Oligo Resource

 

id
string

ID of the oligo

aliases
array

Array of aliases

archiveRecord
nested object

ArchiveRecord Resource if the oligo is archived. This is null if the oligo is not archived.

bases
string

Base pairs of the oligo

createdAt
string

DateTime the oligo was created

creator
nested object

UserSummary Resource of the user who created the oligo

customFields
nested object

Custom fields set on the oligo

entityRegistryId
string or null

Registry ID of the oligo if registered

fields
nested object

See Fields resource

folderId
string

ID of the folder that contains the oligo

length
integer

Number of base pairs in the oligo

modifiedAt
string

DateTime the oligo was last modified

name
string

Name of the oligo

registryId
string or null

Registry the DNA sequence is registered in

schema
nested object or null

Entity schema if set

schema.id
string

ID of the entity schema

schema.name
string

Name of the entity schema

webURL
string

URL of the oligo

{
  "aliases": [],
  "archiveRecord": null,
  "bases": "GATTACA",
  "createdAt": "2017-04-18T05:54:36.388839+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {
    "ACCESSION": {
      "value": "urn.local...1328823972725.496"
    },
    "ORGANISM": {
      "value": "Cloning vector pNEBR-X1 other sequences; artificial sequences; vectors."
    }
  },
  "entityRegistryId": null,
  "fields": {},
  "folderId": "lib_NStcGj3H",
  "id": "seq_RhYGVnHF",
  "length": 7,
  "modifiedAt": "2017-04-18T05:54:36.971650+00:00",
  "name": "pNEBR",
  "registryId": null,
  "schema": null,
  "webURL": "https://benchling.com/benchling/f/NStcGj3H-benchling-lab/seq-RhYGVnHF-pnebr/edit"
}
Suggest Edits

Get an oligo

 
gethttps://benchling.com/api/v2/oligos/oligo_id

Path Params

oligo_id
string
required

ID of the oligo

Response

Returns an Oligo resource.

curl https://benchling.com/api/v2/oligos/seq_asQya4lk \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "aliases": [
    "myAlias"
  ],
  "archiveRecord": null,
  "bases": "GATTACA",
  "createdAt": "2017-04-20T18:11:56.283088+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "authors": [
    {
      "handle": "lpasteur",
      "id": "ent_jdKampO5",
      "name": "Louis Pasteur"
    }
  ],
  "customFields": {
    "Submitter": {
      "value": "Rachel"
    }
  },
  "entityRegistryId": null,
  "fields": {
    "Resistance Gene": {
      "isMulti": true,
      "textValue": null,
      "type": "dropdown",
      "value": []
    },
  },
  "folderId": "lib_qbRUVQIj",
  "id": "seq_asQya4lk",
  "length": 7,
  "modifiedAt": "2017-04-20T19:02:02.789550+00:00",
  "name": "My Sequence",
  "registryId": null,
  "schema": {
    "id": "ts_54KEGtRf",
    "name": "Oligo"
  },
  "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/seq-asQya4lk-my-sequence/edit"
}
 
Suggest Edits

Create an oligo

 
posthttps://benchling.com/api/v2/oligos

Body Params

aliases
array of strings

Aliases to add to the oligo

bases
string
required

Base pairs for the oligo. Must be at least 6 base pairs.

customFields
object

Custom fields to add to the oligo

customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

fields
object

Fields to set on the oligo. Must correspond with the schema's field definitions.

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

folderId
string
required

ID of the folder containing the oligo

name
string
required

Name of the oligo

schemaId
string

ID of the oligo's schema

Response

Returns a Oligo Resource for the created oligo.

curl -XPOST https://benchling.com/api/v2/oligos \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "aliases": ["myAlias"],
    "bases": "GATTACA",
    "customFields": {
      "Submitter": {
      	"value": "Rachel"
      }
    },
    "fields": {},
    "folderId": "lib_NStcGj3H",
    "name": "pBN9999",
    "schemaId": "ts_54KEGtRf"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "aliases": ["myAlias"],
  "archiveRecord": null,
  "bases": "GATTACA",
  "createdAt": "2017-04-25T03:22:34.097153+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {
    "Submitter": {
      "value": "Rachel"
    }
  },
  "entityRegistryId": null,
  "fields": {
    "Long Text": {
      "isMulti": false,
      "textValue": null,
      "type": "long_text",
      "value": null
    },
    "Resistance Gene": {
      "isMulti": true,
      "textValue": null,
      "type": "dropdown",
      "value": []
    },
    "Sequence Link": {
      "isMulti": true,
      "textValue": null,
      "type": "sequence_link",
      "value": []
    }
  },
  "folderId": "lib_NStcGj3H",
  "id": "seq_DhVZ2qld",
  "length": 7,
  "modifiedAt": "2017-04-25T03:22:34.291249+00:00",
  "name": "pBN9999",
  "registryId": null,
  "schema": {
    "id": "ts_54KEGtRf",
    "name": "Oligo"
  },
  "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/seq-DhVZ2qld-pbn9999/edit"
}
 
Suggest Edits

Bulk create oligos

 
posthttps://benchling.com/api/v2/oligos:bulk-create

Body Params

oligos
object
oligos.aliases
array of strings

Aliases to add to the oligo

oligos.bases
string
required

Base pairs for the oligo. Must be at least 6 base pairs.

oligos.customFields
object

Custom fields to add to the oligo

oligos.customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

oligos.fields
object

Fields to set on the oligo. Must correspond with the schema's field definitions.

oligos.fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

oligos.folderId
string
required

ID of the folder containing the oligo

oligos.name
string
required

Name of the oligo

oligos.schemaId
string

ID of the oligo's schema

Response

This endpoint launches a long-running task and returns the Task ID of the launched task.

The task response contains the full list of Oligo resources that were created.

curl -XPOST https://benchling.com/api/v2/oligos:bulk-create \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
  "oligos": [
    {
      "folderId": "lib_zHxiDoPT",
      "name": "Sample primer",
      "bases": "GATTACAGATTACAGATTACA"
    }
  ]
}'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "oligos": [
    {
      "schema": null,
      "folderId": "lib_zHxiDoPT",
      "archiveRecord": null,
      "name": "Sample primer",
      "creator": {
        "handle": "L.Pasteur",
        "id": "ent_SXi104eI",
        "name": "Louis Pasteur"
      },
      "fields": {},
      "webURL": "https://benchling.com/l-pasteur/f/zHxiDoPT-myod-functionality/seq-j2DsGsZt-sample-primer/edit",
      "length": 21,
      "bases": "GATTACAGATTACAGATTACA",
      "modifiedAt": "2018-05-24T16:27:29.162613+00:00",
      "registryId": null,
      "customFields": {},
      "entityRegistryId": null,
      "id": "seq_j2DsGsZt",
      "createdAt": "2018-05-24T16:27:29.037117+00:00",
      "aliases": []
    }
  ]
}
{
  "taskId": "aada9c8d-160f-439e-956f-3e804b942647"
}
 
Suggest Edits

AA Sequences

 

AA Sequences are the working units of cells that make everything run (they help make structures, catalyze reactions and allow for signaling - a kind of internal cell communication). On Benchling, these are comprised of a string of amino acids and collections of other attributes, such as annotations and primers.

 
Suggest Edits

AA Sequence Resource

 

id
string

ID of the AA sequence

aliases
array

Array of aliases

aminoAcids
string

Amino acids of the AA sequence

annotations
array

Array of annotation objects on the AA sequence

archiveRecord
nested object

ArchiveRecord Resource if the AA sequence is archived. This is null if the AA sequence is not archived.

createdAt
string

DateTime the AA sequence was created

creator
nested object

UserSummary Resource of the user who created the AA sequence

customFields
nested object

Custom fields set on the AA sequence

entityRegistryId
string or null

Registry ID of the AA sequence if registered

fields
nested object

See Fields Resource

folderId
string

ID of the folder that contains the AA sequence

length
integer

Number of amino acids in the AA sequence

modifiedAt
string

DateTime the AA sequence was last modified

name
string

Name of the AA sequence

registryId
string or null

Registry the AA sequence is registered in

schema
nested object or null

Entity schema if set

schema.id
string

ID of the entity schema

schema.name
string

Name of the entity schema

webURL
string

URL of the protein

Annotation Resource

color
string

Hexadecimal color of the annotation

start
integer

Index where the annotation starts

end
integer

Index where the annotation stops

name
string

Name of the annotation

type
string

User-defined text label for annotation

{
  "aliases": [],
  "aminoAcids": "MRKDIENIEDIKVLVDTFYGRVQENEFIGPIFNSKLEGRWPEHLEKMYAFWQTILLEEYTYRGKPFPPHAQLPVEGEHFEEWKRIFNGTVDELYEGKIADEAKWRAERMAAMFLSKIEYFREAGMKPLE",
  "annotations": [],
  "archiveRecord": null,
  "createdAt": "2017-04-18T05:56:49.010184+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {},
  "entityRegistryId": null,
  "fields": {},
  "folderId": "lib_cmVjLU16",
  "id": "prtn_QukABITO",
  "length": 129,
  "modifiedAt": "2017-04-18T05:56:49.010184+00:00",
  "name": "Myroides hemoglobin",
  "registryId": null,
  "schema": null,
  "url": "/lpasteur/f/cmVjLU16-myod-functionality/prtn-QukABITO-myroides-hemoglobin/edit"
}
 
{
  "color": "#FF9CCD",
  "end": 1855,
  "name": "bla gene",
  "start": 994,
  "type": "gene"
}
Suggest Edits

List AA sequences

 
gethttps://benchling.com/api/v2/aa-sequences

Query Params

pageSize
string

Number of results to return. Defaults to 50, maximum of 100.

nextToken
string

Token for pagination

sort
string

Method by which to order search results. Valid sorts are modifiedAt (modified time, most recent first) and name (entity name, alphabetical). Optionally add :asc or :desc to specify ascending or descending order. Default is modifiedAt.

aminoAcids
string

String of amino acids. Restricts results to AA sequences exactly matching these amino acids (case-insensitive).

archiveReason
string

Restricts results to those with the specified archive reason. Use “NOT_ARCHIVED” to filter for unarchived AA Sequences.

folderId
string

ID of a folder. Restricts results to those in the folder.

modifiedAt
string

Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those modified in the specified range. e.g. > 2017-04-30.

name
string

Name of a AA Sequence. Restricts results to those with the specified name.

projectId
string

ID of a project. Restricts results to those in the project.

registryId
string

ID of a registry. Restricts results to those registered in this registry.

schemaId
string

ID of a schema. Restricts results to those of the specified schema.

schemaField.<name>
string

Schema field value. For Integer, Float, and Date type fields, supports the >=, and <= operators. If present, the schemaId param must also be present. Restricts results to those with a field of <name> whose value matches the filter specified in <value>.

AA sequences share listing semantics with DNA sequences. Please refer to the list DNA sequences endpoint for more detailed documentation and examples.

Response

Returns a list of AA Sequence resources.

curl https://benchling.com/api/v2/aa-sequences \
?pageSize=2&schemaId=ts_7LNEOjdO&schemaField.Plasmid=seq_CPIPiONl \
	-u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/aa-sequences \
?pageSize=2&modifiedAt=%3E%202012-12-27T04%3A32%3A12.512764 \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/aa-sequences \
?pageSize=2&archiveReason=NOT_ARCHIVED%20OR%20Expended \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/aa-sequences \
?aminoAcids=AARDVARK \
	-u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "aaSequences": [
    {
      "aliases": [],
      "aminoAcids": "AARDVARK",
      "annotations": [],
      "archiveRecord": null,
      "createdAt": "2017-04-18T05:56:49.010184+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {},
      "entityRegistryId": null,
      "fields": {},
      "folderId": "lib_cmVjLU16",
      "id": "prtn_73FNT51c",
      "length": 8,
      "modifiedAt": "2017-04-18T05:56:49.010184+00:00",
      "name": "Protein consensus",
      "registryId": null,
      "schema": null,
      "url": "/lpasteur/f/cmVjLU16-myod-functionality/prtn-73FNT51c-protein-consensus/edit"
    },
    {
      "aliases": [],
      "aminoAcids": "AARDVARK",
      "annotations": [],
      "archiveRecord": null,
      "createdAt": "2017-04-21T07:18:21.311039+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {
        "tag": {
          "value": "myValue"
        }
      },
      "entityRegistryId": null,
      "fields": {},
      "folderId": "lib_qbRUVQIj",
      "id": "prtn_vjP37kbL",
      "length": 8,
      "modifiedAt": "2017-04-21T07:20:54.562473+00:00",
      "name": "New Name",
      "registryId": null,
      "schema": {
        "id": "ts_tXidwoDx",
        "name": "Chain"
      },
      "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/prtn-vjP37kbL-new-name/edit"
    }
  ]
 
Suggest Edits

Get an AA sequence

 
gethttps://benchling.com/api/v2/aa-sequences/aa_sequence_id

Path Params

aa_sequence_id
string
required

ID of the AA sequence

Response

Returns an AA Sequence resource.

curl https://benchling.com/api/v2/aa-sequences/prtn_QukABITO \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

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{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
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{{ results.responseHeaders }}
{
  "aliases": [],
  "aminoAcids": "MRKDIENIEDIKVLVDTFYGRVQENEFIGPIFNSKLEGRWPEHLEKMYAFWQTILLEEYTYRGKPFPPHAQLPVEGEHFEEWKRIFNGTVDELYEGKIADEAKWRAERMAAMFLSKIEYFREAGMKPLE",
  "annotations": [],
  "archiveRecord": null,
  "createdAt": "2017-04-18T05:56:49.010184+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "authors": [
    {
      "handle": "lpasteur",
      "id": "ent_jdKampO5",
      "name": "Louis Pasteur"
    }
  ],
  "customFields": {},
  "entityRegistryId": null,
  "fields": {},
  "folderId": "lib_cmVjLU16",
  "id": "prtn_QukABITO",
  "length": 129,
  "modifiedAt": "2017-04-18T05:56:49.010184+00:00",
  "name": "Myroides hemoglobin",
  "registryId": null,
  "schema": null,
  "webURL": "https://benchling.com/lpasteur/f/cmVjLU16-myod-functionality/prtn-QukABITO-myroides-hemoglobin/edit"
}
 
Suggest Edits

BulkGet AA sequences

 
gethttps://benchling.com/api/v2/aa-sequences:bulk-get

Query Params

aaSequenceIds
string

Comma separated list of AA sequence IDs

Response

Returns an array of AA Sequence resources.

curl https://benchling.com/api/v2/proteins:bulk-get?proteinIds=prtn_73FNT51c,prtn_vjP37kbL \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

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{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "aaSequences": [
    {
      "aliases": [],
      "aminoAcids": "AARDVARKAARDVARKAARDVARKAARDMARKAARDVADKAARDVARKAARDIAKKAARDVARKAAPALARHAALDIARKAAKDMARKAANDPARKAARDVARKAAFDMAKKAAGDQAKAAAMDIARAAAQDIANKAARDVARKAALDVAKKAARDVARKAAKDIAAEAAPDVAKKAARDLALKAAKDVAGDAARDVARKAARDVAEKAARDAAEKAARDVARKAAADIAIKAAKDIAEKAARDVARKAARDVARKAARDVARKAARDVARKAARDVARK",
      "annotations": [],
      "archiveRecord": null,
      "createdAt": "2017-04-18T05:56:49.010184+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {},
      "entityRegistryId": null,
      "fields": {},
      "folderId": "lib_cmVjLU16",
      "id": "prtn_73FNT51c",
      "length": 280,
      "modifiedAt": "2017-04-18T05:56:49.010184+00:00",
      "name": "Protein consensus",
      "registryId": null,
      "schema": null,
      "url": "/lpasteur/f/cmVjLU16-myod-functionality/prtn-73FNT51c-protein-consensus/edit"
    },
    {
      "aliases": [],
      "aminoAcids": "AARDVARK",
      "annotations": [],
      "archiveRecord": null,
      "createdAt": "2017-04-21T07:18:21.311039+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {
        "tag": {
          "value": "myValue"
        }
      },
      "entityRegistryId": null,
      "fields": {},
      "folderId": "lib_qbRUVQIj",
      "id": "prtn_vjP37kbL",
      "length": 8,
      "modifiedAt": "2017-04-21T07:20:54.562473+00:00",
      "name": "New Name",
      "registryId": null,
      "schema": {
        "id": "ts_tXidwoDx",
        "name": "Chain"
      },
      "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/prtn-vjP37kbL-new-name/edit"
    }
  ]
 
Suggest Edits

Create an AA sequence

 
posthttps://benchling.com/api/v2/aa-sequences

Query Params

aliases
array of strings

Aliases to add to the AA sequence

aminoAcids
string
required

Amino acids for the AA sequence

annotations
array

Annotations to create on the AA sequence

customFields
object

Custom fields to add to the AA sequence

customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

fields
object

Schema fields to set on the AA sequence. Must correspond with the schema's field definitions.

