OpenCloning

Import From Anywhere

Your files, NCBI, AddGene, SnapGene, iGEM…

Engineer Anything

Gibson, Golden Gate, Gateway, In vivo assembly…

Automate Everything

Create scripts, notebooks, templates and forms

Share With Anyone

Export cloning workflows in FAIR Open File Format.

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Import from anywhere

From many online repositories and local files.

Access gene sequences from NCBI

Get plasmid sequences from AddGene or SnapGene

Many other repositories supported!

Support for most cloning methods

Primer design for Homologous Recombination, Gibson...

Engineer anything

Supports most cloning methods and has powerful primer design capabilities.

Automate everything

Use scripts, notebook, forms and templates to speed up design

Get started with scripting

Use cloning kit templates

Programmaticly load sequences

addgene_source = AddgeneIdSource(id=1, repository_id="52691", repository_name="addgene")
addgene_result = await get_from_repository_id_addgene(addgene_source)

locus_source = GenomeCoordinatesSource(
    id=2,
    type="GenomeCoordinatesSource",
    assembly_accession="GCF_000146045.2",
    sequence_accession="NC_001147.6",
    start=432688,
    end=437345,
    strand=-1,
)
locus_result = await genome_coordinates(locus_source)

Programmaticly design cloning strategies

# Golden Gate
golden_gate_source = RestrictionAndLigationSource(id=1, restriction_enzymes=["BsaI"])
result = await restriction_and_ligation(
    golden_gate_source,
    [seq1, seq2, seq3],
)

# Gibson Assembly
gibson_source = GibsonAssemblySource(id=2)
result = await gibson_assembly(gibson_source, [seq1, seq2, seq3])

# Homologous Recombination
hom_rec_source = HomologousRecombinationSource(id=3)
result = await homologous_recombination(hom_rec_source, [template, insert])

Capture the entire cloning workflow

Data model for AddGene plasmid

{
    "id": 1,
    "input": [],
    "output": 2,
    "type": "AddGeneIdSource",
    "output_name": null,
    "repository_id": "52691",
    "repository_name": "addgene",
    "sequence_file_url": "https://media.addgene.org/snapgene-media/v2.0.0/sequences/210876/0ad0ffaa-d9b9-48c4-af54-19e87587070e/addgene-plasmid-52691-sequence-210876.gbk",
    "addgene_sequence_type": "addgene-full"
}

Data model for PCR

{
    "id": 7,
    "input": [4],
    "output": 8,
    "type": "PCRSource",
    "circular": false,
    "assembly": [ < You can represent a PCR like and assembly
        {
            "sequence": 12, < primer id
            "left_location": null,
            "right_location": "15..38", < Forward primer hybridization site
            "reverse_complemented": false
        },
        {
            "sequence": 4, < template sequence id
            "left_location": "1170..1193",
            "right_location": "3397..3416",
            "reverse_complemented": false
        },
        {
            "sequence": 13, < primer id
            "left_location": "0..19", < Reverse primer hybridization site
            "right_location": null,
            "reverse_complemented": true
        }
    ]
}