ArashLari Week 9 - Revision history

ArashLari: /* Electronic Workbook */ clarifying what passed means

2017-10-31T06:12:31Z

‎Electronic Workbook: clarifying what passed means

ArashLari: /* Deliverable */ formatting

2017-10-31T06:11:28Z

‎Deliverable: formatting

ArashLari: /* Web Service API Exploration */ Made it generic and added a "how i did it"

2017-10-31T06:10:52Z

‎Web Service API Exploration: Made it generic and added a "how i did it"

ArashLari: /* Ensemble URL */ updated deliverable

2017-10-31T06:03:54Z

‎Ensemble URL: updated deliverable

ArashLari: /* Acknowledgements */ added them

2017-10-31T06:01:35Z

‎Acknowledgements: added them

ArashLari: /* Observations */ uploaded image

2017-10-31T05:59:51Z

‎Observations: uploaded image

ArashLari: observation added

2017-10-31T05:58:12Z

observation added

ArashLari: Results (they all passed)

2017-10-31T05:56:48Z

Results (they all passed)

ArashLari at 05:55, 31 October 2017

2017-10-31T05:55:11Z

ArashLari: All test instructions

2017-10-31T05:53:41Z

All test instructions

@@ Line 5: / Line 5: @@
 *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:

@@ Line 123: / Line 123: @@
 ==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'
+ 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'
+ curl 'http://rest.ensembl.org/lookup/id/ID?expand=1' -H 'Content-type:application/json'
 = Acknowledgements =

@@ Line 120: / Line 120: @@
 = 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 [http://rest.ensembl.org/documentation/info/lookup] 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 "ACT1" in the url with your desired gene name.
+*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/ACT1?' -H 'Content-type:application/json'
+curl 'http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/GENE?' -H 'Content-type:application/json'
 = Acknowledgements =

@@ Line 119: / Line 119: @@
 [[File:ArashObservation.png]]
-= Ensemble URL =
+= Web Service API Exploration =
 curl 'http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/ACT1?' -H 'Content-type:application/json'

@@ Line 123: / Line 123: @@
 = 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.
 [[User:ArashLari|ArashLari]] ([[User talk:ArashLari|talk]]) 15:36, 30 October 2017 (PDT)
 {{Template:ArashLari}}

@@ Line 115: / Line 115: @@
 == 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.
 = Ensemble URL =

@@ Line 113: / Line 113: @@
 *Hide/Show Edge Weights - Select "Never Show Edge Weights"
 Result: '''PASSED'''
 = Ensemble URL =

@@ Line 10: / Line 10: @@
 *Restrict Graph to Viewport - Check
 *Hide/Show Edge Weights - Select "Show With Mouse Over"
-Result:
+Result: '''PASSED'''
 == Test 2 ==
 Instructions:
@@ Line 16: / Line 16: @@
 *Restrict Graph to Viewport - Check
 *Hide/Show Edge Weights - Select "Show With Mouse Over"
 == Test 3 ==
 Instructions:
@@ Line 21: / Line 22: @@
 *Restrict Graph to Viewport - Check
 *Hide/Show Edge Weights - Select "Show With Mouse Over"
 == Test 4 ==
 Instructions:
@@ Line 26: / Line 28: @@
 *Restrict Graph to Viewport - Uncheck
 *Hide/Show Edge Weights - Select "Show With Mouse Over"
 == Test 5 ==
 Instructions:
@@ Line 31: / Line 34: @@
 *Restrict Graph to Viewport - Uncheck
 *Hide/Show Edge Weights - Select "Show With Mouse Over"
 == Test 6 ==
 Instructions:
@@ Line 36: / Line 40: @@
 *Restrict Graph to Viewport - Uncheck
 *Hide/Show Edge Weights - Select "Show With Mouse Over"
 == Test 7 ==
 Instructions:
@@ Line 41: / Line 46: @@
 *Restrict Graph to Viewport - Check
 *Hide/Show Edge Weights - Select "Always Show Edge Weights"
 == Test 8 ==
 Instructions:
@@ Line 46: / Line 52: @@
 *Restrict Graph to Viewport - Check
 *Hide/Show Edge Weights - Select "Always Show Edge Weights"
 == Test 9 ==
 Instructions:
@@ Line 51: / Line 58: @@
 *Restrict Graph to Viewport - Check
 *Hide/Show Edge Weights - Select "Always Show Edge Weights"
 == Test 10 ==
 Instructions:
@@ Line 56: / Line 64: @@
 *Restrict Graph to Viewport - Uncheck
 *Hide/Show Edge Weights - Select "Always Show Edge Weights"
 == Test 11 ==
 Instructions:
@@ Line 61: / Line 70: @@
 *Restrict Graph to Viewport - Uncheck
 *Hide/Show Edge Weights - Select "Always Show Edge Weights"
 == Test 12 ==
 Instructions:
@@ Line 66: / Line 76: @@
 *Restrict Graph to Viewport - Uncheck
 *Hide/Show Edge Weights - Select "Always Show Edge Weights"
 == Test 13 ==
 Instructions:
@@ Line 71: / Line 82: @@
 *Restrict Graph to Viewport - Check
 *Hide/Show Edge Weights - Select "Never Show Edge Weights"
 == Test 14 ==
 Instructions:
@@ Line 76: / Line 88: @@
 *Restrict Graph to Viewport - Check
 *Hide/Show Edge Weights - Select "Never Show Edge Weights"
 == Test 15 ==
 Instructions:
@@ Line 81: / Line 94: @@
 *Restrict Graph to Viewport - Check
 *Hide/Show Edge Weights - Select "Never Show Edge Weights"
 == Test 16 ==
 Instructions:
@@ Line 86: / Line 100: @@
 *Restrict Graph to Viewport - Uncheck
 *Hide/Show Edge Weights - Select "Never Show Edge Weights"
 == Test 17 ==
 Instructions:
@@ Line 91: / Line 106: @@
 *Restrict Graph to Viewport - Uncheck
 *Hide/Show Edge Weights - Select "Never Show Edge Weights"
 == Test 18 ==
 Instructions:
@@ Line 96: / Line 112: @@
 *Restrict Graph to Viewport - Uncheck
 *Hide/Show Edge Weights - Select "Never Show Edge Weights"
 = Ensemble URL =