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 genomic-coordinatesgit 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/genomic-coordinates)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/genomic-coordinates"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/genomic-coordinates/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/genomic-coordinates"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/genomic-coordinates.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk warn
- 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 | $0.00223 | $0.02597 |
| Opus 5 | $0.00112 | $0.01299 |
| Sonnet 5 | $0.00045 | $0.00519 |
| Haiku 4.5 | $0.00022 | $0.00260 |
Grade A, and why
genomic-coordinates 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 8d 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.
Copies of this mod
1 near-identical copy found in the catalogue:
- genomic-coordinates — 100% identical, 19 lines differ
How it starts
The opening of the file, as written. The whole thing — 207 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Genomic Coordinates
When to use
Any time a coordinate crosses a boundary: between two file formats, between two tools, between two assemblies, or between the genome and a transcript.
The rule
A coordinate is three facts, not one: the number, the convention it is written in, and the assembly it was measured against. Carry all three or the number is not interpretable.
Coordinate errors are the quietest class of bug in genomics. An off-by-one BED file parses, sorts, and intersects without complaint. A GRCh37 VCF joined against a GRCh38 annotation returns rows. A right-shifted indel simply fails to match its entry in ClinVar, and the result is a variant reported as novel. Nothing raises an error; the answer is just wrong, and it is wrong in a direction that looks plausible.
So: convert with the table, not from memory, and verify against the reference whenever a reference is available.
The two conversions
1-based inclusive -> 0-based half-open : start - 1, end
0-based half-open -> 1-based inclusive : start + 1, end
The end coordinate never moves. If a conversion changed both numbers, it is wrong.
Which format is which
| 0-based, half-open | 1-based, inclusive |
|---|---|
| BED, bedGraph, bigWig, narrowPeak | GFF3, GTF, VCF |
| BAM/CRAM (binary POS) | SAM (text POS) |
| PSL, genePred, refFlat | WIG, Picard interval_list |
| MAF (UCSC multiple alignment) | MAF (TCGA mutation annotation) |
| PyRanges, pybedtools | GRanges/IRanges, samtools & UCSC & Ensembl region strings |
Both "MAF" formats exist, they mean different things, and they disagree. UCSC
serves 0-based files through a 1-based browser box. references/format-conventions.md
has the full table with per-format detail.
cd skills/genomic-coordinates/scripts
python3 convert_coords.py --list # the table
python3 convert_coords.py --from bed --to gff chr1 999 1000
python3 convert_coords.py --from ucsc --to bed "chr7:5,530,601-5,530,625"
python3 convert_coords.py --from granges --to pyranges --input regions.tsv
What ships with it
9 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/format-conventions.md 9.3 KB
- references/reference-builds.md 7.0 KB
- references/transcript-coordinates.md 6.2 KB
- references/variant-representation.md 6.1 KB
- scripts/_common.py 13 KB runs code
- scripts/audit_intervals.py 19 KB runs code
- scripts/check_contigs.py 16 KB runs code
- scripts/convert_coords.py 6.5 KB runs code
- scripts/normalize_variant.py 9.7 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.
- 8d ago Changed · +17 lines a0a4d9378236
- 12d ago First seen · 190 lines · 223 tokens per session scan A afc6c6f220a8
genomic-coordinates is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (44,220 stars, last pushed 4d ago), licensed MIT. It adds 223 tokens to every session and 2,597 once invoked, about $0.0011 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…
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.
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.
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.