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Table 3 Benchmarking the speed of Gel mathematics on massive graphs

From: Mango: combining and analyzing heterogeneous biological networks

Gel operation.

Time (in seconds)

Average

4 M+=8 K

0.92, 0.35, 0.27, 0.60, 0.56

0.54

8 K+=4 M

1.25, 1.15, 1.03, 1.02, 1.02

1.09

4 M−=8 K

0.52, 0.33, 0.62, 0.33, 0.25

0.41

8 K−=4 M

1.09, 1.28, 1.09, 1.16, 1.19

1.16

4 M.+=8 K

0.69, 0.60, 0.57, 0.31, 0.40

0.51

8 K.+=4 M

12.06, 12.09, 12.05, 12.23, 12.32

12.15

4 M.−=8 K

0.55, 0.41, 0.25, 0.26, 0.32

0.36

8 K.−=4 M

0.90, 0.85, 0.83, 0.98, 0.74

0.86

4 M∗=8 K

22.94, 23.74, 23.35, 22.98, 23.03

23.21

8 K∗=4 M

36.75, 35.33, 35.23, 35.38

35.67

copy=4 M

7.90, 7.76, 7.85, 7.73, 7.87

7.82

copy=8 K

0.30, 0.52, 0.45, 0.34, 0.29

0.38

  1. The 4 M link network is the gene correlation network generated by WGCNA. The 8 K link network is the combined KEGG pathway network. Benchmarks were performed consecutively on a 2010 Mac mini that has 8 Gb and runs 64-bit MacOS X 10.10 with a 2.4 GHz Intel Core 2 Duo processor. The time to copy the networks is also listed. All operations, including the copy operation, were performed using single thread in RAM