Benchling Integration

What it does

When your agent uses it

• Automating lab data with benchling-sdk
• Tasks that involve Data warehousing
• Tasks that involve REST APIs

Example prompts

• “/benchling-integration”

Requirements

• Python 3
• A credential in BENCHLING_API_KEY
• A credential in BENCHLING_CLIENT_SECRET
• Compatibility (from SKILL.md): Requires Python 3.9+, benchling-sdk 1.25.0, network access, a Benchling tenant with API access, and API key or OAuth app credentials.
• Pre-approved tools (allowed-tools): Read, Write, Edit, Bash

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

1. 1Identify the tenant, API version, identity, and permissions. Use OAuth app credentials
2. 2Read the relevant schema and resolve actual folder, registry, status, and dropdown IDs.
3. 3Read a small filtered page before writing. Use typed SDK methods and check their
4. 4Construct and serialize a representative payload. For imports, retain external IDs
5. 5Perform the requested operation and read back the result. Check terminal async status;

What it can do on your machine

Read from SKILL.md and the folder at commit 92ace75. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves these tools, so the agent can use them without asking each time:

  • Read
  • Write
  • Edit
  • Bash

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Shell commands in SKILL.md call:

  • uv

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • docs.benchling.com
  • benchling.com
  • arxiv.org
  • doi.org
  • export.arxiv.org

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names these keys or tokens, usually read from environment variables:

  • BENCHLING_CLIENT_SECRET

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

• Compatibility

  Requires Python 3.9+, benchling-sdk 1.25.0, network access, a Benchling tenant with API access, and API key or OAuth app credentials.

  From compatibility in the SKILL.md frontmatter.

Context cost

Benchling Integration loads about 2.1k tokens when it runs, and up to ~14k if it reads all its reference files. Until then it costs about 58 tokens; SKILL.md has 622 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~58

When it runs · the whole SKILL.md, loaded when a task matches

~2.1k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~14k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

• NotePre-approves every shell command (allowed-tools: Bash)SKILL.md

  allowed-tools: Read, Write, Edit, Bash

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from K-Dense-AI/scientific-agent-skills at commit 92ace75, republished under its MIT licence (© K-Dense-AI). 622 words, ~2,134 tokens.

name

benchling-integration

description

Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.

allowed-tools

Read, Write, Edit, Bash

compatibility

Requires Python 3.9+, benchling-sdk 1.25.0, network access, a Benchling tenant with API access, and API key or OAuth app credentials.

license

MIT

metadata.version

1.7

metadata.last-reviewed

2026-09-30

metadata.skill-author

K-Dense Inc.

uv pip install "benchling-sdk==1.25.0"

import os
from benchling_sdk.benchling import Benchling
from benchling_sdk.auth.client_credentials_oauth2 import ClientCredentialsOAuth2

tenant_url = os.environ["BENCHLING_TENANT_URL"].rstrip("/")
benchling = Benchling(
    url=tenant_url,
    auth_method=ClientCredentialsOAuth2(
        client_id=os.environ["BENCHLING_CLIENT_ID"],
        client_secret=os.environ["BENCHLING_CLIENT_SECRET"],
        token_url=f"{tenant_url}/oauth/token",
    ),
)
for page in benchling.dna_sequences.list(page_size=10, name_includes="plasmid"):
    for sequence in page:
        print(sequence.id, sequence.name)
    break  # deliberate first-page connectivity/permission check

from Bio import SeqIO
from benchling_sdk.models import DnaSequenceCreate

for record in SeqIO.parse("sequences.fasta", "fasta"):
    payload = DnaSequenceCreate(
        name=record.id,
        bases=str(record.seq),
        is_circular=False,
        folder_id="lib_example",
    )
    created = benchling.dna_sequences.create(payload)
    print(record.id, created.id)  # persist this mapping for restart/reconciliation

for page in benchling.containers.list(ancestor_storage_id="box_example"):
    for container in page:
        print(container.id, container.name, container.barcode)

import csv

with open("sequences.csv", "w", newline="", encoding="utf-8") as handle:
    writer = csv.DictWriter(handle, fieldnames=["id", "name", "bases", "length"])
    writer.writeheader()
    for page in benchling.dna_sequences.list(schema_id="ts_example"):
        for seq in page:
            writer.writerow({
                "id": seq.id, "name": seq.name,
                "bases": seq.bases, "length": len(seq.bases),
            })

© K-Dense-AI, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 5 other files (references) in skills/benchling-integration of K-Dense-AI/scientific-agent-skills.

• SKILL.md
• references/api_endpoints.md
• references/authentication.md
• references/core_capabilities.md
• references/eventbridge.md
• references/sdk_reference.md

Open the folder on GitHubat commit 92ace75

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in K-Dense-AI/scientific-agent-skills, which our catalogue first saw on October 7, 2026.

• lingxling/awesome-skills-cnclaude-scientific-skills/skills/benchling-integration