Welcome to SPECIMEN!

SPECIMEN is a Python package that contains a growing collection of workflows for the automated curation of high-quality, ideally strain-specific, genome-scale metabolic models (GEMs).

These workflows are mainly based on the refineGEMs [1] toolbox.

Additionally, most of the functions and steps of the different workflows in SPECIMEN can be used separatly.

Available Workflows

Currently, SPECIMEN includes the following workflows (for a summary refer to Overview of the Workflows):

How to Cite

Warning

Coming soon

Content

• Installation
  • Installation via GitHub/pip
• Overview of the Workflows
  • CarveMe + ModelPolisher based (CMPB) workflow
  • High-quality template based (HQTB) workflow
  • More ideas for workflows
• Contents of SPECIMEN
  • specimen subpackages
  • specimen submodules
• Help & FAQ
  • Known Bugs and Issues
  • FAQs
• Notes for Developers
  • Current Status
  • Developer Information
  • Documentation Notes

[1]

Famke Bäuerle, Gwendolyn O Döbel, Laura Camus, Simon Heilbronner, and Andreas Dräger. Genome-scale metabolic models consistently predict in vitro characteristics of corynebacterium striatum. Frontiers in Bioinformatics, 2023.