benchling-integration

Name: benchling-integration
Author: K-Dense-AI

813installs3.1kforks

How to install benchling-integration?

k-dense-ai/scientific-agent-skills/benchling-integration

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill benchling-integration

Installs into the current project.

Summary

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.

Files · 1

View on GitHub

SKILL.md

1	# Benchling Integration
2
3	## Overview
4
5	Benchling is a cloud platform for life sciences R&D. Access registry entities (DNA, RNA, proteins), inventory, electronic lab notebooks, and workflows programmatically via the Python SDK and REST API.
6
7	Version note: Examples target benchling-sdk 1.25.0 (latest stable on PyPI). Docs: [benchling.com/sdk-docs](https://benchling.com/sdk-docs/). Platform guide: [docs.benchling.com](https://docs.benchling.com/).
8
9	## When to Use This Skill
10
11	This skill should be used when:
12	- Working with Benchling's Python SDK or REST API
13	- Managing biological sequences (DNA, RNA, proteins) and registry entities
14	- Automating inventory operations (samples, containers, locations, transfers)
15	- Creating or querying electronic lab notebook entries
16	- Building workflow automations or Benchling Apps
17	- Syncing data between Benchling and external systems
18	- Querying the Benchling Data Warehouse for analytics
19	- Setting up event-driven integrations with AWS EventBridge
20
21	## Core Capabilities
22
23	### 1. Authentication & Setup
24
25	Python SDK installation:
26
27	```bash
28	uv pip install "benchling-sdk==1.25.0"
29	```
30
31	Preview builds (alpha; not for production):
32
33	```bash
34	uv pip install "benchling-sdk" --prerelease allow
35	```
36
37	Environment variables (scoped reads only):
38
39	Read only the named keys you need — never dump or iterate over the full environment:
40
41	```python
42	import os
43
44	tenant_url = os.environ.get("BENCHLING_TENANT_URL") # e.g. https://your-tenant.benchling.com
45	api_key = os.environ.get("BENCHLING_API_KEY")
46
47	if not tenant_url or not api_key:
48	raise ValueError("Set BENCHLING_TENANT_URL and BENCHLING_API_KEY")
49	```
50
51	Obtain an API key from Profile Settings in Benchling. For OAuth apps, use the [Developer Console](https://docs.benchling.com/docs/getting-started-benchling-apps) and store `BENCHLING_CLIENT_ID` / `BENCHLING_CLIENT_SECRET` separately.
52
53	Authentication methods:
54
55	API key (scripts and personal automation):
56
57	```python
58	from benchling_sdk.benchling import Benchling
59	from benchling_sdk.auth.api_key_auth import ApiKeyAuth
60
61	benchling = Benchling(
62	url=tenant_url,
63	auth_method=ApiKeyAuth(api_key),
64	)
65	```
66
67	OAuth client credentials (multi-user apps and production integrations):
68
69	```python
70	from benchling_sdk.benchling import Benchling
71	from benchling_sdk.auth.client_credentials_oauth2 import ClientCredentialsOAuth2
72
73	benchling = Benchling(
74	url=tenant_url,
75	auth_method=ClientCredentialsOAuth2(
76	client_id=os.environ["BENCHLING_CLIENT_ID"],
77	client_secret=os.environ["BENCHLING_CLIENT_SECRET"],
78	),
79	)
80	```
81
82	**Key poin

People who liked this also viewed

6 picks

Type

benchling-integration

813installs3.1kforks

View on GitHub

How to install benchling-integration?

k-dense-ai/scientific-agent-skills/benchling-integration

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill benchling-integration

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Benchling Integration
2
3	## Overview
4
5	Benchling is a cloud platform for life sciences R&D. Access registry entities (DNA, RNA, proteins), inventory, electronic lab notebooks, and workflows programmatically via the Python SDK and REST API.
6
7	Version note: Examples target benchling-sdk 1.25.0 (latest stable on PyPI). Docs: [benchling.com/sdk-docs](https://benchling.com/sdk-docs/). Platform guide: [docs.benchling.com](https://docs.benchling.com/).
8
9	## When to Use This Skill
10
11	This skill should be used when:
12	- Working with Benchling's Python SDK or REST API
13	- Managing biological sequences (DNA, RNA, proteins) and registry entities
14	- Automating inventory operations (samples, containers, locations, transfers)
15	- Creating or querying electronic lab notebook entries
16	- Building workflow automations or Benchling Apps
17	- Syncing data between Benchling and external systems
18	- Querying the Benchling Data Warehouse for analytics
19	- Setting up event-driven integrations with AWS EventBridge
20
21	## Core Capabilities
22
23	### 1. Authentication & Setup
24
25	Python SDK installation:
26
27	```bash
28	uv pip install "benchling-sdk==1.25.0"
29	```
30
31	Preview builds (alpha; not for production):
32
33	```bash
34	uv pip install "benchling-sdk" --prerelease allow
35	```
36
37	Environment variables (scoped reads only):
38
39	Read only the named keys you need — never dump or iterate over the full environment:
40
41	```python
42	import os
43
44	tenant_url = os.environ.get("BENCHLING_TENANT_URL") # e.g. https://your-tenant.benchling.com
45	api_key = os.environ.get("BENCHLING_API_KEY")
46
47	if not tenant_url or not api_key:
48	raise ValueError("Set BENCHLING_TENANT_URL and BENCHLING_API_KEY")
49	```
50
51	Obtain an API key from Profile Settings in Benchling. For OAuth apps, use the [Developer Console](https://docs.benchling.com/docs/getting-started-benchling-apps) and store `BENCHLING_CLIENT_ID` / `BENCHLING_CLIENT_SECRET` separately.
52
53	Authentication methods:
54
55	API key (scripts and personal automation):
56
57	```python
58	from benchling_sdk.benchling import Benchling
59	from benchling_sdk.auth.api_key_auth import ApiKeyAuth
60
61	benchling = Benchling(
62	url=tenant_url,
63	auth_method=ApiKeyAuth(api_key),
64	)
65	```
66
67	OAuth client credentials (multi-user apps and production integrations):
68
69	```python
70	from benchling_sdk.benchling import Benchling
71	from benchling_sdk.auth.client_credentials_oauth2 import ClientCredentialsOAuth2
72
73	benchling = Benchling(
74	url=tenant_url,
75	auth_method=ClientCredentialsOAuth2(
76	client_id=os.environ["BENCHLING_CLIENT_ID"],
77	client_secret=os.environ["BENCHLING_CLIENT_SECRET"],
78	),
79	)
80	```
81
82	**Key poin

People who liked this also viewed

6 picks

Type