rho.bio.agent

rho.bio.agent exposes declared bioinformatics resources to an agent through the ordinary rho.ext and rho.ai tool contracts. It is downstream of the provider and agent core.

Register and call a bio tool

library(rho.async)
library(rho.ai)
library(rho.bio)
library(rho.ext)
library(rho.bio.agent)

registry <- rho_bio_registry()
rho_register_manifest(registry, rho_manifest(
  id = "example",
  version = "1.0.0",
  title = "Example manifest",
  description = "A registered manifest"
))

runtime <- rho_extension_runtime()
rho_register_bio_extension(rho_extension_api(runtime), registry)
tool <- get("bio_describe_manifest", runtime@state$tools)
result <- rho_execute_tool(
  tool,
  ToolCall("bio-1", "bio_describe_manifest", list()),
  context = NULL
) |>
  rho_await(timeout = 1000)

list(
  tool = tool@name,
  manifests = result@details$count
)
#> $tool
#> [1] "bio_describe_manifest"
#>
#> $manifests
#> [1] 1

The extension translates registry facts into tool results; it does not make the model the authority for those facts. Additional bio workflows can register tools without changing rho.agent.

See the rho.bio.agent reference and the underlying rho.bio substrate.