NAR-2023

This release accompanies the paper "Whole-cell modeling of E. coli confirms that in vitro tRNA aminoacylation measurements are insufficient to support cell growth and predicts a positive feedback mechanism regulating arginine biosynthesis".

New Features

• Add kinetically-informed tRNA charging
• Add aminoacyl-tRNA dependent, codon-based polypeptide elongation
• Add cleavage of initial methionines on nascent polypeptides

Bug Fixes

• Fix mass distribution of tRNAs

Performance Improvements

• Refactor calculation of ribosome initiations from Python to C (using Cython)