Skip to main content

Table 1 Models

From: BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

Model ID

B1

B2

B3

B4

B5

B6

Model Ref

[25]

[23]

[24]

[26]

[27]

[29]

Cell

S. cerevisiae

E. coli

E. coli

CHO

Generic

Drosophila

      

melanogaster

Description

Metabolic:

Metabolic:

Metabolic: CCM

Metabolic

Signal

Developmental

level

genome scale

CCM

& transcription

 

transduction

GRN (spatial)

Parameters

1759

116

178

117

86

37

Dynamic states

276

18

47

34

26

108 –212

Observed states

44

9

47

13

6

108 –212

Experiments

1

1

1

1

10

1

Data points

5280

110

7567

169

96

1804

Data type

simulated

measured

simulated

simulated

simulated

measured

Noise level

σ=5%

real

no noise

variable

σ=5%

real

  1. Main features of the benchmark models. The standard deviation, σ, is given in those cases where artificial noise with constant variance was added to the data.