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 GPTomics/bioSkills --skill combinatorial-screensgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/combinatorial-screens)<a href="https://agentmods.dev/skills/gptomics/bioskills/combinatorial-screens"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/combinatorial-screens/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/gptomics/bioskills/combinatorial-screens"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/combinatorial-screens.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 | $0.00252 | $0.04575 |
| Opus 5 | $0.00126 | $0.02287 |
| Sonnet 5 | $0.00050 | $0.00915 |
| Haiku 4.5 | $0.00025 | $0.00458 |
Grade A, and why
bio-crispr-screens-combinatorial-screens 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:
- bio-crispr-screens-combinatorial-screens — 97% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 265 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: MAGeCK 0.5.9+ (for MLE with interaction terms), Inzolia library annotation (Esmaeili Anvar 2024), pandas 2.2+, numpy 1.26+, scipy 1.12+, matplotlib 3.8+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
mageck --version;mageck mle --help - For Cas12a libraries: verify against published Inzolia / in4mer / Big Papi annotations
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Combinatorial CRISPR Screen Analysis
"Run a combinatorial CRISPR screen to find synthetic-lethal interactions" -> Design a paired or multiplex library, screen for double-knockout fitness, score per-pair genetic interaction (GI = observed_double - expected_additive), and identify synthetic-lethal (negative GI) and synthetic-rescue (positive GI) interactions.
- CLI:
mageck mlewith explicit interaction terms for paired-Cas9 (Big Papi-style) - Python: custom GI scoring for Cas12a multiplex (in4mer / Inzolia)
- Modality: enCas12a / LbCas12a single-array multiplex (preferred for paralog screens)
Combinatorial Architecture Decision Tree
| Goal | Architecture | Library | Why |
|---|---|---|---|
| Paralog buffering, identify synthetic lethal paralog pairs | enCas12a single-array 4-guide multiplex | Inzolia (Esmaeili Anvar 2024) | Cas9 single-KO misses paralog-buffered essentials (42% of constitutively expressed genes never score, Dede 2020) |
| Test specific pathway pair (e.g., DNA repair branches) | Big Papi (orthologous SaCas9 + SpCas9; two sgRNAs from U6 and H1 in pPapi) | Custom | Mature methodology; orthologous enzymes avoid repeated-element recombination |
| Combinatorial 3-way / 4-way knockout | in4mer (4-guide single Cas12a array) | Custom (in4mer) | Single transcript processed by Cas12a; multi-gene |
| Single-cell Perturb-seq with multi-pert per cell | Combinatorial Perturb-seq + Cas9 multiplex | Custom | Single-cell readout of multi-perturbation effects |
| Drug-modifier + KO interaction | Cas9 KO + drug treatment | Standard libraries | Drug as second "perturbation" |
What ships with it
2 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.
- 8d ago First seen · 265 lines · 252 tokens per session scan A d856b3b0e048
bio-crispr-screens-combinatorial-screens is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 252 tokens to every session and 4,575 once invoked, about $0.0013 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 2026-09-03.
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