synthetic-sciences/openscience is an AI workbench that carries out scientific research by reading papers, forming hypotheses, writing and running code, conducting experiments, analyzing results, and preparing reports. Researchers use it for work in machine learning, biology, physics, and chemistry with remote or local models. Catalogue add-ons extend its scientific workflows through skills and 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 synthetic-sciences/openscience --skill dnanexus-integrationgit clone --depth 1 https://github.com/synthetic-sciences/openscienceWrote 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/synthetic-sciences/openscience/dnanexus-integration)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/dnanexus-integration"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/dnanexus-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/synthetic-sciences/openscience/dnanexus-integration"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/dnanexus-integration.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- 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 | $0.00049 | $0.02483 |
| Opus 5.5 | $0.00020 | $0.00993 |
| Sonnet 5.5 | $0.00010 | $0.00497 |
| Haiku 4.5 | $0.00005 | $0.00248 |
Grade A, and why
dnanexus-integration scanned grade A with 1 finding 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 1mo 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.
Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
subprocess.check_call([ Copies of this mod
8 near-identical copies found in the catalogue:
- dnanexus-integration — 98% identical, 9 lines differ
- dnanexus-integration — 98% identical, 14 lines differ
- dnanexus-integration — 98% identical, 9 lines differ
- dnanexus-integration — 98% identical, 14 lines differ
- dnanexus-integration — 95% identical, 10 lines differ
- dnanexus-integration — 95% identical, 7 lines differ
- dnanexus-integration — 88% identical, 10 lines differ
- dnanexus-integration — 88% identical, 10 lines differ
How it starts
The opening of the file, as written. The whole thing — 389 lines — stays where its author put it; the contents beside it link to each section on GitHub.
DNAnexus Integration
Overview
DNAnexus is a cloud platform for biomedical data analysis and genomics. Build and deploy apps/applets, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution.
When to Use This Skill
This skill should be used when:
- Creating, building, or modifying DNAnexus apps/applets
- Uploading, downloading, searching, or organizing files and records
- Running analyses, monitoring jobs, creating workflows
- Writing scripts using dxpy to interact with the platform
- Setting up dxapp.json, managing dependencies, using Docker
- Processing FASTQ, BAM, VCF, or other bioinformatics files
- Managing projects, permissions, or platform resources
Core Capabilities
The skill is organized into five main areas, each with detailed reference documentation:
1. App Development
Purpose: Create executable programs (apps/applets) that run on the DNAnexus platform.
Key Operations:
- Generate app skeleton with
dx-app-wizard - Write Python or Bash apps with proper entry points
- Handle input/output data objects
- Deploy with
dx buildordx build --app - Test apps on the platform
Common Use Cases:
- Bioinformatics pipelines (alignment, variant calling)
- Data processing workflows
- Quality control and filtering
- Format conversion tools
Reference: See references/app-development.md for:
- Complete app structure and patterns
- Python entry point decorators
- Input/output handling with dxpy
- Development best practices
- Common issues and solutions
2. Data Operations
Purpose: Manage files, records, and other data objects on the platform.
Key Operations:
- Upload/download files with
dxpy.upload_local_file()anddxpy.download_dxfile() - Create and manage records with metadata
- Search for data objects by name, properties, or type
- Clone data between projects
- Manage project folders and permissions
Common Use Cases:
- Uploading sequencing data (FASTQ files)
- Organizing analysis results
- Searching for specific samples or experiments
- Backing up data across projects
- Managing reference genomes and annotations
What ships with it
5 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.
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.
- 1mo ago Changed · +6 lines cc070682ea82
- 1mo ago First seen · 383 lines · 49 tokens per session scan A bb84d8f6a053
dnanexus-integration is a skill published in the GitHub repository synthetic-sciences/openscience (4,121 stars, last pushed 2d ago), licensed Apache-2.0. It adds 49 tokens to every session and 2,483 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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