ArashLari Week 9

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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

  • Note: A test passing means that it satisfied all the criteria detailed in the instructions

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:

ArashObservation.png

Web Service API Exploration

While I was originally confused as to what the assignment was asking for, once we figured it out it became much clearer. I simply went to the ensemble api page, and found the command that returned the json file using the gene name. The example given on the website had the species as "homo_sapien", so i changed that to "saccharomyces_cerevisiae" in the url and put the name of a random yeast file to test it. This process worked, but because the instructions pointed to [1] I used the ID retrieved from the first command and placed it in the command given from this page to do it the way the instructions alluded to.

Deliverable

  • Note: to find the json file for any other gene, simply replace the text that says "GENE" in the url with your desired gene name. (this code won't work as it's generic)
curl 'http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/GENE?' -H 'Content-type:application/json'

From there you could put the id retrieved from the json file into the url where it says "ID" in uppercase, but the json file above also returns all the relevant information already. 

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

Acknowledgements

Nicole Kalcic was my partner and we met up once and worked over text message. I also worked with Zach Van Ysseldyk and Antoni Porras on the Web API section and we figured out how to return the desired deliverable together. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. ArashLari (talk) 15:36, 30 October 2017 (PDT) Arash Lari

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments


Journal Entries:

Shared Journals:

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