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

folderId
string
required

ID of the folder containing the AA sequence

name
string
required

Name of the AA sequence

schemaId
string

ID of the entity schema

Response

Returns the AA Sequence resource of the created sequence.

curl -XPOST https://benchling.com/api/v2/aa-sequences \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "aliases": ["myAlias"],
    "annotations": [],
    "aminoAcids": "AARDVARK",
    "customFields": {
      "Submitter": {
      	"value": "Rachel"
      }
    },
    "fields": {
      "Description": {
      	"value": "A heavy chain"
      }
    },
    "folderId": "lib_NStcGj3H",
    "name": "My Test Protein",
    "schemaId": "ts_tXidwoDx"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
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{
  "aliases": [
    "myAlias"
  ],
  "aminoAcids": "AARDVARK",
  "annotations": [],
  "archiveRecord": null,
  "createdAt": "2017-04-25T04:12:57.983452+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {
    "Submitter": {
      "value": "Rachel"
    }
  },
  "entityRegistryId": null,
  "fields": {
    "Description": {
      "isMulti": false,
      "textValue": "A heavy chain",
      "type": "long_text",
      "value": "A heavy chain"
    }
  },
  "folderId": "lib_NStcGj3H",
  "id": "prtn_l0nfixhB",
  "length": 8,
  "modifiedAt": "2017-04-25T04:12:57.983452+00:00",
  "name": "My Test Protein",
  "registryId": null,
  "schema": {
    "id": "ts_tXidwoDx",
    "name": "Chain"
  },
  "webURL": "https://benchling.com/benchling/f/NStcGj3H-benchling-lab/prtn-l0nfixhB-my-test-protein/edit"
}
 
Suggest Edits

Bulk create AA sequences

 
posthttps://benchling.com/api/v2/aa-sequences:bulk-create

Query Params

aaSequences
array

Array of AA sequences to create

aaSequences.aliases
array of strings

Aliases to add to the AA sequence

aaSequences.aminoAcids
string
required

Amino acids for the AA sequence

aaSequences.annotations
array

Annotations to create on the AA sequence

aaSequences.customFields
object

Custom fields to add to the AA sequence

aaSequences.customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

aaSequences.fields
object

Schema fields to set on the AA sequence. Must correspond with the schema's field definitions.

aaSequences.fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

aaSequences.folderId
string
required

ID of the folder containing the AA sequence

aaSequences.name
string
required

Name of the AA sequence

aaSequences.schemaId
string

ID of the entity schema

Response

This endpoint launches a long-running task and returns the Task ID of the launched task.

The task response contains the full list of AA Sequence resources that were created.

curl -XPOST https://benchling.com/api/v2/aa-sequences:bulk-create \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
  "aaSequences": [
    {
      "folderId": "lib_zHxiDoPT",
      "name": "Bradyrhizobium hemoglobin",
      "schemaId": "ts_grm2bHEe",
      "aminoAcids": "MTGAERREQITAEIVAQTGITEAMIAQLVHGFYAKVRRDPMIGPVFEARITDWEPHLAQMCA",
      "annotations": [
        {
          "name": "Binding pocket",
          "start": 8,
          "end": 30
        }
      ]
    }
  ]
}'
A binary file was returned

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{{ results.method }}
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{
  "aaSequences": [
    {
      "schema": {
        "id": "ts_grm2bHEe",
        "name": "Chain"
      },
      "folderId": "lib_zHxiDoPT",
      "archiveRecord": null,
      "name": "Bradyrhizobium hemoglobin",
      "creator": {
        "handle": "L.Pasteur",
        "id": "ent_SXi104eI",
        "name": "Louis Pasteur"
      },
      "url": "/l-pasteur/f/zHxiDoPT-myod-functionality/prtn-w3YDYl5l-bradyrhizobium-hemoglobin/edit",
      "fields": {},
      "webURL": "https://benchling.com/l-pasteur/f/zHxiDoPT-myod-functionality/prtn-w3YDYl5l-bradyrhizobium-hemoglobin/edit",
      "id": "prtn_w3YDYl5l",
      "length": 62,
      "modifiedAt": "2018-05-24T16:23:49.193857+00:00",
      "aminoAcids": "MTGAERREQITAEIVAQTGITEAMIAQLVHGFYAKVRRDPMIGPVFEARITDWEPHLAQMCA",
      "registryId": null,
      "customFields": {},
      "entityRegistryId": null,
      "annotations": [
        {
          "color": "#C7B0E3",
          "start": 8,
          "end": 30,
          "id": "prtnann_CAEr3R2V",
          "name": "Binding pocket"
        }
      ],
      "createdAt": "2018-05-24T16:23:49.193857+00:00",
      "aliases": []
    }
  ]
}
{
  "taskId": "aada9c8d-160f-439e-956f-3e804b942647"
}
 
Suggest Edits

Update an AA sequence

 
patchhttps://benchling.com/api/v2/aa-sequences/aa_sequence_id

Path Params

aa_sequence_id
string
required

ID of the AA sequence to update

Body Params

aliases
array of strings

Aliases to set for the AA sequence. Replaces the existing aliases.

aminoAcids
string

Amino acids of the AA sequence

annnotations
array

Array of annotations on the AA sequence

customFields
object

Custom fields to set on the AA sequence. Creates new fields if field name does not match an existing custom field.

customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

entityRegistryId
string

Registry ID to set for the AA sequence (only works for sequences that are already registered)

fields
object

Fields to set on the AA sequence. Must correspond with the schema's field definitions.

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

folderId
string

ID of the folder containing the AA sequence

name
string

Name of the AA sequence

schemaId
string

ID of the AA sequence's schema

Response

Returns the AA Sequence resource of the updated protein.

curl -XPATCH https://benchling.com/api/v2/aa-sequences/prtn_l0nfixhB \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "aliases": ["myNewAlias"],
    "annotations": [],
    "aminoAcids": "KRAVDRAA",
    "customFields": {},
    "entityRegistryId": "new_registry_id",
    "fields": {
      "Description": {
        "value": "A heavy chain"
    	}
    },   
    "folderId": "lib_cFG1WoHc",
    "name": "aaSeq1923",
    "schemaId": "ts_tXidwoDx"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
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{{ results.data }}
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{
  "aliases": [
    "myNewAlias"
  ],
  "aminoAcids": "KRAVDRAA",
  "annotations": [],
  "archiveRecord": null,
  "createdAt": "2017-04-25T04:12:57.983452+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {
    "Submitter": {
      "value": "Rachel"
    }
  },
  "entityRegistryId": null,
  "fields": {
    "Description": {
      "isMulti": false,
      "textValue": "A heavy chain",
      "type": "long_text",
      "value": "A heavy chain"
    }
  },
  "folderId": "lib_cFG1WoHc",
  "id": "prtn_l0nfixhB",
  "length": 8,
  "modifiedAt": "2017-04-25T04:31:57.983452+00:00",
  "name": "aaSeq1923",
  "registryId": null,
  "schema": {
    "id": "ts_tXidwoDx",
    "name": "Chain"
  },
  "webURL": "https://benchling.com/benchling/f/NStcGj3H-benchling-lab/prtn-l0nfixhB-my-test-protein/edit"
}
 
Suggest Edits

Archive AA sequences

Archives AA sequences and any batches of the AA sequences.

 
posthttps://benchling.com/api/v2/aa-sequences:archive

Body Params

aaSequenceIds
array of strings
required

Array of AA sequence IDs

reason
string
required

Reason that AA sequences are being archived. One of ["Made in error", "Retired", "Expended", "Shipped", "Contaminated", "Expired", "Missing", "Other"].

Response

IDs of all items that were archived, grouped by resource type. This includes the IDs of AA sequences along with any IDs of batches that were archived.

curl -XPOST https://benchling.com/api/v2/aa-sequences:archive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "aaSequenceIds": ["prtn_pJjmug6L"],
    "reason": "Retired"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "aaSequenceIds": ["prtn_pJjmug6L"],
  "batchIds": ["bat_SkxnWL1n"]
}
 
Suggest Edits

Unarchive AA sequences

Unarchives AA sequences and any batches that were archived along with them.

 
posthttps://benchling.com/api/v2/aa-sequences:unarchive

Body Params

aaSequenceIds
array of strings
required

Array of AA sequence IDs

Response

IDs of all items that were unarchived, grouped by resource type. This includes the IDs of AA sequences along with any IDs of batches that were unarchived.

curl -XPOST https://benchling.com/api/v2/aa-sequences:unarchive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "aaSequenceIds": ["prtn_pJjmug6L"]
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "aaSequenceIds": ["prtn_pJjmug6L"],
  "batchIds": ["bat_SkxnWL1n"]
}
 
Suggest Edits

Custom Entities

 

Benchling supports custom entities for biological entities that are neither sequences or proteins. Custom entities must have an entity schema set and can have both schema fields and custom fields.

 
Suggest Edits

Custom Entity Resource

 

id
string

ID of the custom entity

aliases
array

Array of aliases

archiveRecord
nested object

ArchiveRecord Resource if the custom entity is archived. This is null if the custom entity is not archived.

createdAt
string

DateTime the custom entity was created

creator
nested object

UserSummary Resource of the user who created the custom entity

customFields
nested object

Custom fields set on the custom entity

entityRegistryId
string or null

Registry ID of the custom entity if registered

fields
nested object

See Fields resource

folderId
string

ID of the folder that contains the custom entity

modifiedAt
string

DateTime the custom entity was last modified

name
string

Name of the custom entity

registryId
string or null

Registry the custom entity is registered in

schema
nested object or null

Entity schema if set

schema.id
string

ID of the entity schema

schema.name
string

Name of the entity schema

webURL
string

URL of the custom entity

{
  "aliases": [],
  "createdAt": "2017-04-18T05:54:56.247545+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {},
  "entityRegistryId": "sBN000",
  "fields": {
    "Parent Strain": {
      "isMulti": true,
      "textValue": null,
      "type": "entity_link",
      "value": []
    },
    "Plasmid": {
      "isMulti": true,
      "textValue": "pBN000",
      "type": "entity_link",
      "value": [
        "seq_brlYNmAf"
      ]
    }
  },
  "folderId": "lib_R8KcsjhW",
  "id": "bfi_xCUXNVyG",
  "modifiedAt": "2017-04-18T05:55:48.685345+00:00",
  "name": "sBN000",
  "registryId": "src_NetYd96a",
  "schema": {
    "id": "ts_EM122lfJ",
    "name": "Strain"
  },
  "webURL": "https://benchling.com/benchling/f/R8KcsjhW-academic-registry/bfi-xCUXNVyG-sbn000/edit"
}
 
Suggest Edits

List custom entities

 
gethttps://benchling.com/api/v2/custom-entities

Query Params

pageSize
string

Number of results to return. Defaults to 50, maximum of 100.

nextToken
string

Token for pagination

sort
string

Method by which to order search results. Valid sorts are modifiedAt (modified time, most recent first) and name (entity name, alphabetical). Optionally add :asc or :desc to specify ascending or descending order. Default is modifiedAt.

modifiedAt
string

Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those modified in the specified range. e.g. > 2017-04-30.

name
string

Name of a custom entity. Restricts results to those with the specified name.

folderId
string

ID of a folder. Restricts results to those in the folder.

projectId
string

ID of a project. Restricts results to those in the project.

registryId
string

ID of a registry. Restricts results to those registered in this registry.

schemaId
string

ID of a schema. Restricts results to those of the specified schema.

schemaField.<name>
string

Schema field value. For Integer, Float, and Date type fields, supports the >=, and <= operators. If present, the schemaId param must also be present. Restricts results to those with a field of <name> whose value matches the filter specified in <value>.

archiveReason
string

Archive reason. Restricts results to those with the specified archive reason. Use “NOT_ARCHIVED” to filter for unarchived custom entities.

Custom entities share listing semantics with DNA sequences. Please refer to the list DNA sequences endpoint for more detailed documentation and examples.

Response

Returns a list of CustomEntity resources.

curl https://benchling.com/api/v2/custom-entities \
?pageSize=2&schemaId=ts_C8z546g1&schemaField.Species=Human \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/custom-entities \
?pageSize=2&modifiedAt=%3E%202012-12-27T04%3A32%3A12.512764 \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/custom-entities \
?pageSize=2&archiveReason=NOT_ARCHIVED%20OR%20Expended \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "customEntities": [
    {
      "aliases": [],
      "createdAt": "2017-04-18T05:54:56.247545+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {},
      "entityRegistryId": "sBN000",
      "fields": {
        "Parent Strain": {
          "isMulti": true,
          "textValue": null,
          "type": "entity_link",
          "value": []
        },
        "Plasmid": {
          "isMulti": true,
          "textValue": "pBN000",
          "type": "entity_link",
          "value": [
            "seq_brlYNmAf"
          ]
        }
      },
      "folderId": "lib_R8KcsjhW",
      "id": "bfi_xCUXNVyG",
      "modifiedAt": "2017-04-18T05:55:48.685345+00:00",
      "name": "sBN000",
      "registryId": "src_NetYd96a",
      "schema": {
        "id": "ts_EM122lfJ",
        "name": "Strain"
      },
      "webURL": "https://benchling.com/benchling/f/R8KcsjhW-academic-registry/bfi-xCUXNVyG-sbn000/edit"
    },
    {
      "aliases": [
        "sLP065"
      ],
      "createdAt": "2017-04-18T05:54:56.247545+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {},
      "entityRegistryId": "sBN165",
      "fields": {
        "Parent Strain": {
          "isMulti": true,
          "textValue": "sBN164",
          "type": "entity_link",
          "value": [
            "bfi_m9ZcRZye"
          ]
        },
        "Plasmid": {
          "isMulti": true,
          "textValue": "pBN165",
          "type": "entity_link",
          "value": [
            "seq_E9AKgVVf"
          ]
        }
      },
      "folderId": "lib_R8KcsjhW",
      "id": "bfi_x6OFQZh7",
      "modifiedAt": "2017-04-18T05:55:49.465918+00:00",
      "name": "sBN165",
      "registryId": "src_NetYd96a",
      "schema": {
        "id": "ts_EM122lfJ",
        "name": "Strain"
      },
      "webURL": "https://benchling.com/benchling/f/R8KcsjhW-academic-registry/bfi-x6OFQZh7-sbn165/edit"
    }
  ]
}
 
Suggest Edits

Get a custom entity

 
gethttps://benchling.com/api/v2/custom-entities/custom_entity_id

Path Params

custom_entity_id
string
required

Response

Returns a CustomEntity resource.

curl https://benchling.com/api/v2/custom-entities/bfi_xCUXNVyG \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "aliases": [],
  "createdAt": "2017-04-18T05:54:56.247545+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "authors": [
    {
      "handle": "lpasteur",
      "id": "ent_jdKampO5",
      "name": "Louis Pasteur"
    }
  ],
  "customFields": {},
  "entityRegistryId": "sBN000",
  "fields": {
    "Parent Strain": {
      "isMulti": true,
      "textValue": null,
      "type": "entity_link",
      "value": []
    },
    "Plasmid": {
      "isMulti": true,
      "textValue": "pBN000",
      "type": "entity_link",
      "value": [
        "seq_brlYNmAf"
      ]
    }
  },
  "folderId": "lib_R8KcsjhW",
  "id": "bfi_xCUXNVyG",
  "modifiedAt": "2017-04-18T05:55:48.685345+00:00",
  "name": "sBN000",
  "registryId": "src_NetYd96a",
  "schema": {
    "id": "ts_EM122lfJ",
    "name": "Strain"
  },
  "webURL": "https://benchling.com/benchling/f/R8KcsjhW-academic-registry/bfi-xCUXNVyG-sbn000/edit"
}
 
