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. 2021 Nov 10;22:547. doi: 10.1186/s12859-021-04417-9

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 8 — Visualization of the scaling behavior of the sub-models of JCVI-syn3A [31]. The plot shows the correlation between the included number of non-essential uptake reactions, the number of resulting EFMs, and the run times. The sub-models are plotted on the x-axis and referred to by their number e.g. 00 refers to $s m_{00}$ . Y-axis 1 shows the number of calculated/predicted EFMs, y-axis 2 the required/predicted run time in days using 960 threads on the VSC. Both axes are in logarithmic scale. Full symbols (dots and squares) refer to measured run times and computed EFMs (sub-models $s m_{00}$ to $s m_{15}$ ). The corresponding equations for the non-logarithmic representation of the calculated results are $y 1 = 264629 e^{0.6678 x}$ with $R^{2} = 0.9997$ and $y 2 = 3 E^{- 5} e^{0.7508 x}$ with $R^{2} = 0.9986$ . Empty symbols refer to estimated data (sub-models $s m_{16}$ to $s m_{22}$ ) with the assumption that the slopes for both curves remain the same over all sub-models. Sub-model $s m_{00}$ refers to the smallest sub-model that includes none of the 22 non-essential uptake reactions and $s m_{22}$ to the full model that includes all uptake reactions