Nicolekalcic Week 9

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Journal Week 9 - Nicole Kalcic

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


Part 2: Web Service API Exploration

I was confused with this part of the assignment, but Arash and Zach met up to sort out questions, and I was then able to proceed with the information relayed to me. Arash and I used the same genes in order to compare work and URLs, although Arash walked me through what he did because he is more experienced with CS than I am. He explained to me that on the Ensembl API webpage, we could use the gene name to find the command that returned the json file we needed. You can simply change the example gene, "homo_sapien", to the gene we used, "saccharomyces_cerevisiae" in the url. and put the name of a random yeast file to test it. Arash showed this to me first because he found it to be the easiest way. It is important to note that the assignment instructions point to [1]. You can use the ID retrieved from the command number 1 and place it in the command given on this page in order to complete this according to the assignment.

The deliverable is as follows:

(To find the json file for any other gene, replace the text that says "GENE" in the url with your desired gene name.)

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

Put the ID retrieved from the json file into the URL.

(Json file above is sufficient)

curl 'http://rest.ensembl.org/lookup/id/ID?expand=1' -H 'Content-type:application/json'

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


Nicole Kalcic's Homepage


Assignment: Week 1 Shared Journal: Class Journal Week 1 Individual Journal: User Page

Assignment: Week 2 Shared Journal: Class Journal Week 2 Individual Journal: Nicolekalcic Week 2

Assignment: Week 3 Shared Journal: Class Journal Week 3 Individual Journal: Nicolekalcic Week 3

Assignment: Week 4 Shared Journal: Class Journal Week 4 Individual Journal: Nicolekalcic Week 4

Assignment: Week 5 Shared Journal: Class Journal Week 5 Individual Journal: Nicolekalcic Week 5

Assignment: Week 6 Shared Journal: Class Journal Week 6 Individual Journal: Nicolekalcic Week 6

Assignment: Week 7 Shared Journal: Class Journal Week 7 Individual Journal: NicoleKalcic Week 7

Assignment: Week 8 Shared Journal: Class Journal Week 8 Individual Journal: NicoleKalcic Week 8

Assignment: Week 9 Shared Journal: Class Journal Week 9 Individual Journal: Nicolekalcic Week 9

Assignment: Week 10 Shared Journal: Class Journal Week 10 Individual Journal: Nicolekalcic Week 10

Assignment: Week 11 Shared Journal: Not Available Individual Journal: Nicolekalcic Week 11

Assignment: Week 12 Shared Journal: Not Available Individual Journal: Nicolekalcic Week 12

Assignment: Week 14 Shared Journal: Not Available Individual Journal: Nicolekalcic Week 14

Assignment: Week 15 Shared Journal: Not Available Individual Journal: Nicolekalcic Week 15

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