Welcome to aureme’s documentation!

Contents

• How to use Docker?
  • Running a Docker container
  • Some tips about Docker
• How to use the AuReMe workspace (default workflow)
  • Requirements
  • The default workflow
  • Data organization
  • Orthology-based reconstruction
  • Annotation-based reconstruction
  • Merge metabolic networks
  • Gap-filling
  • Manual curation
• FAQ
  • Can I have a sample of AuReMe?
  • How to convert files to different formats?
  • How to manage growth medium?
  • How to manage metabolic network compartment?
  • What are “artefacts”?
  • How to explore the topology of a metabolic network?
  • How to manage the log files?
  • How to reproduce studies?
  • How to create a new ‘à-la-carte’ workflow?
  • How to choose another reference database?
  • What is checked in my input files?
  • What is the Makefile?
  • What is the config.txt file?
  • How to regenerate a new database version?
  • How to map a metabolic network on another database?
  • How to generate report on results?
  • How to generate Wiki?
  • How to connect to Pathway-tools?
  • How to set an objective reaction?
  • How to process Flux Balance Analysis?

Indices and tables

• Index
• Module Index
• Search Page