NAR-2023 (with metadata for Zenodo)

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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)

npj-sba-2022-08-19

This is the newest snapshot release to support the manuscript titled An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control published in npj Systems Biology and Applications, 19 August 2022.

One of the most significant changes is an upgrade from Python 2.7 to Python 3.8.

Biologically, the new version supports several new features by selecting simulation options in runSim.py with the noted flags or in fw_queue.py with the noted environment variables. Additional details are in the Methods section of the paper:

• ppGpp dynamics and regulation of gene expression, RNAP binding, and translation (--ppgpp-regulation or PPGPP_REGULATION=1)
• Dynamics of amino acid biosynthesis (--mechanistic-translation-supply or MECHANISTIC_TRANSLATION_SUPPLY=1)
• Dynamics of amino acid transport (--mechanistic-aa-transport or MECHANISTIC_AA_TRANSPORT=1)
• Dynamics of tRNA charging and ribosome elongation (--trna-charging or TRNA_CHARGING=1)
• tRNA attenuation (--trna-attenuation or TRNA_ATTENUATION=1)
• New environmental conditions (add or remove single amino acids, amino acid combinations, acetate and succinate) with new variants (--variant or VARIANT)

To run simulations as described in the paper with the entire set of new growth rate control options enabled, the following set of parameters should be used with fw_queue.py (along with any other desired options):

TRNA_ATTENUATION=1 PPGPP_REGULATION=1 MECHANISTIC_TRANSLATION_SUPPLY=1 MECHANISTIC_AA_TRANSPORT=1 \
    AA_SUPPLY_IN_CHARGING=1 D_PERIOD_DIVISION=1 MECHANISTIC_REPLISOME=0 TIMESTEP_MAX=1 \
    python runscripts/fireworks/fw_queue.py

Other updates from the previously released version:

• Framework to run simulations with Google Cloud Platform
• Flat files describing genes and reactions have been updated to reflect newer versions on EcoCyc and additional data sources for other parameters have been added
• Many analysis plots have been added or updated
• Improvements to the modeling framework and helper classes and functions
• Bug fixes and performance improvements

Science-2020-07-24

This release snapshot Science-2020-07-24 goes with the paper Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation published in Science, 24 July 2020.

See docs/README.md for info on setting up the Python 2.7 runtime environment to run this release.

(The next release will contain lots of work done since this snapshot forked off, and it runs on Python 3.8.)