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 flowiogit 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/flowio)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/flowio"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/flowio/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/flowio"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/flowio.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 | $0.00088 | $0.02920 |
| Opus 5 | $0.00044 | $0.01460 |
| Sonnet 5 | $0.00018 | $0.00584 |
| Haiku 4.5 | $0.00009 | $0.00292 |
Grade A, and why
flowio 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 — 328 lines — stays where its author put it; the contents beside it link to each section on GitHub.
FlowIO
Purpose
Use FlowIO as a lightweight, low-level reader and writer for Flow Cytometry Standard files. Examples in this skill target FlowIO 1.4.0, the current stable release verified on 2026-07-23.
FlowIO is appropriate for:
- Reading FCS 2.0, 3.0, and 3.1 files
- Inspecting HEADER, TEXT, ANALYSIS, and channel metadata
- Retrieving event data as a two-dimensional NumPy array
- Reading legacy files that contain multiple datasets
- Writing list-mode, single-precision FCS 3.1 files
- Preparing data for pandas, machine-learning, or downstream cytometry tools
FlowIO does not perform compensation, logicle/biexponential transforms, gating, clustering, or FlowJo workspace processing. Use FlowKit or another analysis package for those tasks.
Install
Create or activate a Python environment, then install the verified release:
uv pip install "flowio==1.4.0"
Confirm the runtime version:
uv run python -c "import flowio; print(flowio.__version__)"
FlowIO 1.4.0 supports Python 3.9 through 3.13 and depends on NumPy.
Operating Workflow
- Clarify the operation. Distinguish metadata inventory, event extraction, file repair, conversion, and downstream biological analysis.
- Inspect before loading events. Use
only_text=Truefor metadata-only work, especially with large or unfamiliar files. - Choose event semantics explicitly. Use
as_array(preprocess=True)for gain/log/time scaling from FCS metadata, orpreprocess=Falsefor values as encoded in the DATA segment. Record the choice. - Keep parsing strict by default. Do not automatically suppress offset errors. Relax checks only for a known vendor-format defect, and review the resulting event data.
- Treat metadata as potentially sensitive. FCS TEXT values can include sample, subject, operator, and instrument identifiers. Export only fields needed for the task.
- Validate writes by reopening them. Check event/channel counts, labels, metadata, and representative values after any FCS export.
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.
- 9d ago Changed · +17 lines 69e87a334078
- 13d ago First seen · 311 lines · 88 tokens per session scan A 2b92a5e59edd
flowio is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (44,469 stars, last pushed today), licensed MIT. It adds 88 tokens to every session and 2,920 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.
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…
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.
exploratory-data-analysis
Inspect scientific data and generate a Markdown structure-and-quality report. Use when triaging tabular, array, sequence, HDF5, JSON, or raster files before downstream analysis.