bio-workflows-metabolic-modeling-pipeline
End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA analysis, and gene essentiality prediction. Use when building metabolic models or predicting metabolic phenotypes from genomic data.
npx skills add BioTender-max/awesome-bio-agent-skills --skill metabolic-modeling-pipeline --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+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, seaborn 0.13+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Metabolic Modeling Pipeline **"Build and analyze a metabolic model for my organism"** → Orchestrate CarveMe reconstruction, memote quality scoring, gap-filling, FBA/FVA flux analysis, gene essentiality prediction, and context-specific model building from expression data. Complete workflow for genome-scale metabolic modeling: from protein sequences to flux predictions and phenotype analysis. ## Workflow Overview ``` Protein FASTA (genome annotation) | v [1. Reconstruction] --> CarveMe / gapseq / ModelSEED | v [2. Model Curation] --> memote QC, gap-filling | | <---- Iterative refinement loop v [3. FBA Analysis] --> Growth prediction, flux distribution | +-----------------------+
- Version Compatibility
- Workflow Overview
- Prerequisites
- Primary Path: Bacterial Model from Genome
- Step 1: Automated Reconstruction with CarveMe
- Step 2: Model Validation with Memote
- Step 3: Model Curation (Iterative)
- Step 4: Flux Balance Analysis
- Step 5a: Gene Essentiality Prediction
- Step 5b: Context-Specific Models
- Visualization with Escher
- Parameter Recommendations
- Troubleshooting
- Output Files
pip install cobra carveme memote escher pandas numpy matplotlib seaborn conda install -c bioconda diamond Basic reconstruction from protein sequences carve genome.faa -o model_draft.xml With gram type specification (improves biomass composition) carve genome.faa -o model_draft.xml --gram-neg Gap-fill for specific media carve genome.faa -o model_draft.xml --gram-neg --gapfill M9 Run memote QC memote run --filename model_draft_report.html model_draft.xml
What does the bio-workflows-metabolic-modeling-pipeline skill do?
End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA analysis, and gene essentiality prediction. Use when building metabolic models or predicting metabolic phenotypes from genomic data.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill metabolic-modeling-pipeline --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.