bio-systems-biology-gene-essentiality
Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions. Predict essential genes and identify synthetic lethal pairs for drug target discovery. Use when identifying essential genes or finding synthetic lethal drug targets.
npx skills add BioTender-max/awesome-bio-agent-skills --skill gene-essentiality --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: COBRApy 0.29+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Gene Essentiality Analysis **"Predict which genes are essential for growth in my organism"** → Perform in silico single and double gene knockouts on a metabolic model, identifying genes whose deletion abolishes growth and synthetic lethal pairs for drug target discovery. - Python: `cobra.flux_analysis.single_gene_deletion()`, `cobra.flux_analysis.double_gene_deletion()` (COBRApy) ## Single Gene Knockouts **Goal:** Identify essential genes by simulating single gene deletions and measuring growth impact on a metabolic model. **Approach:** Perform in silico single gene deletions across all model genes, compare post-deletion growth to wild-type, and classify genes as essential (lethal), growth-reducing, or non-essential based on growth ratio thresholds. ```python import cobra from cobra.flux_analysis
- Version Compatibility
- Single Gene Knockouts
- Classify Gene Essentiality
- Synthetic Lethality
- Identify Synthetic Lethal Pairs
- Condition-Specific Essentiality
- Robustness Analysis
- Related Skills
What does the bio-systems-biology-gene-essentiality skill do?
Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions. Predict essential genes and identify synthetic lethal pairs for drug target discovery. Use when identifying essential genes or finding synthetic lethal drug targets.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill gene-essentiality --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.