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 etetoolkitgit 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/etetoolkit)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/etetoolkit"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/etetoolkit/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/etetoolkit"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/etetoolkit.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 3 findings, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Rogue Agent · line 22 Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.Fix: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.
- medium Privilege Escalation · line 372 Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
- medium Privilege Escalation · line 558 Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
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 | $0.00046 | $0.04603 |
| Opus 5.5 | $0.00018 | $0.01841 |
| Sonnet 5.5 | $0.00009 | $0.00921 |
| Haiku 4.5 | $0.00005 | $0.00460 |
Grade B, and why
etetoolkit scanned grade B 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.
Asks for rootmediumPrivilege escalation
A mod that escalates privileges can change anything on the machine, not only the project.
sudo apt-get install python3-pyqt5 python3-pyqt5.qtsvg Copies of this mod
8 near-identical copies found in the catalogue:
- etetoolkit — 97% identical, 10 lines differ
- etetoolkit — 97% identical, 10 lines differ
- etetoolkit — 97% identical, 10 lines differ
- etetoolkit — 97% identical, 10 lines differ
- etetoolkit — 95% identical, 9 lines differ
- etetoolkit — 95% identical, 7 lines differ
- etetoolkit — 95% identical, 9 lines differ
- etetoolkit — 95% identical, 7 lines differ
How it starts
The opening of the file, as written. The whole thing — 629 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ETE Toolkit Skill
Overview
ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analyze evolutionary events, visualize results, and integrate with biological databases for phylogenomic research and clustering analysis.
Core Capabilities
1. Tree Manipulation and Analysis
Load, manipulate, and analyze hierarchical tree structures with support for:
- Tree I/O: Read and write Newick, NHX, PhyloXML, and NeXML formats
- Tree traversal: Navigate trees using preorder, postorder, or levelorder strategies
- Topology modification: Prune, root, collapse nodes, resolve polytomies
- Distance calculations: Compute branch lengths and topological distances between nodes
- Tree comparison: Calculate Robinson-Foulds distances and identify topological differences
Common patterns:
from ete3 import Tree
# Load tree from file
tree = Tree("tree.nw", format=1)
# Basic statistics
print(f"Leaves: {len(tree)}")
print(f"Total nodes: {len(list(tree.traverse()))}")
# Prune to taxa of interest
taxa_to_keep = ["species1", "species2", "species3"]
tree.prune(taxa_to_keep, preserve_branch_length=True)
# Midpoint root
midpoint = tree.get_midpoint_outgroup()
tree.set_outgroup(midpoint)
# Save modified tree
tree.write(outfile="rooted_tree.nw")
Use scripts/tree_operations.py for command-line tree manipulation:
# Display tree statistics
python scripts/tree_operations.py stats tree.nw
# Convert format
python scripts/tree_operations.py convert tree.nw output.nw --in-format 0 --out-format 1
# Reroot tree
python scripts/tree_operations.py reroot tree.nw rooted.nw --midpoint
# Prune to specific taxa
python scripts/tree_operations.py prune tree.nw pruned.nw --keep-taxa "sp1,sp2,sp3"
# Show ASCII visualization
python scripts/tree_operations.py ascii tree.nw
2. Phylogenetic Analysis
Analyze gene trees with evolutionary event detection:
- Sequence alignment integration: Link trees to multiple sequence alignments (FASTA, Phylip)
- Species naming: Automatic or custom species extraction from gene names
- Evolutionary events: Detect duplication and speciation events using Species Overlap or tree reconciliation
- Orthology detection: Identify orthologs and paralogs based on evolutionary events
- Gene family analysis: Split trees by duplications, collapse lineage-specific expansions
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 86318631f1f4
- 1mo ago First seen · 623 lines · 46 tokens per session scan B a38c5740f43b
etetoolkit is a skill published in the GitHub repository synthetic-sciences/openscience (4,266 stars, last pushed yesterday), licensed Apache-2.0. It adds 46 tokens to every session and 4,603 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it B with 1 finding (asks for root). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other skills, from other repositories
songsee
Audio spectrograms/features (mel, chroma, MFCC) via CLI.
arxiv
Search arXiv papers by keyword, author, category, or ID.
research-paper-writing
Write ML papers for NeurIPS/ICML/ICLR: design→submit.
paper-revision-author
Revise independently drafted paper sections into one coherent LaTeX body before the abstract is written.
paper-plot-stub
Plot a results CSV (x, ybaseline, yours) as a two-line matplotlib chart and write a PDF. Demo-only.
knowledge-extension-ecosystem-lsp-code-intelligence
A codebase guide to LSP, the standard protocol behind editor features such as symbol queries, file diagnostics, and language-aware code information.