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Table 2 GFlasso processing pipeline

From: Enhancing the usability and performance of structured association mapping algorithms using automation, parallelization, and visualization in the GenAMap software system

Step No.

Description

Stage

No. Jobs using yeast data

Av. Time/Job on yeast data

Hours:min:sec

Actual time from start to finish

Time saved via parallelization

1

Lasso stage 1

Preprocessing SNPs

23

00:00:25

00:02:59

00:06:36

2

Lasso validation error

Preprocessing SNPs

1

00:02:14

00:02:14

00:00:00

3

Lasso stage 2

Preprocessing SNPs

23

00:01:16

00:03:40

00:25:34

4

Lasso validation error

Preprocessing SNPs

1

00:00:39

00:00:39

00:00:00

5

Marker Processing

Preprocessing SNPs

1

00:00:10

00:00:10

00:00:00

6

Connected component analysis

Preprocessing traits

1

00:00:56

00:00:56

00:00:00

7

Spectral clustering

Preprocessing traits

118

00:00:56

00:06:44

01:43:03

8

Trait Processing

Preprocessing traits

1

00:06:02

00:06:02

00:00:00

9

GFlasso stage 1

GFlasso optimization

130

00:51:34

01:41:36

110:02:30

10

GFlasso validation error stage 1

GFlasso optimization

1

01:43:01

01:43:01

00:00:00

11

GFlasso stage 2

GFlasso optimization

130

05:49:08

29:27:45

726:59:05

12

GFlasso validation error stage 2

GFlasso optimization

1

00:45:26

00:45:26

00:00:00

13

GFlasso stage 3

GFlasso optimization

130

03:18:04

10:56:18

418:12:37

14

GFlasso validation error stage 3

GFlasso optimization

1

00:56:32

00:56:32

00:00:00