Suggest Edits

BulkGet custom entities

 
gethttps://benchling.com/api/v2/custom-entities:bulk-get

Query Params

customEntityIds
string

Comma separated list of custom entity IDs

Response

Returns an array of CustomEntity resources.

curl https://benchling.com/api/v2/custom-entities:bulk-get?customEntityIds=bfi_xCUXNVyG,bfi_x6OFQZh7 \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

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{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "customEntities": [
    {
      "aliases": [],
      "createdAt": "2017-04-18T05:54:56.247545+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {},
      "entityRegistryId": "sBN000",
      "fields": {
        "Parent Strain": {
          "isMulti": true,
          "textValue": null,
          "type": "entity_link",
          "value": []
        },
        "Plasmid": {
          "isMulti": true,
          "textValue": "pBN000",
          "type": "entity_link",
          "value": [
            "seq_brlYNmAf"
          ]
        }
      },
      "folderId": "lib_R8KcsjhW",
      "id": "bfi_xCUXNVyG",
      "modifiedAt": "2017-04-18T05:55:48.685345+00:00",
      "name": "sBN000",
      "registryId": "src_NetYd96a",
      "schema": {
        "id": "ts_EM122lfJ",
        "name": "Strain"
      },
      "webURL": "https://benchling.com/benchling/f/R8KcsjhW-academic-registry/bfi-xCUXNVyG-sbn000/edit"
    },
    {
      "aliases": [
        "sLP065"
      ],
      "createdAt": "2017-04-18T05:54:56.247545+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {},
      "entityRegistryId": "sBN165",
      "fields": {
        "Parent Strain": {
          "isMulti": true,
          "textValue": "sBN164",
          "type": "entity_link",
          "value": [
            "bfi_m9ZcRZye"
          ]
        },
        "Plasmid": {
          "isMulti": true,
          "textValue": "pBN165",
          "type": "entity_link",
          "value": [
            "seq_E9AKgVVf"
          ]
        }
      },
      "folderId": "lib_R8KcsjhW",
      "id": "bfi_x6OFQZh7",
      "modifiedAt": "2017-04-18T05:55:49.465918+00:00",
      "name": "sBN165",
      "registryId": "src_NetYd96a",
      "schema": {
        "id": "ts_EM122lfJ",
        "name": "Strain"
      },
      "webURL": "https://benchling.com/benchling/f/R8KcsjhW-academic-registry/bfi-x6OFQZh7-sbn165/edit"
    }
  ]
}
 
Suggest Edits

Create a custom entity

 
posthttps://benchling.com/api/v2/custom-entities

Body Params

aliases
array of strings

Aliases to add to the custom entity

customFields
object

Custom fields to add to the custom entity

customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

fields
object

Schema fields to set on the custom entity. Must correspond with the schema's field definitions.

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

folderId
string
required

ID of the folder containing the sequence

name
string
required

Name of the custom entity

schemaId
string
required

ID of the custom entity's schema

Response

Returns the CustomEntity resource of the created custom entity.

curl -XPOST https://benchling.com/api/v2/custom-entities \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "aliases": ["myAlias"],
    "customFields": {
      "Submitter": {
      	"value": "Rachel"
      }
    },
    "fields": {
    	"Parent Strain": {
      	"value": "bfi_mbUPSbEm"
      },
      "Plasmids": {
      	"value": ["seq_yiOFpY8k", "seq_55UxcIps"]
      }
    },
    "folderId": "lib_qbRUVQIj",
    "name": "Test Strain",
    "schemaId": "ts_EM122lfJ"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "aliases": ["myAlias"],
  "createdAt": "2017-04-25T04:35:03.521863+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {},
  "entityRegistryId": null,
  "fields": {
    "Parent Strain": {
      "isMulti": false,
      "textValue": "A Parent Strain",
      "type": "entity_link",
      "value": "bfi_mbUPSbEm"
    },
    "Plasmids": {
      "isMulti": true,
      "textValue": "One inserted plasmid, A second inserted plasmid",
      "type": "entity_link",
      "value": ["seq_yiOFpY8k", "seq_55UxcIps"]
    }
  },
  "folderId": "lib_qbRUVQIj",
  "id": "bfi_lQVlEk1l",
  "modifiedAt": "2017-04-25T04:35:03.521863+00:00",
  "name": "Test Strain",
  "registryId": null,
  "schema": {
    "id": "ts_EM122lfJ",
    "name": "Strain"
  },
  "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/bfi-lQVlEk1l-test-strain/edit"
}
 
Suggest Edits

Bulk create custom entities

 
posthttps://benchling.com/api/v2/custom-entities:bulk-create

Body Params

customEntities
object
customEntities.aliases
string

Aliases to add to the custom entity

customEntities.customFields
object

Custom fields to add to the custom entity

customEntities.customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

customEntities.fields
object

Schema fields to set on the custom entity. Must correspond with the schema's field definitions.

customEntities.fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

customEntities.folderId
string
required

ID of the folder containing the sequence

customEntities.name
string
required

Name of the custom entity

customEntities.schemaId
string
required

ID of the custom entity's schema

Response

This endpoint launches a long-running task and returns the Task ID of the launched task.

The task response contains the full list of CustomEntity resources that were created.

curl -XPOST https://benchling.com/api/v2/custom-entities:bulk-create \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "customEntities": [
      {
        "fields": {
          "Test number": {
            "value": 12
          }
        },
        "schemaId": "ts_LTO2dCRl",
        "folderId": "lib_zHxiDoPT",
        "name": "Antibody 1"
      },
      {
        "schemaId": "ts_LTO2dCRl",
        "folderId": "lib_zHxiDoPT",
        "name": "Antibody 2"
      }
    ]
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "response": {
    "customEntities": [
      {
        "aliases": [],
        "archiveRecord": null,
        "createdAt": "2018-05-24T14:43:47.808873+00:00",
        "creator": {
          "handle": "L.Pasteur",
          "id": "ent_SXi104eI",
          "name": "Louis Pasteur"
        },
        "customFields": {},
        "entityRegistryId": null,
        "fields": {
          "Test number": {
            "isMulti": false,
            "textValue": "12",
            "type": "integer",
            "value": 12t
          }
        },
        "folderId": "lib_zHxiDoPT",
        "id": "bfi_rhf4HfDV",
        "modifiedAt": "2018-05-24T14:43:47.808873+00:00",
        "name": "Antibody 1",
        "registryId": null,
        "schema": {
          "id": "ts_LTO2dCRl",
          "name": "Antibody"
        },
        "url":
          "/l-pasteur/f/zHxiDoPT-myod-functionality/bfi-rhf4HfDV-antibody-1/edit",
        "webURL":
          "http://local.bnch.us:5000/l-pasteur/f/zHxiDoPT-myod-functionality/bfi-rhf4HfDV-antibody-1/edit"
      },
      {
        "aliases": [],
        "archiveRecord": null,
        "createdAt": "2018-05-24T14:43:47.808873+00:00",
        "creator": {
          "handle": "L.Pasteur",
          "id": "ent_SXi104eI",
          "name": "Louis Pasteur"
        },
        "customFields": {},
        "entityRegistryId": null,
        "fields": {
          "Test number": {
            "isMulti": false,
            "textValue": "",
            "type": "integer",
            "value": null
          }
        },
        "folderId": "lib_zHxiDoPT",
        "id": "bfi_PaRYzI1y",
        "modifiedAt": "2018-05-24T14:43:47.808873+00:00",
        "name": "Antibody 2",
        "registryId": null,
        "schema": {
          "id": "ts_LTO2dCRl",
          "name": "Antibody"
        },
        "url":
          "/l-pasteur/f/zHxiDoPT-myod-functionality/bfi-PaRYzI1y-antibody-2/edit",
        "webURL":
          "http://local.bnch.us:5000/l-pasteur/f/zHxiDoPT-myod-functionality/bfi-PaRYzI1y-antibody-2/edit"
      }
    ]
  },
  "status": "SUCCEEDED"
}

{
  "taskId": "aada9c8d-160f-439e-956f-3e804b942647"
}
 
Suggest Edits

Update custom entity

 
patchhttps://benchling.com/api/v2/custom-entities/custom_entity_id

Path Params

custom_entity_id
string
required

Body Params

aliases
array of strings

Aliases to set for the custom entity. Replaces the existing aliases.

customFields
object

Custom fields to set on the custom entity. Creates new fields if field name does not match an existing custom field.

customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

entityRegistryId
string

Registry ID to set for the custom entity (only works for entities that are already registered)

fields
object

Schema fields to set on the custom entity

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

folderId
string

ID of the folder containing the custom entity

name
string

Name of the custom entity

schemaId
string

ID of the custom entity's schema

Response

Returns the CustomEntity resource of the updated custom entity.

curl -XPATCH https://benchling.com/api/v2/custom-entities/bfi_lQVlEk1l \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "aliases": ["myNewAlias"],
    "customFields": {},
    "entityRegistryId": "new_registry_id",
    "fields": {
      "Parent Strain": {
        "value": "bfi_mbUPSbEm"
      },
      "Plasmids": {
        "value": ["seq_yiOFpY8k", "seq_55UxcIps"]
      }
    },
		"folderId": "lib_cFG1WoHc",
    "isCircular": false,
    "name": "antibody20991",
    "schemaId": "ts_RDaALAwC"
}'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "aliases": ["myNewAlias"],
  "createdAt": "2017-04-25T04:35:03.521863+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "customFields": {},
  "entityRegistryId": null,
  "fields": {
    "Parent Strain": {
      "isMulti": false,
      "textValue": "A Parent Strain",
      "type": "entity_link",
      "value": "bfi_mbUPSbEm"
    },
    "Plasmids": {
      "isMulti": true,
      "textValue": "One inserted plasmid, A second inserted plasmid",
      "type": "entity_link",
      "value": ["seq_yiOFpY8k", "seq_55UxcIps"]
    }
  },
  "folderId": "lib_cFG1WoHc",
  "id": "bfi_lQVlEk1l",
  "modifiedAt": "2017-04-25T07:35:03.521863+00:00",
  "name": "antibody20991",
  "registryId": null,
  "schema": {
    "id": "ts_RDaALAwC",
    "name": "Antibody"
  },
  "webURL": "https://benchling.com/lpasteur/f/qbRUVQIj-misc/bfi-lQVlEk1l-test-strain/edit"
}
 
Suggest Edits

Bulk update custom entities

 
posthttps://benchling.com/api/v2/custom-entities:bulk-update

Body Params

customEntities
object
customEntities.id
string

ID of the custom entity

customEntities.aliases
array of strings

Aliases to set on the custom entity

customEntities.customFields
object

Custom fields to set on the custom entity. Creates new fields if field name does not match an existing custom field.

customEntities.customFields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

customEntities.fields
object

Schema fields to set on the custom entity

customEntities.fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

customEntities.name
string

Name of the custom entity

customEntities.schemaId
string

ID of the custom entity's schema

Note that folderId and authorIds are not currently supported.

Response

This endpoint launches a long-running task and returns the Task ID of the launched task.

The task response contains the full list of CustomEntity resources that were updated.

curl -XPOST https://benchling.com/api/v2/custom-entities:bulk-update \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "customEntities": [
      {
        "id": "bfi_rhf4HfDV",
        "aliases": ["foo", "bar"],
        "customFields": {
          "foo": "bar"
        },
        "fields": {
          "Test number": {
            "value": 12
          }
        },
        "name": "Antibody 1"
      },
      {
        "id": "bfi_PaRYzI1y",
        "name": "Antibody 2"
      }
    ]
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "response": {
    "customEntities": [
      {
        "aliases": ["foo", "bar"],
        "archiveRecord": null,
        "createdAt": "2018-05-24T14:43:47.808873+00:00",
        "creator": {
          "handle": "L.Pasteur",
          "id": "ent_SXi104eI",
          "name": "Louis Pasteur"
        },
        "customFields": {
          "foo": "bar"
        },
        "entityRegistryId": null,
        "fields": {
          "Test number": {
            "isMulti": false,
            "textValue": "12",
            "type": "integer",
            "value": 12
          }
        },
        "folderId": "lib_zHxiDoPT",
        "id": "bfi_rhf4HfDV",
        "modifiedAt": "2018-05-24T14:43:47.808873+00:00",
        "name": "Antibody 1",
        "registryId": null,
        "schema": {
          "id": "ts_LTO2dCRl",
          "name": "Antibody"
        },
        "url":
          "/l-pasteur/f/zHxiDoPT-myod-functionality/bfi-rhf4HfDV-antibody-1/edit",
        "webURL":
          "http://benchling.com/l-pasteur/f/zHxiDoPT-myod-functionality/bfi-rhf4HfDV-antibody-1/edit"
      },
      {
        "aliases": [],
        "archiveRecord": null,
        "createdAt": "2018-05-24T14:43:47.808873+00:00",
        "creator": {
          "handle": "L.Pasteur",
          "id": "ent_SXi104eI",
          "name": "Louis Pasteur"
        },
        "customFields": {},
        "entityRegistryId": null,
        "fields": {
          "Test number": {
            "isMulti": false,
            "textValue": "",
            "type": "integer",
            "value": null
          }
        },
        "folderId": "lib_zHxiDoPT",
        "id": "bfi_PaRYzI1y",
        "modifiedAt": "2018-05-24T14:43:47.808873+00:00",
        "name": "Antibody 2",
        "registryId": null,
        "schema": {
          "id": "ts_LTO2dCRl",
          "name": "Antibody"
        },
        "url":
          "/l-pasteur/f/zHxiDoPT-myod-functionality/bfi-PaRYzI1y-antibody-2/edit",
        "webURL":
          "http://benchling.com/l-pasteur/f/zHxiDoPT-myod-functionality/bfi-PaRYzI1y-antibody-2/edit"
      }
    ]
  },
  "status": "SUCCEEDED"
}
{
  "taskId": "aada9c8d-160f-439e-956f-3e804b942647"
}
 
Suggest Edits

Archive custom entities

Archives custom entities and any batches of the custom entities.

 
posthttps://benchling.com/api/v2/custom-entities:archive

Body Params

customEntityIds
array of strings
required

Array of custom entity IDs

reason
string
required

Reason that custom entities are being archived. One of ["Made in error", "Retired", "Expended", "Shipped", "Contaminated", "Expired", "Missing", "Other"].

