Does it support pathway enrichment analysis?

It offers structured strategies for grouping significant metabolites into pathways and calculating enrichment scores using resources like KEGG and BioCyc.

What metabolic patterns can this skill identify?

The skill provides diagnostic patterns for identifying substrate depletion, enzymatic bottlenecks, pathway shutdowns, and shifts between de novo and salvage pathways.

Can I calculate cellular energy charge with this skill?

Yes, the skill includes specific formulas and Python snippets for calculating the Adenylate Energy Charge (AEC) and evaluating redox states (NAD+/NADH ratios).

How does this skill help with metabolite naming?

It provides standardized guidance on IUPAC names, common names, and abbreviations to ensure accurate identification and cross-referencing between biological databases.

Metabolomics Analysis

Name: Metabolomics Analysis
Author: justaddcoffee

byjustaddcoffee

0•

Data Science & ML

Provides expert strategies and domain knowledge for analyzing metabolic pathways, flux measurements, and biochemical mechanisms.

The Metabolomics Analysis skill empowers researchers and data scientists to perform sophisticated metabolic profiling by providing structured guidance on metabolite identification, pathway enrichment, and flux index calculations. It assists in interpreting complex biochemical patterns—such as substrate depletion, enzymatic bottlenecks, and pathway shifts—and offers ready-to-use Python snippets for calculating critical metrics like Adenylate Energy Charge (AEC) and redox states. By integrating domain-specific logic and literature search strategies, this skill helps transform raw metabolic data into meaningful biological insights while helping users avoid common pitfalls like compartmentalization errors or isomer confusion.

Key Features

01Diagnostic patterns for identifying metabolic bottlenecks and salvage shifts

02Structured templates for generating testable biochemical hypotheses

03Ready-to-use formulas for Adenylate Energy Charge and redox state assessment

04Standardized metabolite identification mapping across IUPAC and common names

050 GitHub stars

06Automated strategies for pathway enrichment and flux index calculations

Use Cases

01Calculating cellular energy states and oxidative stress markers from metabolite pools

02Mapping differentially abundant metabolites to KEGG and HMDB pathway contexts

03Interpreting metabolic flux and enzymatic bottlenecks in complex experimental datasets

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add justaddcoffee/open-science-skills metabolomics

For use in Claude.ai and ChatGPT

Download Skill