Index of papers in PLOS Comp. Biol. that mention

**parameter sets**

Abstract | This thermodynamically safe parameterization relies on the definition of a reference state upon which feasible parameter sets can be efficiently sampled. |

Dissecting enzyme catalysis: assessing the impact of reaction molecularity | For the aforementioned cases, the sums of the blue and red areas represent the 95% confidence region of all the thermodynamically feasible parameter sets . |

Dissecting enzyme catalysis: assessing the impact of reaction molecularity | Such increased area point to a greater diversity of feasible parameter sets under more thermodynamically favourable conditions. |

Dissecting enzyme catalysis: assessing the impact of reaction molecularity | On the contrary, more homogeneous parameter sets can be found closer to equilibrium, i.e. |

Introduction | All use simplified kinetic expressions (loss of generality) and most ignore intrinsic thermodynamic constraints between kinetic parameters, hence they will sample infeasible parameter sets . |

Parameterization and sampling of the catalytic mechanism | This sampling strategy ensures that any parameter set sampled satisfies both pattern and kinetic constraints (Fig. |

Sampling functional contributions: catalytic and regulatory effects | Parameter set accuracy check |

Sampling functional contributions: catalytic and regulatory effects | The sampling procedure generates only feasible parameter sets . |

Sampling functional contributions: catalytic and regulatory effects | Since this parameterization is built upon a reference point, this can be validated by confirming that the parameter set produces the reference flux at the reference point, i.e. |

parameter sets is mentioned in 18 sentences in this paper.

Topics mentioned in this paper:

- rate constants (19)
- parameter sets (18)
- substrates (15)

Gene expression simulations | Using evolutionary optimization, we found parameter sets that show excellent agreement with the fluorescence in situ hybridization (FISH) data for sna, vnd, 50g, and zen (Fig. |

Optimization | .p15]N, are evaluated and compared to the data using a residual sum of squares calculation: where th = dl-Venus data, clth 2 measurement uncertainty—both corresponding to simulated nucleus h and timepoint k—and SN is the ordinary least squares estimate of the scale factor that minimizes the difference between X and Y across all time and space coordinates and for parameter set N. Um“; and Wnuc are the dimensionless versions of nuclear dl and nuclear dl/ Cact complex, respectively (see Equations (1) and (3)). |

Optimization | After the 25th generation, we keep the top 100 parameter sets as the end product of each evolutionary optimization run. |

Optimization | A similar method is used to find parameter sets for simulations of gene eXpression, with l = 250, [,4 = 50. |

Parameter analysis of extended dI/Cact model | Each evolutionary optimization run that was used to fit our model to the dl-Venus data set resulted in 100 closely-clustered parameter sets . |

Parameter analysis of extended dI/Cact model | We represent each evolutionary optimization run by an average parameter set , in which we calculate the mean and standard deviation (weighted by RSS error; see Methods and 81 Text) for each parameter, across all 100 sets. |

Parameter analysis of extended dI/Cact model | We collected 254 such runs, resulting in 254 average parameter sets that are nearly indistinguishable in terms of their average RSS error (see Methods and 81 Text), yet vary in the values of their parameters, as has been observed previously for biological models [25, 26]. |

Simulations of dI/Cact dynamics | We thus fit the sum of free nuclear d1 (1) and nuclear dl/Cact complex (3) in our extended model to the dl-Venus data set in both space and time, revealing parameter sets that show an excellent fit to the data (see Fig. |

parameter sets is mentioned in 10 sentences in this paper.

Topics mentioned in this paper:

- gene expression (42)
- parameter sets (10)
- Sensitivity analysis (6)

Power calculation for large forest surveys | For these forests with k = 10“, there were two distinct parameter sets that match the characteristics of the empirical data. |

Power calculation for large forest surveys | Pasoh is not included because no parameter sets consistent with the empirical data were found with k 2 10—4. |

Power calculation for large forest surveys | While there were two discrete parameter sets each that matched the richness and evenness of Pasoh and Lambir (one where 6 was low and m high, and one where 6 was higher and m lower), the power of the test with these parameters was always low. |

Power calculations for particular experiments | Here, we choose parameter sets such that the model best describes a set of summary statistics of empirical data sets, specifically: species richness and Shannon index. |

Power calculations for particular experiments | There will therefore be a discrete set of parameter values where the mean species richness and mean Shannon index of samples from the model match the empirical data sets; in most cases we found only one such parameter set , though in some cases there were two and in others there were none because the model produced a Shannon index that was always higher than, or always lower than, the empirical data. |

Power calculations for particular experiments | We performed this procedure, for a set of candidate values of the non-neutral parameter, to generate parameter sets resembling three tropical forest data sets belonging to the CTFS network to which neutral theory has successfully been fitted in the past [46]: Barro Colorado Island, Pasoh Forest Reserve, and Lambir Hills National Park [37—39]. |

Testing the neutral null model | For the i’th sample neutral data set, compute the corresponding maximum likelihood estimate parameter set ijN) and maximum likelihood L(X | mm, 03%,) using the same procedure as used for XT. |

parameter sets is mentioned in 7 sentences in this paper.

Topics mentioned in this paper:

- model parameters (16)
- null model (9)
- sample size (8)

Supporting Information | The correlation with tumor survival in this case is lower than the correlation of tumor survival with MP1 across the entire parameter set (Fig. |

Supporting Information | The correlation with tumor survival in this case is higher than that observed across the entire parameter set . |

Supporting Information | This movie shows a representative simulation that results in tumor survival under the base parameter set . |

Systematic characterization of TME network robustness and the role of heterogeneities | With a few exceptions (detailed in the caption of SS Fig), the sensitivity of simulation outcomes to the parameters was found to be less informative over this larger parameter set, and for this reason we focused our analysis on the initial parameter set (above). |

parameter sets is mentioned in 5 sentences in this paper.

Topics mentioned in this paper:

- immune cells (9)
- sensitivity analysis (8)
- tumor growth (8)

Ordinary differential equation modeling | To find the optimal parameter sets that describe the experimental data for each model structure, we performed parameter estimations. |

Ordinary differential equation modeling | To prove the validity of our optimization procedure, a Latin hypercube sampling approach with 1000 initial parameter sets has been performed (S7 Fig). |

Ordinary differential equation modeling | Therefore, the best performing model structure in combination with the estimated parameter set is described by the lowest -Zlog(L). |

Supporting Information | Multistart optimization with 1000 initial parameter sets for model 4_8_12. |

Supporting Information | A) Mul-tistart optimization has been performed With 1000 initial parameter sets . |

parameter sets is mentioned in 5 sentences in this paper.

Topics mentioned in this paper:

- phosphorylation (52)
- signaling pathways (32)
- MAPK (29)

Cell-specific models | In neuronal modeling, it has become clear that different combinations of conductance parameter sets can give rise to the same activity pattern and that using average values of the conductances may fail to generate that pattern [10,11,37]. |

Complex driving protocols and objectives | Finally, the iterative optimization approach [31] refined our in silico parameter estimation by decreasing the spread of the returned parameter sets , which caused the prediction error to again decrease by an order of magnitude. |

GA optimization using a single action potential | Although the optimized model action potential matches the optimization objective to a very high degree, the estimated parameter set does not match that of the FR model (Fig 1E). |

parameter sets is mentioned in 3 sentences in this paper.

Topics mentioned in this paper:

- action potential (38)
- experimental data (21)
- parameter estimation (19)