Response

IDs of all items that were archived, grouped by resource type. This includes the IDs of custom entities along with any IDs of batches that were archived.

curl -XPOST https://benchling.com/api/v2/custom-entities:archive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "customEntityIds": ["bfi_pJjmug6L"],
    "reason": "Made in error"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "customEntityIds": ["bfi_pJjmug6L"],
  "batchIds": ["bat_SkxnWL1n"]
}
 
Suggest Edits

Unarchive custom entities

Unarchives custom entities and any batches that were archived along with them.

 
posthttps://benchling.com/api/v2/custom-entities:unarchive

Body Params

customEntityIds
array of strings
required

Array of custom entity IDs

Response

IDs of all items that were unarchived, grouped by resource type. This includes the IDs of custom entities along with any IDs of batches that were unarchived.

curl -XPOST https://benchling.com/api/v2/custom-entities:unarchive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "customEntityIds": ["bfi_pJjmug6L"]
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "customEntityIds": ["bfi_pJjmug6L"],
  "batchIds": ["bat_SkxnWL1n"]
}
 
Suggest Edits

Registry Resource

 

id
string

ID of the registry

name
string

Name of the registry

owner.id
string

ID of the registry's owner

owner.handle
string

Handle of the registry's owner

owner.name
string

Name of the registry's owner

{
  "id": "src_gfNcj1gd",
  "name": "Benchling Lab Registry",
  "owner": {
    "handle": "benchling",
    "id": "ent_DyeDbv66",
    "name": "Benchling Lab"
  }
}
Suggest Edits

List registries

 
gethttps://benchling.com/api/v2/registries

Response

Returns an array of Registry resources.

curl https://benchling.com/api/v2/registries \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "registries": [
    {
      "id": "src_gfNcj1gd",
      "name": "Benchling Lab Registry",
      "owner": {
        "handle": "benchling",
        "id": "ent_DyeDbv66",
        "name": "Benchling Lab"
      }
    }
  ]
}
{
  "invalidFiles": {
    "seq_kqBKWECP": {
      "errors": ['"es-456,789" is already the name or alias of another file in the registry'],
      "warnings": []
      }
    }
  }
}
 
Suggest Edits

BulkGet registered entities

 
gethttps://benchling.com/api/v2/registries/registry_id/registered-entities:bulk-get

Path Params

registry_id
string
required

Query Params

entityRegistryIds
string

Comma separated list of entity Registry IDs

Response

Returns an array of entity (Sequence, Protein, CustomEntity) resources.

curl https://benchling.com/api/v2/registries/src_NetYd96a/registered-entities:bulk-get?entityRegistryIds=pBN000,sBN000 \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "entities": [
    {
      "aliases": [],
      "annotations": [],
      "archiveRecord": null,
      "bases": "GATTACA",
      "createdAt": "2017-04-18T05:54:56.247545+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {
        "test": {
          "value": "test"
        }
      },
      "entityRegistryId": "pBN000",
      "fields": {
        "Long Text": {
          "isMulti": false,
          "textValue": "This is a paragraph.",
          "type": "long_text",
          "value": "This is a paragraph."
        },
        "Resistance Gene": {
          "isMulti": true,
          "textValue": "Kanamycin",
          "type": "dropdown",
          "value": [
            "sfso_DCPHEbI2"
          ]
        },
        "Sequence Link": {
          "isMulti": true,
          "textValue": "pBN088",
          "type": "sequence_link",
          "value": [
            "seq_yv5KShpj"
          ]
        }
      },
      "folderId": "lib_R8KcsjhW",
      "id": "seq_brlYNmAf",
      "isCircular": false,
      "length": 0,
      "modifiedAt": "2017-04-18T19:58:44.259145+00:00",
      "name": "pBN000",
      "primers": [],
      "registryId": "src_NetYd96a",
      "schema": {
        "id": "ts_54KEGtRf",
        "name": "Plasmid"
      },
      "url": "/benchling/f/R8KcsjhW-academic-registry/seq-brlYNmAf-pbn000/edit"
    },
    {
      "aliases": [],
      "archiveRecord": null,
      "createdAt": "2017-04-18T05:54:56.247545+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "customFields": {},
      "entityRegistryId": "sBN000",
      "fields": {
        "Parent Strain": {
          "isMulti": true,
          "textValue": null,
          "type": "entity_link",
          "value": []
        },
        "Plasmid": {
          "isMulti": true,
          "textValue": "pBN000",
          "type": "entity_link",
          "value": [
            "seq_brlYNmAf"
          ]
        }
      },
      "folderId": "lib_R8KcsjhW",
      "id": "bfi_xCUXNVyG",
      "modifiedAt": "2017-04-18T05:55:48.685345+00:00",
      "name": "sBN000",
      "registryId": "src_NetYd96a",
      "schema": {
        "id": "ts_EM122lfJ",
        "name": "Strain"
      },
      "url": "/benchling/f/R8KcsjhW-academic-registry/bfi-xCUXNVyG-sbn000/edit"
    }
  ]
}
 
Suggest Edits

Registration

 
 
 
Suggest Edits

Bulk register entities

 
posthttps://benchling.com/api/v2/registries/registry_id:bulk-register-entities

Path Params

registry_id
string
required

ID for the registry

Query Params

entityIds
array of strings
required

Array of entity IDs

namingStrategy
string
required

One of NEW_IDS, IDS_FROM_NAMES, DELETE_NAMES, SET_FROM_NAME_PARTS, REPLACE_NAMES_FROM_PARTS, KEEP_NAMES

Attempts to move entities into the registry.

namingStrategy specifies the behavior for how to name an entity when registering it:

- NEW_IDS (default): Generates new registry IDs, and leaves entity name as-is
- IDS_FROM_NAMES: Converts names into registry IDs. Conversion has the following rules:
    - If the name ends in a number, use the schema's prefix, followed by that number, as the registry ID
    - If the name does not end in a number, use the name as-is for the registry ID
- DELETE_NAMES: Generates new registry IDs and sets entity name to new registry ID, and does not keep old names as aliases
- SET_FROM_NAME_PARTS: Generates new registry IDs and generates new entity name based on the entity schema's name template, if it has one. Old name is converted into an alias.
- REPLACE_NAMES_FROM_PARTS: Generates new registry IDs and generates new entity name based on the entity schema's name template, if it has one. Old name is deleted.
- KEEP_NAMES: Use name as registry ID

This endpoint will first check that the entities are all valid to be moved into the registry, given the namingStrategy. If any entities fail validation, no files will be moved and errors describing invalid entities is returned.

If all entities pass validation, the entities are moved into the registry.

Response

This endpoint launches a long-running task and returns the Task ID of the launched task.

When successful, the task has an empty response.

Benchling cannot always process two registration attempts within the same registry at the same time, so it's possible for the task to return an error response that indicates another attempt is already in progress and currently blocking this one. Benchling will automatically retry the task up to 3 times, and in the unlikely event that it is still failing, the task status will be “FAILED” and the error message will read:

Another registration attempt is in progress. Please try again in a few moments. If this problem persists, please wait 1-2 minutes before trying again.

curl -XPOST https://benchling.com/api/v2/registries/src_faCwxYz:bulk-register-entities \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "entityIds": ["seq_kqBKWECP", "prtn_vvCtjCy0", "bfi_TTyl4LH2"],
    "namingStrategy": "NEW_IDS"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{"taskId": "102ff3d5-ade5-4121-890f-8229c77bbce1"}
{ }

{
  "errors": {
    "seq_kqBKWECP": {
      "errors": [
       ' "es-456,789" is already the name or alias of another entity in the registry'
      ],
      "warnings": []
    }
  },
  "message": "The entities you attempted to register failed validation.",
  "status": "FAILED"
}
 
Suggest Edits

Unregister entities

 
posthttps://benchling.com/api/v2/registries/registry_id:unregister-entities

Path Params

registry_id
string
required

ID for the registry

Query Params

entityIds
array of strings
required

Array of entity IDs

folderId
string
required

ID of the folder that the entities should be moved to

Unregisters entities and moves them to a folder.

Response

Returns empty response ({}) if successful.

curl -XPOST https://benchling.com/api/v2/registries/src_faCwxYz:unregister-entities \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "entityIds": ["seq_kqBKWECP", "prtn_vvCtjCy0", "bfi_TTyl4LH2"],
    "folderId": "lib_ZCJqyQz1"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "error": {
    "message": "Entities (seq_mpveSwMX) are not registered in registry (src_JK1ktG3S).",
    "type": "invalid_request_error",
    "userMessage": "Entities (seq_mpveSwMX) are not registered in registry (src_JK1ktG3S)."
  }
}
 
Suggest Edits

Batches

 

Batches represent physical quantities of a sequence, protein, or other biological entity. A batch is identified by its biological entity's name (or Registry ID, if the entity is registered), its date of creation, and an optional inventory number.

 
Suggest Edits

Batch Resource

 

archiveRecord
nested object

ArchiveRecord Resource if the batch is archived. This is null if the batch is not archived.

createdAt
string

DateTime the batch was created

creator
object

UserSummary Resource of the user who created the batch

entity
object

Entity the batch is created on

entity.id
string

ID of the batch's entity

entity.type
string

The type of the entity (DNA sequence, AA sequence, or custom entity)

fields
object

See Fields resource

id
string

ID of the batch

modifiedAt
string

DateTime the batch was last modified

name
string

Name of the batch. Batch name formatting can be customized per-deployment, but usually is {entity_name}-{incrementing_number}, starting from 001.

schema
object

Batch schema

schema.id
string

ID of batch schema

schema.name
string

Name of batch schema ({entity_schema_name} Batch)

webURL
string

URL of the batch

{
  "archiveRecord": null,
  "createdAt": "2017-04-23T04:33:24.903812+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_UU3GOusY",
    "name": "Louis Pasteur"
  },
  "entity": {
    "id": "seq_uVXfsEnF",
    "type": "sequence",
  },
  "fields": {
    "Titer": {
      "isMulti": false,
      "textValue": "8.7",
      "type": "text",
      "value": "8.7"
    }
  },
  "id": "bat_UOIr8IjL",
  "modifiedAt": "2017-04-23T04:33:24.903812+00:00",
  "name": "pBN000-20170423-3",
  "schema": {
    "id": "batsch_k0JUctvW",
    "name": "Plasmid Batch"
  },
  "webURL": "https://benchling.com/lpasteur/f/55UxcIps-registry/bfi-dOVQJY0G-viral-cells/edit?batch=bat_ohKNVeJm&tab=samples"
}
 
Suggest Edits

List batches

 
gethttps://benchling.com/api/v2/batches

Query Params

pageSize
string

Number of results to return. Defaults to 50, maximum of 100.

nextToken
string

Token for pagination

sort
string

Method by which to order search results. Valid sorts are modifiedAt (modified time, most recent first) and name (entity name, alphabetical). Optionally add :asc or :desc to specify ascending or descending order. Default is modifiedAt.

schemaId
string

ID of a schema. Restricts results to those of the specified schema.

schemaField.<name>
string

Schema field value. For Integer, Float, and Date type fields, supports the >=, and <= operators. If present, the schemaId param must also be present. Restricts results to those with a field of <name> whose value matches the filter specified in <value>.

modifiedAt
string

Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those modified in the specified range. e.g. > 2017-04-30.

archiveReason
string

Archive reason. Restricts results to those with the specified archive reason. Use “NOT_ARCHIVED” to filter for unarchived batches.

Response

Returns a list of Batch resources.

curl https://benchling.com/api/v2/batches \
?pageSize=2&schemaId=ts_PIcDCm0c&schemaField.Verifier=Emma \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/batches \
?pageSize=2&modifiedAt=%3E%202012-12-27T04%3A32%3A12.512764 \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/batches \
?pageSize=2&archiveReason=NOT_ARCHIVED%20OR%20Expended \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "batches": [
    {
      "archiveRecord": null,
      "createdAt": "2017-08-07T23:45:30.593284+00:00",
      "creator": {
        "handle": "L.Pasteur",
        "id": "ent_VnQ20zg8",
        "name": "Louis Pasteur"
      },
      "entity": {
        "id": "seq_OqhAhvvr",
        "type": "dna_sequence"
      },
      "fields": {
        "Created": {
          "isMulti": false,
          "textValue": "",
          "type": "date",
          "value": null
        },
        "batch assay": {
          "isMulti": false,
          "textValue": "1.234",
          "type": "text",
          "value": "1.234"
        },
        "batch volume": {
          "isMulti": false,
          "textValue": "5E6",
          "type": "text",
          "value": "5E6"
        },
        "Verifier": {
          "isMulti": false,
          "textValue": "Emma",
          "type": "text",
          "value": "Emma"
        }
      },
      "id": "bat_5Nj15JWc",
      "modifiedAt": "2017-08-07T23:45:30.593284+00:00",
      "name": "pBN000-002",
      "schema": {
        "id": "batsch_6nwbaSWn",
        "name": "Plasmid Batch"
      },
      "webURL": "http://benchling.com/benchling/f/bXDQg8lb-academic-registry/seq-OqhAhvvr-pbn000/edit?batch=bat_5Nj15JWc&tab=samples"
    }
  ]
}
 
Suggest Edits

Get a batch

 
gethttps://benchling.com/api/v2/batches/batch_id

Path Params

batch_id
string
required

ID of the batch

Response

Returns a Batch resource.

curl https://benchling.com/api/v2/batches/bat_5Nj15JWc \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "archiveRecord": null,
  "createdAt": "2017-08-07T23:45:30.593284+00:00",
  "creator": {
    "handle": "L.Pasteur",
    "id": "ent_VnQ20zg8",
    "name": "Louis Pasteur"
  },
  "defaultConcentration": {
    "units": "mg/mL",
    "value": 1.3    
  },
  "entity": {
    "id": "seq_OqhAhvvr",
    "type": "dna_sequence"
  },
  "fields": {
    "Created": {
      "isMulti": false,
      "textValue": "",
      "type": "date",
      "value": null
    },
    "batch assay": {
      "isMulti": false,
      "textValue": "1.234",
      "type": "text",
      "value": "1.234"
    },
    "batch volume": {
      "isMulti": false,
      "textValue": "5E6",
      "type": "text",
      "value": "5E6"
    }
  },
  "id": "bat_5Nj15JWc",
  "modifiedAt": "2017-08-07T23:45:30.593284+00:00",
  "name": "pBN000-002",
  "schema": {
    "id": "batsch_6nwbaSWn",
    "name": "Plasmid Batch"
  },
  "webURL": "http://benchling.com/benchling/f/bXDQg8lb-academic-registry/seq-OqhAhvvr-pbn000/edit?batch=bat_5Nj15JWc&tab=samples"
}
 
Suggest Edits

Get an entity's batches

 
gethttps://benchling.com/api/v2/entities/entity_id/batches

Path Params

entity_id
string
required

ID of the entity

Response

Returns an array of Batch resources for the entity's batches.

curl https://benchling.com/api/v2/entities/seq_9p1Q5ICC/batches \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "batches": [
    {
      "archiveRecord": null,
      "createdAt": "2017-05-22T23:36:24.519341+00:00",
      "creator": {
        "handle": "rachel",
        "id": "ent_ZVNt8ewH",
        "name": "Rachel Wang"
      },
      "entity": {
        "id": "seq_9p1Q5ICC",
        "type": "dna_sequence"
      },
      "fields": {
        "batch link": {
          "isMulti": true,
          "textValue": null,
          "type": "batch_link",
          "value": []
        }
      },
      "id": "bat_CgfIEZRJ",
      "modifiedAt": "2017-05-22T23:36:24.519341+00:00",
      "name": "pBN000-20170522",
      "schema": {
        "id": "batsch_lT9rKZ0q",
        "name": "Plasmid Batch"
      },
      "webURL": "https://benchling.com/lpasteur/f/55UxcIps-registry/bfi-dOVQJY0G-viral-cells/edit?batch=bat_ohKNVeJm&tab=samples"
    }
  ]
}
 
Suggest Edits

BulkGet batches

Batches can be queried by their IDs or their names. Querying by name requires specifying a registryId since batch names are not necessarily unique across registries. Batches must be registered to query by name.

 
gethttps://benchling.com/api/v2/batches:bulk-get

Body Params

batchIds
string

Comma-separated list of batch IDs

batchNames
string

Comma-separated list of batch names. Batch names have the format {file name}-{creation date as YYYYMMDD}-{optional inventory number}. Must specify registryId with batchNames.

registryId
string

ID of the registry that batches are registered in. Required if querying by batchNames.

