ArashLari Week 9

Electronic Workbook

For the purposes of testing I used the following files:

• 21-genes_31-edges_Schade-data_estimation_output.xlsx
• 21-genes_31-edges_Schade-data_estimation_output.sif
• 21-genes_31-edges_Schade-data_estimation_output.graphml

Then proceed to the GRNSight-beta from the link provided in the instructions for this assignment

Test 1

Instructions:

• Load Graph - File Menu -> Open
• Restrict Graph to Viewport - Check
• Hide/Show Edge Weights - Select "Show With Mouse Over"

Result: PASSED

Test 2

Instructions:

• Load Graph - File Menu -> Import SIF
• Restrict Graph to Viewport - Check
• Hide/Show Edge Weights - Select "Show With Mouse Over"

Result: PASSED

Test 3

Instructions:

• Load Graph - File Menu -> Import GraphML
• Restrict Graph to Viewport - Check
• Hide/Show Edge Weights - Select "Show With Mouse Over"

Result: PASSED

Test 4

Instructions:

• Load Graph - File Menu -> Open
• Restrict Graph to Viewport - Uncheck
• Hide/Show Edge Weights - Select "Show With Mouse Over"

Result: PASSED

Test 5

Instructions:

• Load Graph - File Menu -> Import SIF
• Restrict Graph to Viewport - Uncheck
• Hide/Show Edge Weights - Select "Show With Mouse Over"

Result: PASSED

Test 6

Instructions:

• Load Graph - File Menu -> Import GraphML
• Restrict Graph to Viewport - Uncheck
• Hide/Show Edge Weights - Select "Show With Mouse Over"

Result: PASSED

Test 7

Instructions:

• Load Graph - File Menu -> Open
• Restrict Graph to Viewport - Check
• Hide/Show Edge Weights - Select "Always Show Edge Weights"

Result: PASSED

Test 8

Instructions:

• Load Graph - File Menu -> Import SIF
• Restrict Graph to Viewport - Check
• Hide/Show Edge Weights - Select "Always Show Edge Weights"

Result: PASSED

Test 9

Instructions:

• Load Graph - File Menu -> Import GraphML
• Restrict Graph to Viewport - Check
• Hide/Show Edge Weights - Select "Always Show Edge Weights"

Result: PASSED

Test 10

Instructions:

• Load Graph - File Menu -> Open
• Restrict Graph to Viewport - Uncheck
• Hide/Show Edge Weights - Select "Always Show Edge Weights"

Result: PASSED

Test 11

Instructions:

• Load Graph - File Menu -> Import SIF
• Restrict Graph to Viewport - Uncheck
• Hide/Show Edge Weights - Select "Always Show Edge Weights"

Result: PASSED

Test 12

Instructions:

• Load Graph - File Menu -> Import GraphML
• Restrict Graph to Viewport - Uncheck
• Hide/Show Edge Weights - Select "Always Show Edge Weights"

Result: PASSED

Test 13

Instructions:

• Load Graph - File Menu -> Open
• Restrict Graph to Viewport - Check
• Hide/Show Edge Weights - Select "Never Show Edge Weights"

Result: PASSED

Test 14

Instructions:

• Load Graph - File Menu -> Import SIF
• Restrict Graph to Viewport - Check
• Hide/Show Edge Weights - Select "Never Show Edge Weights"

Result: PASSED

Test 15

Instructions:

• Load Graph - File Menu -> Import GraphML
• Restrict Graph to Viewport - Check
• Hide/Show Edge Weights - Select "Never Show Edge Weights"

Result: PASSED

Test 16

Instructions:

• Load Graph - File Menu -> Open
• Restrict Graph to Viewport - Uncheck
• Hide/Show Edge Weights - Select "Never Show Edge Weights"

Result: PASSED

Test 17

Instructions:

• Load Graph - File Menu -> Import SIF
• Restrict Graph to Viewport - Uncheck
• Hide/Show Edge Weights - Select "Never Show Edge Weights"

Result: PASSED

Test 18

Instructions:

• Load Graph - File Menu -> Import GraphML
• Restrict Graph to Viewport - Uncheck
• Hide/Show Edge Weights - Select "Never Show Edge Weights"

Result: PASSED

Observations

While they all passed, it should be noted that for tests 7 through 12, the user can technically see all the numbers, but sometimes they might overlap and become hard to read. This can be seen in the following image:

Ensemble URL

curl 'http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/ACT1?' -H 'Content-type:application/json'

Acknowledgements

ArashLari (talk) 15:36, 30 October 2017 (PDT) Arash Lari

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 13
• Week 14
• Week 15
• Week 16

Journal Entries:

• ArashLari Week 2
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• ArashLari Week 4
• ArashLari Week 5
• ArashLari Week 6
• ArashLari Week 7
• ArashLari Week 8
• ArashLari Week 9
• ArashLari Week 10
• ArashLari Week 11
• ArashLari Week 12
• ArashLari Week 13
• ArashLari Week 14
• ArashLari Week 15
• ArashLari Week 16

Shared Journals:

• ArashLari Week 1 Journal
• ArashLari Week 2 Journal
• ArashLari Week 3 Journal
• ArashLari Week 4 Journal
• ArashLari Week 5 Journal
• ArashLari Week 6 Journal
• ArashLari Week 7 Journal
• ArashLari Week 8 Journal
• ArashLari Week 9 Journal
• ArashLari Week 10 Journal
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