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 genomic-coordinatesgit 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/genomic-coordinates)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/genomic-coordinates"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/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/synthetic-sciences/openscience/genomic-coordinates"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/genomic-coordinates.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.02902 |
| Opus 5.5 | $0.00089 | $0.01161 |
| Sonnet 5.5 | $0.00045 | $0.00580 |
| Haiku 4.5 | $0.00022 | $0.00290 |
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 20d 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.
This is a copy
91% identical to genomic-coordinates — 115 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
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.
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.
- 20d ago Changed · +15 lines 7f41234352f7
- 1mo ago Changed · +5 lines 2972662826ee
- 1mo ago First seen · 209 lines · 223 tokens per session scan A c507b019caed
genomic-coordinates is a skill published in the GitHub repository synthetic-sciences/openscience (4,025 stars, last pushed today), licensed Apache-2.0. It adds 223 tokens to every session and 2,902 once invoked, about $0.0009 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 91% identical to genomic-coordinates, differing in 115 lines, and is treated as a copy.
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