Response

Returns an array of Batch resources.

curl https://benchling.com/api/v2/batches:bulk-get?batchIds=bat_Dd68FOGF,bat_GkvoNF4Q \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/batches:bulk-get?batchNames=pBN000-20170418,pBN000-20170418-2&registyId=src_NetYd96a \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "batches": [
    {
      "archiveRecord": null,
      "createdAt": "2017-08-07T23:45:30.593284+00:00",
      "creator": {
        "handle": "L.Pasteur",
        "id": "ent_VnQ20zg8",
        "name": "Louis Pasteur"
      },
      "entity": {
        "id": "seq_OqhAhvvr",
        "type": "dna_sequence"
      },
      "fields": {
        "Created": {
          "isMulti": false,
          "textValue": "",
          "type": "date",
          "value": null
        },
        "batch assay": {
          "isMulti": false,
          "textValue": "1.234",
          "type": "text",
          "value": "1.234"
        },
        "batch volume": {
          "isMulti": false,
          "textValue": "5E6",
          "type": "text",
          "value": "5E6"
        },
        "Verifier": {
          "isMulti": false,
          "textValue": "Emma",
          "type": "text",
          "value": "Emma"
        }
      },
      "id": "bat_Dd68FOGF",
      "modifiedAt": "2017-08-07T23:45:30.593284+00:00",
      "name": "pBN000-002",
      "schema": {
        "id": "batsch_6nwbaSWn",
        "name": "Plasmid Batch"
      },
      "webURL": "http://benchling.com/benchling/f/bXDQg8lb-academic-registry/seq-OqhAhvvr-pbn000/edit?batch=bat_5Nj15JWc&tab=samples"
    }
  ]
}
 
Suggest Edits

Create a batch

 
posthttps://benchling.com/api/v2/batches

Body Params

entityId
string
required

API identifier for the entity that the batch will be added to

fields
object

The fields that will be added to the batch

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

defaultConcentration
object

Concentration of the batch

defaultConcentration.units
string
required

Units of measurement (e.g. uL)

defaultConcentration.value
integer
required

Amount of measurement

Response

Returns the Batch resource of the created batch.

curl -XPOST https://benchling.com/api/v2/batches \
  -u sk_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "entityId": "seq_uVXfsEnF",
    "defaultConcentration": {
      "value": 10,
      "units": "M"
    },
    "fields": {
      "Titer": {
        "value": "8.7"
      }
    }
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "archiveRecord": null,
  "createdAt": "2017-04-23T04:33:24.903812+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_UU3GOusY",
    "name": "Louis Pasteur"
  },
  "defaultConcentration": {
    "value": 10,
    "units": "M"
  },
  "entity": {
    "id": "seq_uVXfsEnF",
    "type": "sequence"
  },
  "fields": {
    "Titer": {
      "isMulti": false,
      "textValue": "8.7",
      "type": "text",
      "value": "8.7"
    }
  },
  "id": "bat_UOIr8IjL",
  "modifiedAt": "2017-04-23T04:33:24.903812+00:00",
  "name": "pBN000-20170423-3",
  "schema": {
    "id": "batsch_k0JUctvW",
    "name": "Plasmid Batch"
  },
  "webURL": "https://benchling.com/lpasteur/f/55UxcIps-registry/bfi-dOVQJY0G-viral-cells/edit?batch=bat_ohKNVeJm&tab=samples"
}
 
Suggest Edits

Update a batch

 
patchhttps://benchling.com/api/v2/batches/batch_id

Path Params

batch_id
string
required

Body Params

fields
object

The fields that will be updated on the batch

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

defaultConcentration
object

Concentration of the batch

defaultConcentration.units
string
required

Units of measurement (e.g. uL)

defaultConcentration.value
integer
required

Amount of measurement

Response

Returns the Batch resource of the updated batch.

curl -XPATCH https://benchling.com/api/v2/batches/bat_M8ojkds0 \
  -u sk_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "defaultConcentration": {
      "units": "mg/mL",
      "value": 1.5    
    },
    "fields": {
      "Titer": {
        "value": "8.7"
      }
    }
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "archiveRecord": null,
  "createdAt": "2017-04-23T04:33:24.903812+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_UU3GOusY",
    "name": "Louis Pasteur"
  },
  "entity": {
    "id": "seq_uVXfsEnF",
    "type": "sequence"
  },
  "fields": {
    "Titer": {
      "isMulti": false,
      "textValue": "8.7",
      "type": "text",
      "value": "8.7"
    }
  },
  "id": "bat_M8ojkds0",
  "modifiedAt": "2017-04-23T04:33:24.903812+00:00",
  "name": "pBN000-20170423-3",
  "schema": {
    "id": "batsch_k0JUctvW",
    "name": "Plasmid Batch"
  },
  "webURL": "https://benchling.com/lpasteur/f/55UxcIps-registry/bfi-dOVQJY0G-viral-cells/edit?batch=bat_ohKNVeJm&tab=samples"
}
 
Suggest Edits

Archive batches

 
posthttps://benchling.com/api/v2/batches:archive

Body Params

batchIds
array of strings
required

Array of batch IDs

reason
string
required

Reason that batches are being archived. One of ["Made in error", "Retired", "Expended", "Shipped", "Contaminated", "Expired", "Missing", "Other"].

Response

IDs of all items that were archived, grouped by resource type. This includes the IDs of batches that were archived.

curl -XPOST https://benchling.com/api/v2/batches:archive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "batchIds": ["bat_SkxnWL1n"],
    "reason": "Contaminated"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "batchIds": ["bat_SkxnWL1n"]
}
 
Suggest Edits

Unarchive batches

 
posthttps://benchling.com/api/v2/batches:unarchive

Body Params

batchIds
array of strings
required

Array of batch IDs

Response

IDs of all items that were unarchived, grouped by resource type. This includes the IDs of batches that were unarchived.

curl -XPOST https://benchling.com/api/v2/batches:unarchive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "batchIds": ["bat_SkxnWL1n"]
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "batchIds": ["bat_SkxnWL1n"]
}
 
Suggest Edits

DNA Alignments

A DNA alignment is a Benchling object representing an alignment of multiple DNA sequences.

 
 
 
Suggest Edits

DNA Alignment Resource

 

id
string

ID of the DNA alignment

alignedSequences
List of objects

A list of bases and metadata, including sequence ID if the sequence exists in Benchling (null otherwise), for each sequence in an alignment, and the sequence name. The name will be autogenerated from the .ab1 file if one was used to create the alignment.

name
string

Name of the DNA alignment

{
  "id": "seqanl_6ZVdX98t",
  "alignedSequences": [
    {
      "bases": "NNNNNNNNNNNGNN-GTAGCAAAGANTAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATG--",
      "dnaSequenceId": "seq_9TORP6VT",
      "trimEnd": 60,
      "trimStart": 5,
      "name": "Gene001",
    },
    {
      "bases": "NNNNNNNNNNNGNNAGTAGCAAAGANTAGTAGC-AGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATGGT",
      "dnaSequenceId": "seq_MYmsnS1u",
      "trimEnd": 65,
      "trimStart": 0,
      "name": "Gene002 (Gene002)",
    }
  ],
  "name": "My Alignment"
}
Suggest Edits

Get a DNA alignment

 
gethttps://benchling.com/api/v2/dna-alignments/dna_alignment_id

Path Params

dna_alignment_id
string
required

ID of the DNA alignment

Response

Returns a DNA Alignment Resource

curl https://benchling.com/api/v2/dna-alignments/seqanl_6ZVdX98t \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "alignedSequences": [
    {
      "bases": "NNNNNNNNNNNGNN-GTAGCAAAGANTAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATG--",
      "dnaSequenceId": "seq_9TORP6VT",
      "trimEnd": 60,
      "trimStart": 5
    },
    {
      "bases": "NNNNNNNNNNNGNNAGTAGCAAAGANTAGTAGC-AGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATGGT",
      "dnaSequenceId": "seq_MYmsnS1u",
      "trimEnd": 65,
      "trimStart": 0
    }
  ],
  "id": "seqanl_6ZVdX98t",
  "name": "My Alignment"
}
 
Suggest Edits

Create a template DNA alignment

 
posthttps://benchling.com/api/v2/dna-alignments:create-template-alignment

Body Params

algorithm
string
required

The algorithm with which to perform the DNA alignment. Either "mafft" or "clustalo"

templateSequenceId
string
required

ID of the DNA sequence to align against. The alignment will be created as part of this sequence (and requires edit access to the sequence).

files
array of mixed types
required

Each "file" should either be a reference to another Benchling Sequence ({"sequenceId": "seq_7acauH8"}), or the name and base64-encoded contents of a DNA file ({"name": "my_sequence.gb", "data": "TE9DVVMgICAgICAgVW50aXRsZWQgI"})

name
string

Name for the newly created alignment

Response

This endpoint launches a long-running task and returns the Task ID of the launched task.

The task response contains the DNA Alignment Resource that was created.

curl -XPOST https://benchling.com/api/v2/dna-alignments:create-template-alignment \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '
  {
    "name": "my new alignment",
    "algorithm": "mafft",
    "templateSequenceId": "seq_rXqq0IHU",
    "files": [
      {
        "sequenceId": "seq_3cxbVcCf"
      },
      {
        "name": "pNEBR.gb",
        "data": "TE9DVVMgICAgICAgcE5FQlIgICAgICAgICAgICAgICAgICAgNDI4NyBicCBkcy1ETkEgICAgIGNp\ncmN1bGFyICAgICAxNi1KVUwtMjAxMg0KREVGSU5JVElPTiAgQ2xvbmluZyB2ZWN0b3IgcE5FQlIt\nWDEsIGNvbXBsZXRlIHNlcXVlbmNlLg0KS0VZV09SRFMgICAgLg0KT1JJR0lODQogICAgICAgIDEg\nQVRHQ1RBR1RDVCBBR0NUQUdUQ0FDIEFHR1RDVENBVEcgQ1RBR1RDR1RHQyBUQUdUQ0dBVEdDIFRB\nR1RDR0FUR0MNCiAgICAgICA2MSBUQUdDVEFHVENHIEFUR0NUQUdDVEcgQVRHVEdUR0FHRyBDQ1RD\nQVRHQ1RBIEdDR1RBR1RDQVQgR0NUQUdDQUdBVA0KICAgICAgMTIxIENHQVRDQQ0KLy8NCg==\n"
      }
    ]
  }'


A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "alignedSequences": [
    {
      "bases": "------------------------------------------------------------------------actgac--atctctgagattcccatagagct-----------------------",
      "dnaSequenceId": "seq_9TORP6VT",
      "trimEnd": 126,
      "trimStart": 0
    },
    {
      "bases": "ATGCTAGTCTAGCTAGTCACAGGTCTCATGCTAGTCGTGCTAGTCGATGCTAGTCGATGCTAGCTAGTCGATGCTAGCTGATGTGTGAGGCCTCATGCTAGCGTAGTCATGCTAGCAGATCGATCA",
      "dnaSequenceId": null,
      "trimEnd": 126,
      "trimStart": 0
    },
    {
      "bases": "------------------------------------------------------------------------ATCGCG--ATC-------------------------------------------",
      "dnaSequenceId": "seq_MYmsnS1u",
      "trimEnd": 126,
      "trimStart": 0
    }
  ],
  "id": "seqanl_Jp1GGoHF",
  "name": "my new alignment"
}
{
  "taskId": "aada9c8d-160f-439e-956f-3e804b942647"
}
 
Suggest Edits

Create a consensus DNA alignment

 
posthttps://benchling.com/api/v2/dna-alignments:create-consensus-alignment

Body Params

algorithm
string
required

The algorithm with which to perform the DNA alignment. Either "mafft" or "clustalo"

files
array of mixed types
required

Each "file" should either be a reference to another Benchling Sequence ({"sequenceId": "seq_7acauH8"}), or the name and base64-encoded contents of a DNA file ({"name": "my_sequence.gb", "data": "TE9DVVMgICAgICAgVW50aXRsZWQgI"})

newSequence
object

Information about the new sequence to create. The bases of this sequence will correspond to the consensus of the DNA alignment. Exactly one of sequenceId or newSequence must be specified.

newSequence.folderId
string

ID of the folder to create the DNA sequence in.

sequenceId
string

ID of an existing DNA sequence to replace the consensus bases with. This sequence must be empty (0bp). Exactly one of sequenceId or newSequence must be specified.

name
string

Name for the newly created alignment

Response

This endpoint launches a long-running task and returns the Task ID of the launched task.

The task response contains the DNA Alignment Resource that was created.

curl -XPOST https://benchling.com/api/v2/dna-alignments:create-consensus-alignment \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '
  {
    "algorithm": "mafft",
    "sequenceId": "seq_0zD9sWGO",
    "files": [
      {
        "sequenceId": "seq_MYmsnS1u"
      },
      {
        "name": "pNEBR.gb",
        "data": "TE9DVVMgICAgICAgcE5FQlIgICAgICAgICAgICAgICAgICAgNDI4NyBicCBkcy1ETkEgICAgIGNp\ncmN1bGFyICAgICAxNi1KVUwtMjAxMg0KREVGSU5JVElPTiAgQ2xvbmluZyB2ZWN0b3IgcE5FQlIt\nWDEsIGNvbXBsZXRlIHNlcXVlbmNlLg0KS0VZV09SRFMgICAgLg0KT1JJR0lODQogICAgICAgIDEg\nQVRHQ1RBR1RDVCBBR0NUQUdUQ0FDIEFHR1RDVENBVEcgQ1RBR1RDR1RHQyBUQUdUQ0dBVEdDIFRB\nR1RDR0FUR0MNCiAgICAgICA2MSBUQUdDVEFHVENHIEFUR0NUQUdDVEcgQVRHVEdUR0FHRyBDQ1RD\nQVRHQ1RBIEdDR1RBR1RDQVQgR0NUQUdDQUdBVA0KICAgICAgMTIxIENHQVRDQQ0KLy8NCg==\n"
      }
    ]
  }'


curl -XPOST https://benchling.com/api/v2/dna-alignments:create-consensus-alignment \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '
  {
    "algorithm": "mafft",
    "newSequence": {"folderId": "lib_j3Jb8Ed6"},
    "files": [
      {"sequenceId": "seq_qsw83w2J"},
      {
        "name": "pNEBR.gb",
        "data": "TE9DVVMgICAgICAgcE5FQlIgICAgICAgICAgICAgICAgICAgNDI4NyBicCBkcy1ETkEgICAgIGNp\ncmN1bGFyICAgICAxNi1KVUwtMjAxMg0KREVGSU5JVElPTiAgQ2xvbmluZyB2ZWN0b3IgcE5FQlIt\nWDEsIGNvbXBsZXRlIHNlcXVlbmNlLg0KS0VZV09SRFMgICAgLg0KT1JJR0lODQogICAgICAgIDEg\nQVRHQ1RBR1RDVCBBR0NUQUdUQ0FDIEFHR1RDVENBVEcgQ1RBR1RDR1RHQyBUQUdUQ0dBVEdDIFRB\nR1RDR0FUR0MNCiAgICAgICA2MSBUQUdDVEFHVENHIEFUR0NUQUdDVEcgQVRHVEdUR0FHRyBDQ1RD\nQVRHQ1RBIEdDR1RBR1RDQVQgR0NUQUdDQUdBVA0KICAgICAgMTIxIENHQVRDQQ0KLy8NCg==\n"
      }
    ]
  }'


A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "alignedSequences": [
    {
      "bases": "ATGCTAGTCTAGCTAGTCACAGGTCTCATGCTAGTCGTGCTAGTCGATGCTAGTCGATGCTAGCTAGTCGATGCTAGCTGATGTGTGAGGCCTCATGCTAGCGTAGTCATGCTAGCAGATCGATCA",
      "dnaSequenceId": "seq_C2oxEHDQ",
      "trimEnd": 126,
      "trimStart": 0
    },
    {
      "bases": "AT--------------------------------------------------------------------------------------------------------------------CGCGATC-",
      "dnaSequenceId": "seq_MYmsnS1u",
      "trimEnd": 126,
      "trimStart": 0
    },
    {
      "bases": "ATGCTAGTCTAGCTAGTCACAGGTCTCATGCTAGTCGTGCTAGTCGATGCTAGTCGATGCTAGCTAGTCGATGCTAGCTGATGTGTGAGGCCTCATGCTAGCGTAGTCATGCTAGCAGATCGATCA",
      "dnaSequenceId": null,
      "trimEnd": 126,
      "trimStart": 0
    }
  ],
  "id": "seqanl_6ZyipyQc",
  "name": "TESTSEQ1, pNEBR (pNEBR.gb), Untitled Consensus"
}
{
  "taskId": "aada9c8d-160f-439e-956f-3e804b942647"
}
 
Suggest Edits

Delete DNA alignment

 
deletehttps://benchling.com/api/v2/dna-alignments/dna_alignment_id

Path Params

dna_alignment_id
string
required

ID of the DNA alignment to delete

 
curl -XDELETE https://benchling.com/api/v2/dna-alignments/seqanl_Al1dDYa0 \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
No response examples available
 
Suggest Edits

Containers

 

Containers are the backbone of sample management in Benchling. They represent physical containers, such as tubes or wells, that hold quantities of biological samples (represented by the batches inside the container). The container itself tracks its total volume, and the concentration of every batch inside of it.

