nVmaxBuilder documentation

VmaxBuilder is a modular Python toolbox for converting expression and model inputs into condition-specific reaction capacity estimates.

Pipeline overview

The pipeline is structured as modular stages:

1. Expression preprocessing.

2. Model preprocessing.

3. Protein abundance estimation.

4. Kcat estimation and resolution.

5. Allocation and Vmax calculation.

Start here

• New users: Getting Started

• Installation options: Installation

• Worked examples: Examples

• Practical scenarios: Use Cases

• API details: VmaxBuilder (API)

Note

This project is under active development.

Contents

• Getting Started
  • Who this is for
  • What VmaxBuilder does
  • Quick path
  • Current project status
  • See also
• Installation
  • Recommended setup (uv)
  • Install from package index
  • Development install (local repository)
  • Optional extras
  • Notes
• Examples
  • Planned examples
  • Placeholder status
  • Example template (to be expanded)
  • See also
• Use Cases
  • Research scenarios
  • Developer scenarios
  • Current scope
  • Related pages
• Usage
  • Primary docs entry points
  • Refactor note
• VmaxBuilder (API)
  • api
  • config
  • core
  • expression
  • model
  • protein
  • Kcat
  • allocation
  • Vmax
  • diagnostics
  • registries
  • database_retrieval
  • cobrapy_overwrites
  • utils