Nicolekalcic Week 9

Journal Week 9 - Nicole Kalcic

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Part 1: GRNsight Testing

For the purposes of testing I used these 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

A test passing means that it satisfied all the criteria detailed in the instructions.

Arash and I used the same files in order to compare after testing.

• Test 1:
  • Instructions:
    • Load Graph - File Menu > Open
    • Restrict Graph to Viewport - Check
    • Hide/Show Edge Weights - Select "Show With Mouse Over"
  • PASSED
• Test 2:
  • Instructions:
    • Load Graph - File Menu > Import SIF
    • Restrict Graph to Viewport - Check
    • Hide/Show Edge Weights - Select "Show With Mouse Over"
  • PASSED
• Test 3:
  • Instructions:
    • Load Graph - File Menu > Import GraphML
    • Restrict Graph to Viewport - Check
    • Hide/Show Edge Weights - Select "Show With Mouse Over"
  • PASSED
• Test 4:
  • Instructions:
    • Load Graph - File Menu > Open
    • Restrict Graph to Viewport - Uncheck
    • Hide/Show Edge Weights - Select "Show With Mouse Over"
  • PASSED
• Test 5:
  • • Load Graph - File Menu > Import SIF
    • Restrict Graph to Viewport - Uncheck
    • Hide/Show Edge Weights - Select "Show With Mouse Over"
  • Instructions:
  • PASSED
• Test 6:
  • Instructions:
    • Load Graph - File Menu > Import GraphML
    • Restrict Graph to Viewport - Uncheck
    • Hide/Show Edge Weights - Select "Show With Mouse Over"
  • PASSED
• Test 7:
  • Instructions:
    • Load Graph - File Menu > Open
    • Restrict Graph to Viewport - Check
    • Hide/Show Edge Weights - Select "Always Show Edge Weights"
  • PASSED
• Test 8:
  • Instructions:
    • Load Graph - File Menu > Import SIF
    • Restrict Graph to Viewport - Check
    • Hide/Show Edge Weights - Select "Always Show Edge Weights"
  • PASSED
• Test 9:
  • Instructions
    • Load Graph - File Menu > Import GraphML
    • Restrict Graph to Viewport - Check
    • Hide/Show Edge Weights - Select "Always Show Edge Weights"
  • PASSED
• Test 10:
  • Instructions:
    • Load Graph - File Menu > Open
    • Restrict Graph to Viewport - Uncheck
    • Hide/Show Edge Weights - Select "Always Show Edge Weights"
  • PASSED
• Test 11:
  • Instructions:
    • Load Graph - File Menu > Import SIF
    • Restrict Graph to Viewport - Uncheck
    • Hide/Show Edge Weights - Select "Always Show Edge Weights"
  • PASSED
• Test 12:
  • Instructions:
    • Load Graph - File Menu > Import GraphML
    • Restrict Graph to Viewport - Uncheck
    • Hide/Show Edge Weights - Select "Always Show Edge Weights"
  • PASSED
• Test 13:
  • Instructions:
    • Load Graph - File Menu > Open
    • Restrict Graph to Viewport - Check
    • Hide/Show Edge Weights - Select "Never Show Edge Weights"
  • PASSED
• Test 14:
  • Instructions:
    • Load Graph - File Menu > Import SIF
    • Restrict Graph to Viewport - Check
    • Hide/Show Edge Weights - Select "Never Show Edge Weights"
  • PASSED
• Test 15:
  • Instructions:
    • Load Graph - File Menu > Import GraphML
    • Restrict Graph to Viewport - Check
    • Hide/Show Edge Weights - Select "Never Show Edge Weights"
  • PASSED
• Test 16:
  • Instructions:
    • Load Graph - File Menu > Open
    • Restrict Graph to Viewport - Uncheck
    • Hide/Show Edge Weights - Select "Never Show Edge Weights"
  • PASSED
• Test 17:
  • Instructions:
    • Load Graph - File Menu > Import SIF
    • Restrict Graph to Viewport - Uncheck
    • Hide/Show Edge Weights - Select "Never Show Edge Weights"
  • PASSED
• Test 18:
  • Instructions:
    • Load Graph - File Menu > Import GraphML
    • Restrict Graph to Viewport - Uncheck
    • Hide/Show Edge Weights - Select "Never Show Edge Weights"
  • PASSED

Acknowledgements

• I communicated with my partner Arash Lari about the assignment. We met once and then texted about the rest of the assignment. Arash met with Zach Van Ysseldyk and Antoni Porras in order to help us complete the second part of the assignment.
• Dr. Dondi gave in class lectures on how to begin the API web service exploration and provided the class with several online resources.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Nicolekalcic (talk) 18:35, 30 October 2017 (PDT)

References

• LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9

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