Containers are all associated with schemas, which define the type of the container (e.g. "Tube") along with the fields that are tracked.

Like all storage, every container has a barcode that is unique across the registry.

 
Suggest Edits

Container Resource

 

id
string

ID of the container

archiveRecord
nested object

ArchiveRecord Resource if the container is archived. This is null if the container is not archived.

barcode
string

Barcode of the container

contents
array

Array of container contents, each with a batch and concentration

createdAt

DateTime the container was created

creator
object

UserSummary Resource of the user who created the container

fields
object

See Fields resource

modifiedAt
string

DateTime the container was last modified

name
string

Name of the container, defaults to barcode if name is not provided.

parentStorageId
string

ID of containing parent storage, either a location (e.g. loc_k2lNspzS) or a plate well with a coordinate (`plt_2bAks9dx:a2).

projectId
string or null

ID of the project if set

schema
object

Container schema

schema.id
string

ID of the container schema

schema.name
string

Name of the container schema

volume
object

Volume of container's contents

volume.value
number

Value of the volume (e.g 2)

volume.units
string

Units of the volume (e.g. 'mL')

webURL
string

URL of the container

{
  "archiveRecord": null,
  "barcode": "V001",
  "contents": [
    {
      "batch": {
        "archiveRecord": null,
        "createdAt": "2017-04-18T05:56:11.232568+00:00",
        "creator": {
          "handle": "lpasteur",
          "id": "ent_jDKampO5",
          "name": "Louis Pasteur"
        },
        "entity": {
          "id": "seq_brlYNmAf",
          "type": "sequence"
        },
        "fields": {
          "Batch Assay": {
            "isMulti": false,
            "textValue": "0.5",
            "type": "text",
            "value": "0.5"
          },
          "Batch Volume": {
            "isMulti": false,
            "textValue": "1000",
            "type": "text",
            "value": "1000"
          }
        },
        "id": "bat_Dd68FOGF",
        "modifiedAt": "2017-04-18T05:56:11.232568+00:00",
        "name": "pBN000-20170418",
        "schema": {
          "id": "batsch_OKxmlsLX",
          "name": "Plasmid Batch"
        }
      },
      "concentration": {
        "units": "g/mL",
        "value": 0.0002
      }
    }
  ],
  "createdAt": "2017-04-18T05:56:11.232568+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "fields": {
    "Vial Assay": {
      "isMulti": false,
      "textValue": "0.6",
      "type": "text",
      "value": "0.6"
    },
    "Vial Volume": {
      "isMulti": false,
      "textValue": "990",
      "type": "text",
      "value": "990"
    }
  },
  "id": "con_ZBL9QQWD",
  "modifiedAt": "2017-04-18T05:56:11.232568+00:00",
  "name": "V001",
  "parentStorageId": null,
  "projectId": null,
  "schema": {
    "id": "consch_yebqQk9k",
    "name": "Vial"
  },
  "volume": {
  	"value": 2,
    "units": "mL"
  },
  "webURL": "https://benchling.com/samples/containers/Wzay8Nob"
}
 
Suggest Edits

List containers

 
gethttps://benchling.com/api/v2/containers

Query Params

pageSize
string

Number of results to return. Defaults to 50, maximum of 100.

nextToken
string

Token for pagination

sort
string

Method by which to order search results. Valid sorts are barcode (bar code, alphabetical) modifiedAt (modified time, most recent first) and name (entity name, alphabetical). Optionally add :asc or :desc to specify ascending or descending order. Default is modifiedAt.

schemaId
string

ID of a schema. Restricts results to those of the specified schema.

schemaField.<name>
string

Schema field value. If present, the schemaId param must also be present. Restricts results to those with a field of <name> whose value matches the filter specified in <value>. See below for more information.

modifiedAt
string

Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those modified in the specified range. e.g. > 2017-04-30.

name
string

Name of a container. Restricts results to those with the specified name.

ancestorStorageId
string

ID of a plate, box, or location. Restricts results to those located in the specified storage.

storageContentsId
string

ID of a batch, entity, or entity schema. Restricts results to those that contain the specified batches, batches of the specified entities, or batches of entities of the specified schema

archiveReason
string

Archive reason. Restricts results to those with the specified archive reason. Use “NOT_ARCHIVED” to filter for unarchived containers.

Operators

Some query params support operators, which allow for more complex filtering logic. Operators should be separated from values by a space (+ in URL encoding). Operators are considered keywords, and any values that match an operator must be escaped with double quotes.

The following operators are supported:

  • >, greater than. Precedes a value.
  • >=, greater than or equal to. Precedes a value.
  • <, less than. Precedes a value.
  • <=, less than or equal to. Precedes a value.

See sample requests for examples of operator use.

Schema Field Filters

For the following field types, the filter does an exact match on the provided value, ignoring case:

  • String
  • Long Text

For the following field types, value should be specified as the ID of the linked item or dropdown option:

  • Entity Link
  • Part Link
  • Translation Link
  • Dropdown

The following field types support <= and => operators:

  • Integer
  • Float
  • Date

Response

Returns a list of Container resources.

curl https://benchling.com/api/v2/containers \
?pageSize=2&storageContentsId=bat_rgNUSXmS \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/containers \
?pageSize=2&modifiedAt=%3E%202016-12-27T04%3A32%3A12.512764 \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/containers \
?pageSize=2&archiveReason=NOT_ARCHIVED%20OR%20Expended \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "containers": [
    {
      "archiveRecord": null,
      "barcode": "V001",
      "contents": [
        {
          "batch": {
            "archiveRecord": null,
            "createdAt": "2017-04-18T05:56:11.232568+00:00",
            "creator": {
              "handle": "lpasteur",
              "id": "ent_jDKampO5",
              "name": "Louis Pasteur"
            },
            "entity": {
              "id": "seq_brlYNmAf",
              "type": "sequence"
            },
            "fields": {
              "Batch Assay": {
                "isMulti": false,
                "textValue": "0.5",
                "type": "text",
                "value": "0.5"
              },
              "Batch Volume": {
                "isMulti": false,
                "textValue": "1000",
                "type": "text",
                "value": "1000"
              }
            },
            "id": "bat_Dd68FOGF",
            "modifiedAt": "2017-04-18T05:56:11.232568+00:00",
            "name": "pBN000-20170418",
            "schema": {
              "id": "batsch_OKxmlsLX",
              "name": "Plasmid Batch"
            }
          },
          "concentration": {
            "units": "g/mL",
            "value": 0.0002
          }
        },
      ],
      "createdAt": "2017-04-18T05:56:11.232568+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Vial Assay": {
          "isMulti": false,
          "textValue": "0.6",
          "type": "text",
          "value": "0.6"
        },
        "Vial Volume": {
          "isMulti": false,
          "textValue": "990",
          "type": "text",
          "value": "990"
        }
      },
      "id": "con_ZBL9QQWD",
      "modifiedAt": "2017-04-18T05:56:11.232568+00:00",
      "name": "V001",
      "parentStorageId": null,
      "projectId": null,
      "schema": {
        "id": "consch_yebqQk9k",
        "name": "Vial"
      },
      "volume": {
        "value": 20,
        "units": "uL"
      },
      "webURL": "https://benchling.com/samples/containers/Wzay8Nob"
    },
    {
      "archiveRecord": null,
      "barcode": "V002",
      "contents": [
        {
          "batch": {
            "archiveRecord": null,
            "createdAt": "2017-04-18T05:56:11.232568+00:00",
            "creator": {
              "handle": "lpasteur",
              "id": "ent_jDKampO5",
              "name": "Louis Pasteur"
            },
            "entity": {
              "id": "seq_brlYNmAf",
              "type": "sequence"
            },
            "fields": {
              "Batch Assay": {
                "isMulti": false,
                "textValue": "0.5",
                "type": "text",
                "value": "0.5"
              },
              "Batch Volume": {
                "isMulti": false,
                "textValue": "1000",
                "type": "text",
                "value": "1000"
              }
            },
            "id": "bat_Dd68FOGF",
            "modifiedAt": "2017-04-18T05:56:11.232568+00:00",
            "name": "pBN000-20170418",
            "schema": {
              "id": "batsch_OKxmlsLX",
              "name": "Plasmid Batch"
            }
          },
          "concentration": {
            "units": "g/mL",
            "value": 0.0004
          }
        }
      ],
      "createdAt": "2017-04-18T05:56:11.232568+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Vial Assay": {
          "isMulti": false,
          "textValue": "1.60",
          "type": "text",
          "value": "1.60"
        },
        "Vial Volume": {
          "isMulti": false,
          "textValue": "500",
          "type": "text",
          "value": "500"
        }
      },
      "id": "con_6txspOz7",
      "modifiedAt": "2017-04-18T05:56:11.232568+00:00",
      "name": "V002",
      "parentStorageId": null,
      "projectId": null,
      "schema": {
        "id": "consch_yebqQk9k",
        "name": "Vial"
      },
      "volume": {
        "value": 25,
        "units": "uL"
      },
      "webURL": "https://benchling.com/samples/containers/p4TLGLgQ"
    }
  ]
}
 
Suggest Edits

Get a container

 
gethttps://benchling.com/api/v2/containers/container_id

Path Params

container_id
string
required

ID of the container

Response

Returns a Container resource.

curl -XGET https://benchling.com/api/v2/containers/con_cg8NwV90 \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "archiveRecord": null,
  "barcode": "V001",
  "contents": [
    {
      "batch": {
        "archiveRecord": null,
        "createdAt": "2017-08-07T23:45:30.593284+00:00",
        "creator": {
          "handle": "L.Pasteur",
          "id": "ent_VnQ20zg8",
          "name": "Louis Pasteur"
        },
        "entity": {
          "id": "seq_OqhAhvvr",
          "type": "dna_sequence"
        },
        "fields": {
          "Created": {
            "isMulti": false,
            "textValue": "",
            "type": "date",
            "value": null
          },
          "batch assay": {
            "isMulti": false,
            "textValue": "0.5",
            "type": "text",
            "value": "0.5"
          },
          "batch volume": {
            "isMulti": false,
            "textValue": "1000",
            "type": "text",
            "value": "1000"
          }
        },
        "id": "bat_yuMd3KyQ",
        "modifiedAt": "2017-08-07T23:45:30.593284+00:00",
        "name": "pBN000-001",
        "schema": {
          "id": "batsch_6nwbaSWn",
          "name": "Plasmid Batch"
        },
        "webURL": "http://benchling.com/benchling/f/bXDQg8lb-academic-registry/seq-OqhAhvvr-pbn000/edit?batch=bat_yuMd3KyQ&tab=samples"
      },
      "concentration": {
        "units": "g/mL",
        "value": 0.0002
      }
    },
    {
      "batch": {
        "archiveRecord": null,
        "createdAt": "2017-08-07T23:45:30.593284+00:00",
        "creator": {
          "handle": "L.Pasteur",
          "id": "ent_VnQ20zg8",
          "name": "Louis Pasteur"
        },
        "entity": {
          "id": "seq_OqhAhvvr",
          "type": "dna_sequence"
        },
        "fields": {
          "Created": {
            "isMulti": false,
            "textValue": "",
            "type": "date",
            "value": null
          },
          "batch assay": {
            "isMulti": false,
            "textValue": "1.234",
            "type": "text",
            "value": "1.234"
          },
          "batch volume": {
            "isMulti": false,
            "textValue": "5E6",
            "type": "text",
            "value": "5E6"
          }
        },
        "id": "bat_5Nj15JWc",
        "modifiedAt": "2017-08-07T23:45:30.593284+00:00",
        "name": "pBN000-002",
        "schema": {
          "id": "batsch_6nwbaSWn",
          "name": "Plasmid Batch"
        },
        "webURL": "http://benchling.com/benchling/f/bXDQg8lb-academic-registry/seq-OqhAhvvr-pbn000/edit?batch=bat_5Nj15JWc&tab=samples"
      },
      "concentration": {
        "units": "g/mL",
        "value": 0.0003
      }
    }
  ],
  "createdAt": "2017-08-07T23:45:30.593284+00:00",
  "creator": {
    "handle": "L.Pasteur",
    "id": "ent_VnQ20zg8",
    "name": "Louis Pasteur"
  },
  "fields": {
    "vial assay": {
      "isMulti": false,
      "textValue": "0.6",
      "type": "text",
      "value": "0.6"
    },
    "vial volume": {
      "isMulti": false,
      "textValue": "990",
      "type": "text",
      "value": "990"
    }
  },
  "id": "con_cg8NwV90",
  "modifiedAt": "2017-08-07T23:45:30.593284+00:00",
  "name": "V001",
  "parentStorageId": null,
  "projectId": null,
  "schema": {
    "id": "consch_V5IvNk4B",
    "name": "Vial"
  },
  "volume": {
    "units": "uL",
    "value": 0
  },
  "webURL": "http://benchling.com/samples/containers/cg8NwV90"
}
 
Suggest Edits

BulkGet containers

Containers can be queried by either their IDs or their barcodes.

 
gethttps://benchling.com/api/v2/containers:bulk-get

Query Params

containerIds
string

Comma-separated list of container IDs

barcodes
string

Comma-separated list of container barcodes

Response

Returns a list of Container resources.

curl -XGET https://benchling.com/api/v2/containers:bulk-get?containerIds=con_ZBL9QQWD,con_6txspOz7 \
  -u sk_YOUR_SECRET_KEY:
curl -XGET https://benchling.com/api/v2/containers:bulk-get?barcodes=V001,V002 \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "containers": [
    {
      "archiveRecord": null,
      "barcode": "V001",
      "contents": [
        {
          "batch": {
            "archiveRecord": null,
            "createdAt": "2017-04-18T05:56:11.232568+00:00",
            "creator": {
              "handle": "lpasteur",
              "id": "ent_jDKampO5",
              "name": "Louis Pasteur"
            },
            "entity": {
              "id": "seq_brlYNmAf",
              "type": "sequence"
            },
            "fields": {
              "Batch Assay": {
                "isMulti": false,
                "textValue": "0.5",
                "type": "text",
                "value": "0.5"
              },
              "Batch Volume": {
                "isMulti": false,
                "textValue": "1000",
                "type": "text",
                "value": "1000"
              }
            },
            "id": "bat_Dd68FOGF",
            "modifiedAt": "2017-04-18T05:56:11.232568+00:00",
            "name": "pBN000-20170418",
            "schema": {
              "id": "batsch_OKxmlsLX",
              "name": "Plasmid Batch"
            }
          },
          "concentration": {
            "units": "g/mL",
            "value": 0.0002
          }
        },
      ],
      "createdAt": "2017-04-18T05:56:11.232568+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Vial Assay": {
          "isMulti": false,
          "textValue": "0.6",
          "type": "text",
          "value": "0.6"
        },
        "Vial Volume": {
          "isMulti": false,
          "textValue": "990",
          "type": "text",
          "value": "990"
        }
      },
      "id": "con_ZBL9QQWD",
      "modifiedAt": "2017-04-18T05:56:11.232568+00:00",
      "name": "V001",
      "parentStorageId": null,
      "projectId": null,
      "schema": {
        "id": "consch_yebqQk9k",
        "name": "Vial"
      },
      "volume": {
        "value": 20,
        "units": "uL"
      },
      "webURL": "https://benchling.com/samples/containers/Wzay8Nob"
    },
    {
      "archiveRecord": null,
      "barcode": "V002",
      "contents": [
        {
          "batch": {
            "archiveRecord": null,
            "createdAt": "2017-04-18T05:56:11.232568+00:00",
            "creator": {
              "handle": "lpasteur",
              "id": "ent_jDKampO5",
              "name": "Louis Pasteur"
            },
            "entity": {
              "id": "seq_brlYNmAf",
              "type": "sequence"
            },
            "fields": {
              "Batch Assay": {
                "isMulti": false,
                "textValue": "0.5",
                "type": "text",
                "value": "0.5"
              },
              "Batch Volume": {
                "isMulti": false,
                "textValue": "1000",
                "type": "text",
                "value": "1000"
              }
            },
            "id": "bat_Dd68FOGF",
            "modifiedAt": "2017-04-18T05:56:11.232568+00:00",
            "name": "pBN000-20170418",
            "schema": {
              "id": "batsch_OKxmlsLX",
              "name": "Plasmid Batch"
            }
          },
          "concentration": {
            "units": "g/mL",
            "value": 0.0004
          }
        }
      ],
      "createdAt": "2017-04-18T05:56:11.232568+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_jDKampO5",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Vial Assay": {
          "isMulti": false,
          "textValue": "1.60",
          "type": "text",
          "value": "1.60"
        },
        "Vial Volume": {
          "isMulti": false,
          "textValue": "500",
          "type": "text",
          "value": "500"
        }
      },
      "id": "con_6txspOz7",
      "modifiedAt": "2017-04-18T05:56:11.232568+00:00",
      "name": "V002",
      "parentStorageId": null,
      "projectId": null,
      "schema": {
        "id": "consch_yebqQk9k",
        "name": "Vial"
      },
      "volume": {
        "value": 25,
        "units": "uL"
      },
      "webURL": "https://benchling.com/samples/containers/p4TLGLgQ"
    }
  ]
}
 
