Scientific Agent Skills is a collection of reusable procedures that give AI agents capabilities for scientific research across areas such as biology, chemistry, medicine, and drug discovery. It is used by researchers and by people building AI scientist workflows with compatible coding agents. The catalogue contains many of the project's skills and supporting instructions.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add K-Dense-AI/scientific-agent-skills --skill opentrons-integrationgit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/opentrons-integration)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/opentrons-integration"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/opentrons-integration/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/opentrons-integration"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/opentrons-integration.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk pass
- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00079 | $0.03395 |
| Opus 5 | $0.00039 | $0.01698 |
| Sonnet 5 | $0.00016 | $0.00679 |
| Haiku 4.5 | $0.00008 | $0.00340 |
Grade A, and why
opentrons-integration scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 340 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Opentrons Integration
Overview
Create production-minded Python Protocol API v2 protocols for Opentrons Flex and OT-2. This skill covers protocol structure, hardware and deck configuration, liquid handling, runtime customization, module control, simulation, and safe deployment.
The verified baseline as of 2026-07-23 is:
opentrons==9.1.1for reproducible Flex simulation.opentrons==9.0.0for local OT-2 API 2.28 compatibility simulation.- Flex supports API levels 2.15 through 2.29 on current software.
- OT-2 supports API levels 2.0 through 2.28 on current software.
- API 2.29 is Flex-only at this baseline. Do not put
2.29in an OT-2 protocol.
Read references/sources.md for the upstream documentation used for this
snapshot. Recheck the official versioning page before targeting newer robot
software.
Safety Boundary
Opentrons protocols control physical equipment. Never treat successful Python syntax or local simulation as permission to run on a robot.
Before live execution:
- Simulate locally with the same pinned
opentronsversion used for authoring. - Import the protocol into the correct Opentrons App and require successful analysis.
- Verify robot model, software, pipettes, mounts, modules, adapters, labware definitions, deck fixtures, tip count, source volumes, dead volumes, and destination capacity.
- Review the run preview and deck map with the operator.
- Perform a slow dry run with nonhazardous liquid when geometry, custom labware, partial tip pickup, or gripper moves are new.
- Keep the emergency stop accessible and follow site-specific biosafety, chemical-safety, and contamination-control procedures.
Simulation cannot verify physical calibration, liquid properties, meniscus behavior, labware manufacturing tolerances, cap or seal removal, tubing, or all possible collisions.
Choose the Right Interface
Use this skill for Python files imported into the Opentrons App and run through the Protocol API.
- Use Protocol Designer for supported no-code workflows.
- Use PyLabRobot for a hardware-agnostic workflow spanning vendors.
- Treat the robot's HTTP API as a separate integration surface. If direct HTTP control is explicitly required, use the OpenAPI document served by the target robot and do not infer endpoints from Protocol API methods.
What ships with it
15 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- references/api_reference.md 12 KB
- references/liquid_handling.md 11 KB
- references/migration-api-2-19-to-2-29.md 8.1 KB
- references/modules_and_deck.md 11 KB
- references/protocol_authoring.md 11 KB
- references/sources.md 7.5 KB
- references/validation_and_operations.md 9.6 KB
- requirements-flex.txt 17 B
- requirements-ot2.txt 17 B
- scripts/absorbance_reader_template.py 2.3 KB runs code
- scripts/basic_protocol_template.py 1.8 KB runs code
- scripts/ot2_basic_protocol_template.py 1.7 KB runs code
- scripts/pcr_setup_template.py 4.3 KB runs code
- scripts/runtime_parameters_template.py 3.1 KB runs code
- scripts/serial_dilution_template.py 3.2 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 340 lines · 79 tokens per session scan A 6d647ecd7205
opentrons-integration is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (44,469 stars, last pushed today), licensed MIT. It adds 79 tokens to every session and 3,395 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
Other skills, from other repositories
discovery-toolbox
A routed repertoire of 90 scientific thinking operators for biological research agents - visual reasoning, detectability and information budgets, search reframing, causal identification, competing explanations, observation and selection processes, pipeline artifact diagnosis, effort allocation, and confirmation…
discovery-director
Operate as a research director making original discoveries from a given biological question and dataset. Use when the task is open-ended scientific research, exploring omics or experimental data for findings, hypothesis generation and testing, screening a large candidate space of genes, variants, features or…
OT / ICS / SCADA Security
Operational Technology and industrial control system security — Purdue model segmentation, industrial protocol analysis (Modbus, DNP3, S7, EtherNet/IP), PLC/HMI exposure, IEC 62443 alignment, and MITRE ATT&CK for ICS, for authorized and safety-conscious assessments.
bio-interdomain-hgt
Detect and polarize interdomain horizontal gene transfer with homology, context, and phylogenetic checks. Use when studying lateral gene transfer, virus-host gene exchange, endogenous viral elements, or donor direction.
polars-dovmed
Search PMC Open Access and bioRxiv corpora with polars-dovmed. Use when structured, reproducible literature queries should run through the hosted API or local parquet indexes.
csag-extraction
Extract a Conditional Scientific Argumentation Graph and grounded Q&A from a manuscript. Use when representing assertions, contexts, evidence links, and inference steps in machine-readable form.