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Table 1 Overview of metabolic models and general polyhedra used for performance tests and comparisons of efmtool [12] and mplrs [1]. For metabolic models the number of rows corresponds to the number of metabolites and the number of columns to the number of reactions with numbers in brackets referring to the number of reversible reactions. For the metabolic models the dimensions of the original uncompressed model and a comparison between the compressions of efmtool and EFMlrs are given. For the polytopes, the matrix dimensions of the original uncompressed (uncmp.) polytope P, the transformed uncompressed and via efmtool compressed model in the flux cone FC are shown. All polytopes were obtained from the lrs homepage [27]. comp., compression; Deg., degree of degeneracy

From: EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search

Model

uncmp. P

uncmp. FC

efmtool comp.

EFMIrs comp.

EFMs

Deg.

Columns

Rows

Columns

Rows

Columns

Rows

Columns

Rows

EColiCentral [28]

  

71 (15)

53

44 (11)

26

44 (11)

21

429,276

High

EColiCore2 [29]

  

82 (22)

54

58 (18)

30

58 (18)

30

34,896,477

High

iPS189 [30]

  

277 (21)

271

67 (13)

42

63 (13)

35

3,252,686

High

JCVI-syn3A [31]

  

316 (8)

286

100 (7)

50

100 (7)

48

?

High

cp6 [27]

16 (15)

368

384 (15)

368

384 (15)

368

  

32

High

bv7 [27]

57 (56)

69

106 (56)

69

49 (0)

12

  

5,040

High

mit71 [27]

61 (60)

71

132 (60)

71

132 (60)

71

  

3,149,579

Moderate

fq48-19 [27]

19 (18)

48

67 (18)

48

48 (0)

29

  

119,184

Moderate

mit [27]

9 (8)

729

738 (8)

729

729 (0)

720

  

4,862

Moderate

perm10 [27]

11 (10)

1023

1033 (10)

1023

1033 (10)

1023

  

3628800

Simple