Suggest Edits

Create a container

 
posthttps://benchling.com/api/v2/containers

Body Params

barcode
string

A barcode to assign to the created container. This takes the place of the barcode Benchling would generate

fields
object

The fields for the created container

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

name
string

Name of the container

parentStorageId
string

API identifier for the storage (either box or location) that this will live in. May require a coordinate or position appended -- e.g., "(id):a1".

projectId
string

Optional ID of the project to associate with the container. Only users with read access to the project will be able to read the container.

schemaId
string
required

API identifier for the container schema for the created container

Response

Returns the Container resource of the created container.

curl -XPOST https://benchling.com/api/v2/containers \
  -u sk_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "barcode": "V113",
    "fields": {
      "Vial Volume": {
        "value": "8.7"
      }
    },
    "name": "My Test Vial",
    "parentStorageId": "plt_c2WWIPoF:a9",
    "schemaId": "consch_ITkgwiZb"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "archiveRecord": null,
  "barcode": "V113",
  "contents": [],
  "createdAt": "2017-04-25T06:30:08.691402+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "fields": {
    "Vial Volume": {
      "isMulti": false,
      "textValue": "8.7",
      "type": "text",
      "value": "8.7"
    }
  },
  "id": "con_qsxbSLLq",
  "modifiedAt": "2017-04-25T06:30:08.691402+00:00",
  "name": "My Test Vial",
  "parentStorageId": "plt_c2WWIPoF:a9",
  "projectId": null,
  "schema": {
    "id": "consch_ITkgwiZb",
    "name": "Vial"
  },
  "volume": {
  	"value": 0,
    "units": "uL"
  },
  "webURL": "https://benchling.com/samples/containers/p4TLGLgQ"
}
 
Suggest Edits

Update a container

 
patchhttps://benchling.com/api/v2/containers/container_id

Path Params

container_id
string
required

ID of the container to update

Body Params

fields
object

The fields for the created container

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

name
string

Name of the container

projectId
string

Optional ID of the project to associate with the container. Only users with read access to the project will be able to read the container.

parentStorageId
string

API identifier for the storage (either box or location) that this will live in.

volume
object

Volume of the container

volume.units
string
required

Units of measurement (e.g. uL)

volume.value
integer
required

Amount of measurement

Response

Returns the Container resource of the updated container.

curl -XPATCH https://benchling.com/api/v2/containers/con_0e1ZR3iD \
  -u sk_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "fields": {
      "Color": {
        "value": "green"
      }
    },
    "name": "My Vial",
    "parentStorageId": "plt_c2WWIPoF:a9",
    "volume": {
    	"value": 2,
      "units": "mL
    }
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "archiveRecord": null,
  "barcode": "V113",
  "contents": [],
  "createdAt": "2017-04-25T06:30:08.691402+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_jDKampO5",
    "name": "Louis Pasteur"
  },
  "fields": {
    "Vial Volume": {
      "isMulti": false,
      "textValue": "green",
      "type": "text",
      "value": "green"
    }
  },
  "id": "con_qsxbSLLq",
  "modifiedAt": "2017-04-25T06:30:08.691402+00:00",
  "name": "My Vial",
  "parentStorageId": "plt_c2WWIPoF:a9",
  "projectId": null,
  "schema": {
    "id": "consch_ITkgwiZb",
    "name": "Vial"
  },
  "volume": {
  	"value": 2,
    "units": "mL"
  },
  "webURL": "https://benchling.com/samples/containers/p4TLGLgQ"
}
 
Suggest Edits

Print labels

 
posthttps://benchling.com/api/v2/containers:print-labels

Body Params

containerIds
array of strings

List of IDs of containers that will have labels printed (one label will be printed per container)

labelTemplateId
string

ID of label template to use (same template will be used for all labels printed)

printerId
string

ID of printer to use (same printer will be used for all labels printed)

 
curl -XPOST https://benchling.com/api/v2/containers:print-labels \
-u sk_YOUR_SECRET_KEY: \
-H 'Content-Type: application/json' \ 
-d '{
    "labelTemplateId": "lbltmp_0wGnNMWo",
    "printerId": "print_YJQkilOJ",
    "containerIds": ["con_NrzzPv4S"]
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
"error": {
  "message": "Could not connect to printer",
  "type": "invalid_request_error",
  "userMessage": "Could not connect to printer"
}
 
Suggest Edits

Archive containers

 
posthttps://benchling.com/api/v2/containers:archive

Body Params

containerIds
array of strings
required

Array of container IDs

reason
string
required

Reason that containers are being archived. One of ["Made in error", "Retired", "Expended", "Shipped", "Contaminated", "Expired", "Missing", "Other"].

shouldRemoveBarcodes
boolean

Remove barcodes. Removing barcodes from archived storage that contain items will also remove barcodes from the contained items.

Response

IDs of all items that were archived, grouped by resource type. This includes the IDs of containers that were archived.

curl -XPOST https://benchling.com/api/v2/containers:archive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "containerIds": ["con_pSgZAxIm"],
    "reason": "Made in error",
    "shouldRemoveBarcodes": false
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "containerIds": ["con_pSgZAxIm"]
}
 
Suggest Edits

Unarchive containers

 
posthttps://benchling.com/api/v2/containers:unarchive

Body Params

containerIds
array of strings
required

Array of container IDs

Response

IDs of all items that were unarchived, grouped by resource type. This includes the IDs of containers that were unarchived.

curl -XPOST https://benchling.com/api/v2/containers:unarchive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "containerIds": ["con_pSgZAxIm"]
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "containerIds": ["con_pSgZAxIm"]
}
 
Suggest Edits

Plates

 

Plates are a structured storage type, grids of wells that each function like containers. Plates come in two types: a traditional "fixed" type, where the wells cannot move, and a "matrix" type. A matrix plate has similar functionality to a box, where the containers inside can be moved around and removed altogether.

Plates are all associated with schemas, which define the type of the plate (e.g. "96 Well Plate") along with the fields that are tracked, the dimensions of the plate, and whether or not the plate is a matrix plate or a traditional well plate.

Like all storage, every Plate has a barcode that is unique across the registry.

 
Suggest Edits

Plate Resource

 

id
string

ID of the plate

archiveRecord
nested object

ArchiveRecord Resource if the plate is archived. This is null if the plate is not archived.

barcode
string

Barcode of the plate

createdAt

DateTime the container was created

creator
object

UserSummary Resource of the user who created the plate

fields
object

See Fields resource

modifiedAt
string

DateTime the plate was last modified

name
string

Name of the plate, defaults to barcode is name is not provided.

parentStorageId
string

ID of containing parent storage (e.g. loc_k2lNspzS).

projectId
string or null

ID of the project if set

schema
object

Plate schema

schema.id
string

ID of the plate schema

schema.name
string

Name of the plate schema

wells
object

Well contents of the plate

wells.<position>
object

Well Resource

Well Resource

id
string

ID of the well

barcode
string

Barcode of the well

contents
array

Array of well contents, each with a batch and concentration

createdAt

DateTime the well was created

creator
object

UserSummary resource of the user who created the well

fields
object

See Fields resource

modifiedAt
string

DateTime the well was last modified

name
string

Name of the well, defaults to barcode is name is not provided.

parentStorageId
string

ID of containing parent storage, a plate well with a coordinate (`plt_2bAks9dx:a2).

projectId
string or null

ID of the project if set

schema
object

Well schema

schema.id
string

ID of the well schema

schema.name
string

Name of the well schema

volume
object

Volume of well's contents

volume.value
number

Value of the volume (e.g 2)

volume.units
string

Units of the volume (e.g. 'mL')

{
  "archiveRecord": null,
  "barcode": "MP001",
  "createdAt": "2017-02-10T20:48:27.898648+00:00",
  "creator": {
    "handle": "bench_reed",
    "id": "ent_d5UTwEry",
    "name": "Reed"
  },
  "fields": {},
  "id": "plt_90cishO7",
  "modifiedAt": "2017-02-10T20:48:27.898648+00:00",
  "name": "Test Matrix Plate",
  "parentStorageId": null,
  "projectId": null,
  "schema": {
    "id": "pltsch_HRFsaSl4",
    "name": "Matrix Plate"
  },
  "type": "matrix_plate",
  "wells": {
    "a1": {
      "archiveRecord": null,
      "barcode": "tube003",
      "contents": [],
      "createdAt": "2017-04-12T23:09:09.729865+00:00",
      "creator": {
        "handle": "somakrdas",
        "id": "ent_HiPWJk3d",
        "name": "Somak Das"
      },
      "fields": {},
      "id": "con_Y9HooOZF",
      "modifiedAt": "2017-04-12T23:09:09.729865+00:00",
      "name": "container2",
      "parentStorageId": "plt_90cishO7:a1",
      "projectId": null,
      "schema": {
        "id": "consch_C1PNJGNH",
        "name": "Tube"
      },
      "volume": {
        "units": "uL",
        "value": 0
      }
    }
  }
}
Suggest Edits

List plates

 
gethttps://benchling.com/api/v2/plates

Query Params

pageSize
string

Number of results to return. Defaults to 50, maximum of 100.

nextToken
string

Token for pagination

sort
string

Method by which to order search results. Valid sorts are barcode (bar code, alphabetical) modifiedAt (modified time, most recent first) and name (entity name, alphabetical). Optionally add :asc or :desc to specify ascending or descending order. Default is modifiedAt.

schemaId
string

ID of a schema. Restricts results to those of the specified schema.

schemaField.<name>
string

Schema field value. For Integer, Float, and Date type fields, supports the >=, and <= operators. If present, the schemaId param must also be present. Restricts results to those with a field of <name> whose value matches the filter specified in <value>.

modifiedAt
string

Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those modified in the specified range. e.g. > 2017-04-30.

name
string

Name of a plate. Restricts results to those with the specified name.

ancestorStorageId
string

ID of a location. Restricts results to those located in the specified storage.

storageContentsId
string

ID of a batch, entity, or entity schema. Restricts results to those that hold batches encompassed by the specified batches, entities, or schemas.

archiveReason
string

Archive reason. Restricts results to those with the specified archive reason. Use “NOT_ARCHIVED” to filter for unarchived plates.

Response

Returns a list of Plate resources.

curl https://benchling.com/api/v2/plates \
?pageSize=2&storageContentsId=bat_rgNUSXmS \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/plates \
?pageSize=2&modifiedAt=%3E%202012-12-27T04%3A32%3A12.512764 \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/plates \
?pageSize=2&archiveReason=NOT_ARCHIVED%20OR%20Expended \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "plates": [
    {
      "archiveRecord": null,
      "barcode": "mp001",
      "createdAt": "2017-06-01T02:44:45.411619+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_RcdjkqyM",
        "name": "Louis Pasteur"
      },
      "fields": {},
      "id": "plt_Y8EaPle1",
      "modifiedAt": "2017-06-01T02:44:45.411619+00:00",
      "name": "Matrix Plate for My Experiment",
      "parentStorageId": "loc_jIFm9sDj",
      "projectId": null,
      "schema": {
        "id": "pltsch_eDG0i7Wc",
        "name": "Matrix Plate"
      },
      "type": "matrix_plate",
      "webURL": "https://benchling.com/samples/plates/oJTILSpj",
      "wells": {},
    },
    {
      "archiveRecord": null,
      "barcode": "mp002",
      "createdAt": "2017-06-02T21:02:36.308233+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_RcdjkqyM",
        "name": "Louis Pasteur"
      },
      "fields": {},
      "id": "plt_n0Ovj1Z6",
      "modifiedAt": "2017-06-02T21:02:36.308233+00:00",
      "name": "mp002",
      "parentStorageId": "loc_jIFm9sDj",
      "projectId": null,
      "schema": {
        "id": "pltsch_eDG0i7Wc",
        "name": "Matrix Plate"
      },
      "type": "matrix_plate",
      "webURL": "https://benchling.com/samples/plates/q4xGloqS",
      "wells": {
        "a1": {
          "archiveRecord": null,
          "barcode": "c111",
          "contents": [],
          "createdAt": "2017-06-02T21:02:36.308233+00:00",
          "creator": {
            "handle": "lpasteur",
            "id": "ent_RcdjkqyM",
            "name": "Louis Pasteur"
          },
          "fields": {
            "vial assay": {
              "isMulti": false,
              "textValue": null,
              "type": "text",
              "value": null
            },
            "vial volume": {
              "isMulti": false,
              "textValue": null,
              "type": "text",
              "value": null
            }
          },
          "id": "con_upIdUiFV",
          "modifiedAt": "2017-06-02T21:02:36.308233+00:00",
          "name": "c111",
          "parentStorageId": "plt_n0Ovj1Z6:a1",
          "projectId": null,
          "schema": {
            "id": "consch_O9gxzk20",
            "name": "Vial"
          },
          "webURL": "https://biotechtx.benchling.com/samples/containers/HRP8P4Nt"
        }
      }
    }
  ]
}
 
Suggest Edits

Get a plate

 
gethttps://benchling.com/api/v2/plates/plate_id

Path Params

plate_id
string
required

ID of the plate

Response

Returns a Plate resource.

curl -XGET https://benchling.com/api/v2/plates/plt_90cishO7 \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "archiveRecord": null,
  "barcode": "MP001",
  "createdAt": "2017-02-10T20:48:27.898648+00:00",
  "creator": {
    "handle": "bench_reed",
    "id": "ent_d5UTwEry",
    "name": "Reed"
  },
  "fields": {},
  "id": "plt_90cishO7",
  "modifiedAt": "2017-02-10T20:48:27.898648+00:00",
  "name": "MP001",
  "parentStorageId": null,
  "projectId": null,
  "schema": {
    "id": "pltsch_HRFsaSl4",
    "name": "Matrix Plate"
  },
  "type": "matrix_plate",
  "webURL": "https://benchling.com/samples/plates/q4xGloqS",
  "wells": {
    "a1": {
      "archiveRecord": null,
      "barcode": "tube003",
      "contents": [],
      "createdAt": "2017-04-12T23:09:09.729865+00:00",
      "creator": {
        "handle": "somakrdas",
        "id": "ent_HiPWJk3d",
        "name": "Somak Das"
      },
      "fields": {},
      "id": "con_Y9HooOZF",
      "modifiedAt": "2017-04-12T23:09:09.729865+00:00",
      "name": "container2",
      "parentStorageId": "plt_90cishO7:a1",
      "projectId": null,
      "schema": {
        "id": "consch_C1PNJGNH",
        "name": "Tube"
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvKL"
    }
  }
}
 
Suggest Edits

BulkGet plates

Plates can be queried by either their IDs or their barcodes.

 
gethttps://benchling.com/api/v2/plates:bulk-get

Query Params

plateIds
string

Comma-separated list of plate IDs

barcodes
string

Comma-separated list of plate barcodes

Response

Returns an array of Plate resources.

