OpenBioMed is an agent platform and toolkit collection for biomedical research and drug discovery, covering areas such as molecular design, protein analysis, and single-cell data analysis. It is intended for researchers and provides the biomedical skills listed in the catalogue as workflows for Claude Code.
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 PharMolix/OpenBioMed --skill biomed-skill-creatorgit clone --depth 1 https://github.com/PharMolix/OpenBioMedWrote 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/pharmolix/openbiomed/biomed-skill-creator)<a href="https://agentmods.dev/skills/pharmolix/openbiomed/biomed-skill-creator"><img src="https://agentmods.dev/badge/skills/pharmolix/openbiomed/biomed-skill-creator/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/pharmolix/openbiomed/biomed-skill-creator"><img src="https://agentmods.dev/badge/skills/pharmolix/openbiomed/biomed-skill-creator.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 | $0.00089 | $0.01955 |
| Opus 5 | $0.00044 | $0.00978 |
| Sonnet 5 | $0.00018 | $0.00391 |
| Haiku 4.5 | $0.00009 | $0.00196 |
Grade A, and why
biomed-skill-creator 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 12d 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 — 229 lines — stays where its author put it; the contents beside it link to each section on GitHub.
BioMed Skill Creator
A meta-skill for creating and improving skills in the OpenBioMed biomedical toolkit.
Overview
This skill guides you through creating biomedical skills with interactive validation. Biomedical workflows require domain-specific validation with real data before finalization.
Workflow:
1. Capture Intent → 2. Design Workflow → 3. Interactive Validation → 4. Finalize → 5. Evaluate
↑ ↓
└──────────────────── Iterate if needed ←─────────────────────┘
Step 1: Capture Intent
Ask clarifying questions:
- What biomedical task should this skill perform?
- What inputs will users provide? (molecule name/SMILES, protein ID, text)
- What outputs should the skill produce? (reports, files, predictions, visualizations)
- Are there edge cases or constraints?
Input Types
| Input Type | Factory Method | Example |
|---|---|---|
| Molecule | Molecule.from_smiles() |
"CC(=O)OC1=CC=CC=C1C(=O)O" |
| Protein | Protein.from_fasta() |
"MKFLILLFNILCLFPVLAADNH..." |
Pocket.from_protein_ref_ligand() |
Protein + reference ligand | |
| Text | Text.from_str() |
"What is this molecule?" |
Step 2: Design Workflow
Identify tools and steps. See references/tools_reference.md for available tools.
Common Workflow Patterns
| Pattern | Tools Flow |
|---|---|
| Drug-likeness | molecule_name_request → molecule_qed/sa/logp/lipinski → summarize |
| Protein Mutation | protein_uniprot_request → mutation_explanation → protein_folding → visualize |
| Structure-Based Design | protein_pdb_request → extract_molecules → structure_based_drug_design → docking |
| Molecule Q&A | molecule_name_request → molecule_question_answering → format |
Basic Workflow Code Pattern
from open_biomed.tools.tool_registry import TOOLS
# Get entity
tool = TOOLS["tool_name"]
result, message = tool.run(parameter=value)
entity = result.get("protein") or result.get("molecule")
# Process with other tools
another_tool = TOOLS["another_tool"]
output, msg = another_tool.run(entity=entity)
What ships with it
6 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.
- 12d ago First seen · 229 lines · 89 tokens per session scan A a7f74fe8346d
biomed-skill-creator is a skill published in the GitHub repository PharMolix/OpenBioMed (1,106 stars, last pushed 1mo ago), licensed MIT. It adds 89 tokens to every session and 1,955 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 2026-08-30.
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