Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly ================================================================================== Tyler M. Earnest[1,2], Jonathan Lai[3], Ke Chen[3,4], Michael J. Hallock[5], James R. Williamson[6,7,8], Zaida Luthey-Schulten[1,2,3,*] [1] Center for the Physics of Living Cells, [2] Department of Physics, and [3] Department of Chemistry, University of Illinois, Urbana, Illinois; [4] Department of Bioengineering, University of California, San Diego, La Jolla, California; and [5] School of Chemical Sciences, University of Illinois, Urbana, Illinois; [6] Department of Integrative Structural and Computational Biology, [7] Department of Chemistry, and [8] Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California, [*] Correspondence to zan@illinois.edu doi:10.1016/j.bpj.2015.07.030 Description of model files ========================== We provide our models described in this publication in the hopes that they will be of further use to the community. Please direct any general inquiries to Zan Luthey-Schulten . In vitro assembly models ------------------------ The full and reduced models for the in vitro assembly process are provided in the files * highTfull.xml * highTreduced.xml * lowTfull.xml * lowTreduced.xml where "highT" refers to the model fit to the 40°C experiment, and "lowT" refers to the low temperature experiment at 15°C. The files provided for the in vitro model are in SBML Level 2 Version 4. Our published results were computed using a custom code to allow for faster global optimization, however similar results can be obtained using COPASI. These files are capable of reproducing the data necessary to compute the pulse/chase time courses presented in figures 2 and 5, as well as the integrated reaction fluxes presented in figures 3 and 6, using an integration time of 6e4 seconds. Please contact Tyler Earnest regarding any difficulties that arise in using these SBML files. In vivo biogenesis model ------------------------ The in vivo biogenesis model is provided in the native Lattice Microbes format (based on HDF5) and is found in * wholeCell.lm The oldest version of Lattice Microbes capable of executing this simulation is LM 2.2.1 due to changes necessary to accommodate the number of reactions in this model. This model file will reproduce the data necessary to reproduce the results presented in figures 7 and 8 using a simulation time of 7200 seconds. Please contact Tyler Earnest and Mike Hallock regarding any trouble using this input file with Lattice Microbes.