curl https://benchling.com/api/v2/plates:bulk-get?plateIds=plt_Y8EaPle1,plt_n0Ovj1Z6 \
  -u sk_YOUR_SECRET_KEY:
curl https://benchling.com/api/v2/plates:bulk-get?barcodes=mp001,mp002 \
  -u sk_YOUR_SECRET_KEY:
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "plates": [
    {
      "archiveRecord": null,
      "barcode": "mp001",
      "createdAt": "2017-06-01T02:44:45.411619+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_RcdjkqyM",
        "name": "Louis Pasteur"
      },
      "fields": {},
      "id": "plt_Y8EaPle1",
      "modifiedAt": "2017-06-01T02:44:45.411619+00:00",
      "name": "Matrix Plate for My Experiment",
      "parentStorageId": "loc_jIFm9sDj",
      "projectId": null,
      "schema": {
        "id": "pltsch_eDG0i7Wc",
        "name": "Matrix Plate"
      },
      "type": "matrix_plate",
      "webURL": "https://benchling.com/samples/plates/oJTILSpj",
      "wells": {}
    },
    {
      "archiveRecord": null,
      "barcode": "mp002",
      "createdAt": "2017-06-02T21:02:36.308233+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_RcdjkqyM",
        "name": "Louis Pasteur"
      },
      "fields": {},
      "id": "plt_n0Ovj1Z6",
      "modifiedAt": "2017-06-02T21:02:36.308233+00:00",
      "name": "mp002",
      "parentStorageId": "loc_jIFm9sDj",
      "projectId": null,
      "schema": {
        "id": "pltsch_eDG0i7Wc",
        "name": "Matrix Plate"
      },
      "type": "matrix_plate",
      "webURL": "https://benchling.com/samples/plates/q4xGloqS",
      "wells": {
        "a1": {
          "archiveRecord": null,
          "barcode": "c111",
          "contents": [],
          "createdAt": "2017-06-02T21:02:36.308233+00:00",
          "creator": {
            "handle": "lpasteur",
            "id": "ent_RcdjkqyM",
            "name": "Louis Pasteur"
          },
          "fields": {
            "vial assay": {
              "isMulti": false,
              "textValue": null,
              "type": "text",
              "value": null
            },
            "vial volume": {
              "isMulti": false,
              "textValue": null,
              "type": "text",
              "value": null
            }
          },
          "id": "con_upIdUiFV",
          "modifiedAt": "2017-06-02T21:02:36.308233+00:00",
          "name": "c111",
          "parentStorageId": "plt_n0Ovj1Z6:a1",
          "projectId": null,
          "schema": {
            "id": "consch_O9gxzk20",
            "name": "Vial"
          },
          "webURL": "https://benchling.com/samples/containers/8iraMvKL"
        }
      }
    }
  ]
}
 
Suggest Edits

Create a plate

 
posthttps://benchling.com/api/v2/plates

Body Params

barcode
string

Barcode to assign the plate (will be auto-generated otherwise)

containerSchemaId
string

The ID of the schema to be used for the plate's wells. Only used if wells is also specified. Required for matrix plates.

fields
object

Fields to associate with the plate

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

name
string

Name of the plate

parentStorageId
string

ID of the location that this plate should be stored in. If left blank, it will be stored at the root location.

projectId
string

Optional ID of the project to associate with the plate. Only users with read access to the project will be able to read the plate.

schemaId
string
required

ID of the schema to use for this plate

wells
object

A mapping of positions where containers should be created inside of the plate, and barcodes to associate with them (barcode can be assigned to "null" to autogenerate a barcode). Required for matrix plates.

wells.position
object

Either the coordinate (e.g. B5) or numeric (e.g. 17) position of the well

Well plates hold collections of individual container wells. Each plate is identified by a unique alphanumeric barcode.

curl -XPOST https://benchling.com/api/v2/plates \
  -u sk_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "barcode": "FP1023988",
    "fields": {
      "Format": {
        "value": "PCR"
      },
      "Color": {
        "value": "Red"
      }
    },
    "parentStorageId": "loc_seZefMpV",
    "name": "Test Plate",
    "schemaId": "pltsch_NshXXO5Y"
  }'
curl -XPOST https://benchling.com/api/v2/plates \
-u sk_SECRET_KEY: \
-H 'Content-Type: application/json' \
-d '{
  "barcode": "MP1009448", 
  "parentStorageId": "loc_seZefMpV", 
  "name": "Test Matrix Plate", 
  "schemaId": "pltsch_SJPOWVHW", 
  "containerSchemaId": "consch_kWPjvVRG", 
  "wells": {"A1": {"barcode": "V1002"}, "A2": {"barcode": null}}
}'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "archiveRecord": null,
  "barcode": "FP1023987",
  "createdAt": "2017-07-05T22:05:06.843426+00:00",
  "creator": {
    "handle": "lpasteur",
    "id": "ent_GcNm7s4m",
    "name": "Louis Pasteur"
  },
  "fields": {
    "Color": {
      "isMulti": false,
      "textValue": "Red",
      "type": "text",
      "value": "Red"
    },
    "Format": {
      "isMulti": false,
      "textValue": "PCR",
      "type": "text",
      "value": "PCR"
    }
  },
  "id": "plt_uT2M5JGV",
  "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
  "name": "Test Plate",
  "parentStorageId": "loc_seZefMpV",
  "projectId": null,
  "schema": {
    "id": "pltsch_NshXXO5Y",
    "name": "96 Well Plate"
  },
  "type": "well_plate",
  "webURL": "https://benchling.com/samples/plates/q4xGloqS",
  "wells": {
    "a1": {
      "archiveRecord": null,
      "barcode": "w385",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_mplS9qru",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w385",
      "parentStorageId": "plt_uT2M5JGV:a1",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvKL"
    },
    "a10": {
      "archiveRecord": null,
      "barcode": "w394",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_c9PKTg5L",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w394",
      "parentStorageId": "plt_uT2M5JGV:a10",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvAA"
    },
    "a11": {
      "archiveRecord": null,
      "barcode": "w395",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_qXDTziux",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w395",
      "parentStorageId": "plt_uT2M5JGV:a11",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvBB"
    },
    "a12": {
      "archiveRecord": null,
      "barcode": "w396",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_uqo64not",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w396",
      "parentStorageId": "plt_uT2M5JGV:a12",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvCC"
    },
    "a2": {
      "archiveRecord": null,
      "barcode": "w386",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_Xc3O8FDw",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w386",
      "parentStorageId": "plt_uT2M5JGV:a2",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvDD"
    },
    "a3": {
      "archiveRecord": null,
      "barcode": "w387",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_WqwmNxvj",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w387",
      "parentStorageId": "plt_uT2M5JGV:a3",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvEE"
    },
    "a4": {
      "archiveRecord": null,
      "barcode": "w388",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_sygaOgWz",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w388",
      "parentStorageId": "plt_uT2M5JGV:a4",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvFF"
    },
    "a5": {
      "archiveRecord": null,
      "barcode": "w389",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_aiCptH0A",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w389",
      "parentStorageId": "plt_uT2M5JGV:a5",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvGG"
    },
    "a6": {
      "archiveRecord": null,
      "barcode": "w390",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_Ch45GSXI",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w390",
      "parentStorageId": "plt_uT2M5JGV:a6",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvHH"
    },
    "a7": {
      "archiveRecord": null,
      "barcode": "w391",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_vYJRnxbh",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w391",
      "parentStorageId": "plt_uT2M5JGV:a7",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvII"
    },
    "a8": {
      "archiveRecord": null,
      "barcode": "w392",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_oYvVNlbo",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w392",
      "parentStorageId": "plt_uT2M5JGV:a8",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvJJ"
    },
    "a9": {
      "archiveRecord": null,
      "barcode": "w393",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_3B4Aegly",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w393",
      "parentStorageId": "plt_uT2M5JGV:a9",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvKK"
    },
    "b1": {
      "archiveRecord": null,
      "barcode": "w397",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
        "name": "Louis Pasteur"
      },
      "fields": {
        "Well Color": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        },
        "Well Format": {
          "isMulti": false,
          "textValue": null,
          "type": "text",
          "value": null
        }
      },
      "id": "con_FCMCbfid",
      "modifiedAt": "2017-07-05T22:05:06.843426+00:00",
      "name": "w397",
      "parentStorageId": "plt_uT2M5JGV:b1",
      "projectId": null,
      "schema": {
        "id": "consch_vKUaffqD",
        "name": "well"
      },
      "volume": {
        "units": "uL",
        "value": 0
      },
      "webURL": "https://benchling.com/samples/containers/8iraMvLL"
    },
    "b10": {
      "archiveRecord": null,
      "barcode": "w406",
      "contents": [],
      "createdAt": "2017-07-05T22:05:06.843426+00:00",
      "creator": {
        "handle": "lpasteur",
        "id": "ent_GcNm7s4m",
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  }
}
{
  "barcode": "MP001",
  "createdAt": "2017-06-15T16:20:18.124946+00:00",
  "creator": {
    "handle": "neena",
    "id": "ent_zdWHDmsH",
    "name": "neena"
  },
  "fields": {},
  "id": "plt_ZOB2G3Vi",
  "modifiedAt": "2017-06-15T16:20:18.124946+00:00",
  "name": "MP001",
  "parentStorageId": "loc_eftK3TUV",
  "projectId": null,
  "schema": {
    "id": "pltsch_dUzkRPyJ",
    "name": "Matrix Plate"
  },
  "type": "matrix_plate",
  "webURL": "https://benchling.com/samples/plates/ZOB2G3Vi",
  "wells": {
    "a1": {
      "barcode": "EP032",
      "contents": [
        {
          "batch": {
            "createdAt": "2017-07-17T03:01:22.446526+00:00",
            "creator": {
              "handle": "damon",
              "id": "ent_1rDTdDZ2",
              "name": "Damon Doucet"
            },
            "entity": {
              "id": "bfi_UOvdBTf1",
              "type": "custom_entity"
            },
            "fields": {
              "Manufacture Date": {
                "isMulti": false,
                "textValue": "",
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            },
            "id": "bat_ydPLuuo3",
            "modifiedAt": "2017-07-17T03:01:22.446526+00:00",
            "name": "SAMP008-001",
            "schema": {
              "id": "batsch_PorXEcdB",
              "name": "Clinical Sample Batch"
            },
            "webURL": "https://benchling.com/biotechtx/f/55UxcIps-registry/bfi-UOvdBTf1-samp008/edit?batch=bat_ydPLuuo3&tab=samples"
          },
          "concentration": {
            "units": "uM",
            "value": 1.0
          }
        }
      ],
      "createdAt": "2017-06-20T06:12:39.127446+00:00",
      "creator": {
        "handle": "norseboar",
        "id": "ent_g1uat6YD",
        "name": "Reed Molbak"
      },
      "fields": {},
      "id": "con_mD5j1wa3",
      "modifiedAt": "2017-06-20T06:12:39.127446+00:00",
      "name": "EP032",
      "parentStorageId": "plt_ZOB2G3Vi:a1",
      "projectId": null,
      "schema": {
        "id": "consch_B0k6is3M",
        "name": "Vial"
      },
      "volume": {
        "units": "mL",
        "value": 1.4
      },
      "webURL": "https://benchling.com/samples/containers/mD5j1wa3"
    }
  }
}
{
  "error": {
    "message": "Found duplicate barcode: newbarcode.",
    "type": "invalid_request_error",
    "userMessage": "Found duplicate barcode: newbarcode."
  }
}
 
Suggest Edits

Update a plate

 
patchhttps://benchling.com/api/v2/plates/plate_id

Path Params

plate_id
string
required

ID of the plate to update

Body Params

fields
object

Fields to update

fields.<field name>
object

Every field should have its name as a key, mapping to an object with information about the value of the field.

name
string

Name of the plate

projectId
string

Optional ID of the project to associate with the plate. Only users with read access to the project will be able to read the plate.

parentStorageId
string

API identifier for the location that this will live in.

Response

Returns the Plate resource of the updated plate.

curl -XPATCH https://benchling.com/api/v2/plates/plt_bU3AsFCQ \
  -u sk_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "fields": {
      "Color": {
        "value": "Red"
      }
    },
    "name": "My Plate",
    "parentStorageId": "loc_2vB0pxok",
    "projectId": "src_30QSFwGr"
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "archiveRecord": null,
  "barcode": "mp001",
  "createdAt": "2018-05-06T00:45:12.382839+00:00",
  "creator": {
    "handle": "L.Pasteur",
    "id": "ent_PLqzw9R2",
    "name": "Louis Pasteur"
  },
  "fields": {
    "Color": {
      "isMulti": false,
      "textValue": "Red",
      "type": "text",
      "value": "Red"
    }
  },
  "id": "plt_bU3AsFCQ",
  "modifiedAt": "2018-05-23T06:56:15.947535+00:00",
  "name": "My Plate",
  "parentStorageId": "loc_2vB0pxok",
  "projectId": "src_30QSFwGr",
  "schema": {
    "id": "pltsch_0Ti45ALa",
    "name": "Matrix Plate"
  },
  "type": "matrix_plate",
  "webURL": "https://benchling.com/samples/plates/bU3AsFCQ",
  "wells": {}
}
 
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Archive plates

Archives plates and any containers of the plates.

 
posthttps://benchling.com/api/v2/plates:archive

Body Params

plateIds
array of strings
required

Array of plate IDs

reason
string
required

Reason that plates are being archived. One of ["Made in error", "Retired", "Expended", "Shipped", "Contaminated", "Expired", "Missing", "Other"].

shouldRemoveBarcodes
boolean

Remove barcodes. Removing barcodes from archived storage that contain items will also remove barcodes from the contained items.

Response

IDs of all items that were archived, grouped by resource type. This includes the IDs of plates along with any IDs of containers that were archived.

curl -XPOST https://benchling.com/api/v2/plates:archive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "plateIds": ["plt_i5LZtX8z"],
    "reason": "Made in error",
    "shouldRemoveBarcodes": false
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "plateIds": ["plt_i5LZtX8z"],
  "containerIds": ["con_pSgZAxIm"]
}
 
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Unarchive plates

Unarchives plates and the containers that were archived along with them.

 
posthttps://benchling.com/api/v2/plates:unarchive

Body Params

plateIds
array of strings
required

Array of plate IDs

Response

IDs of all items that were unarchived, grouped by resource type. This includes the IDs of plates along with any IDs of containers that were unarchived.

curl -XPOST https://benchling.com/api/v2/plates:unarchive \
  -u sk_YOUR_SECRET_KEY: \
  -H 'Content-Type: application/json' \
  -d '{
    "plateIds": ["plt_i5LZtX8z"]
  }'
A binary file was returned

You couldn't be authenticated

{{ results.method }}
{{ results.url }}
{{ results.requestHeaders }}
{{ results.data }}
{{ results.responseHeaders }}
{
  "plateIds": ["plt_i5LZtX8z"],
  "containerIds": ["con_pSgZAxIm"]
}
 
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Boxes

 

Boxes are a structured storage type, consisting of a grid of positions that can each hold one container. Unlike locations, there are a maximum number of containers that a box can hold (one per position).

Boxes are all associated with schemas, which define the type of the box (e.g. "10x10 Cryo Box") along with the fields that are tracked and the dimensions of the box.

Like all storage, every Box has a barcode that is unique across the registry.

 
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Box Resource

 

id
string

ID of the box

archiveRecord
nested object

ArchiveRecord Resource if the box is archived. This is null if the box is not archived.

barcode
string

Barcode of the box

createdAt

DateTime the container was created

creator
object

UserSummary Resource of the user who created the box

fields
object

See Fields resource

modifiedAt
string

DateTime the box was last modified

name
string

Name of the box, defaults to barcode is name is not provided.

parentStorageId
string

ID of containing parent storage (e.g. loc_k2lNspzS).

projectId
string or null

ID of the project if set

schema
object

Box schema

schema.id
string

ID of the box schema

schema.name
string

Name of the box schema

webURL
string

URL of the box

{
  "archiveRecord": null,
  "barcode": "vb001",
  "createdAt":