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Table 4 Generation of sampling warmup points using dynamic load balancing

From: VFFVA: dynamic load balancing enables large-scale flux variability analysis

Model

createWarmupMATLAB

createWarmupVF

Cores

1

1

2

4

8

16

32

Ecoli_core

149

2.8

1.8

0.8

0.7

0.5

0.5

P_putida

385

12.5

13

8

4

2

2

EcoliK12

801

49

43

23

10.4

9.5

9.1

Recon2

11346

288

186

30

32

24

21

E_Matrix

NA*

602

508

130

52

43

43

Ec_Matrix

NA*

5275

4986

924

224

118

117

  1. *The generation of warmup points of E_Matrix and Ec_Matrix models did not converge after 20000s. The creation of warmup points can vary widely between runs as it involves the generation of a random c vector in the linear program. The runs were repeated three times and the average was reported.
  2. The run times of the generation of 30,0000 warmup points for sampling of six metabolic models using the standard serial implementation createWarmupMATLAB and the dynamic load balanced implementation createWarmupVF
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BMC Bioinformatics

ISSN: 1471-2105

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