BioPhi API

Humanize antibody sequences or estimate their humanness.

Prepares paired antibody FASTA and invokes BioPhi Sapiens or OASis.

Web form Home page ↗ Paper ↗ Source code ↗ License ↗

Submit POST /api/biophi/

Queues a run and returns 202 with the job.

Schema GET /api/biophi/

Returns this tool's metadata and the fields below, as JSON.

Request body

Fields

The same names the web form posts. See the field type table for what each kind means over HTTP.

Name	Type	Required	Default	Description
`job_name`	string text	no	`mouse-4d5`	Antibody name
`heavy_sequence`	string textarea	yes	`DVQLQESGPGLVRPSQTLSLTCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDT …`	Heavy-chain sequence Variable domain only. The placeholder is the murine 4D5 heavy chain, the mouse parent of trastuzumab.
`light_sequence`	string textarea	yes	`DIVMTQSHKFMSTSVGDRVSITCKASQDVNTAVAWYQQKPGHSPKLLIYSASFRYTGVPDRFTGSRSGTDFTFTISSVQAEDLAVYYCQQ …`	Light-chain sequence Variable domain only. The placeholder is the murine 4D5 light chain.
`operation`	string select	no	`humanize`	Operation One of: `humanize`, `mean_score`, `oasis`.

Example

A request that runs

These are the defaults, exactly as the web form would post them.

curl -X POST https://athanortools.com/api/biophi/ \
  -H 'Content-Type: application/json' \
  -d '{
  "job_name": "mouse-4d5",
  "heavy_sequence": "DVQLQESGPGLVRPSQTLSLTCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYNTPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSA",
  "light_sequence": "DIVMTQSHKFMSTSVGDRVSITCKASQDVNTAVAWYQQKPGHSPKLLIYSASFRYTGVPDRFTGSRSGTDFTFTISSVQAEDLAVYYCQQHYTTPPTFGGGTKVEIK",
  "operation": "humanize"
}'

The reply is 202 with a queued job; poll its status_url until status is succeeded or failed. See the quick start for the whole exchange.

Responses

What comes back

status	Meaning
`queued`	Accepted, waiting for the jobs ahead of it. `position` counts how many those are.
`running`	The tool is executing now.
`succeeded`	Finished; `result` holds the tool's output and `license` the terms it came under.
`failed`	Finished; `error` holds a code and a message.
`cancelled`	Abandoned at the submitter's request; there is no result. A job cancelled before its turn never ran at all.

Errors

code	Meaning
`invalid_input`	The client supplied invalid or incomplete input.
`tool_unavailable`	The requested third-party dependency is not available on this host.
`execution_failed`	A configured third-party tool exited unsuccessfully.
`internal_error`	An adapter failed in a way it does not describe. The detail is in the server log, not the response.
`not_found`	No job has that id. Finished jobs are dropped eventually.