Dbashour Week 9 - Revision history

Dbashour: /* Acknowledgements */

2017-10-31T06:07:37Z

‎Acknowledgements

Dbashour: /* References */ updated

2017-10-31T06:06:50Z

‎References: updated

Dbashour: /* Acknowledgements */ added signature

2017-10-31T06:03:47Z

‎Acknowledgements: added signature

Dbashour: /* Web Service API Exploration */ syntax fix

2017-10-31T06:02:08Z

‎Web Service API Exploration: syntax fix

Dbashour: /* Web Service API Exploration */ syntax fix

2017-10-31T06:00:12Z

‎Web Service API Exploration: syntax fix

Dbashour: /* Electronic Journal */ updated api exploratoin

2017-10-31T05:58:35Z

‎Electronic Journal: updated api exploratoin

Dbashour: updated acknowledgements and template

2017-10-30T23:43:55Z

updated acknowledgements and template

Dbashour: /* Electronic Journal */ syntax fix

2017-10-30T23:13:29Z

‎Electronic Journal: syntax fix

Dbashour: /* Electronic Journal */ updated files used

2017-10-30T23:12:53Z

‎Electronic Journal: updated files used

Dbashour: /* GRNsight Beta Version Test: Edge Weights + Normalization */ syntax fix

2017-10-30T22:50:41Z

‎GRNsight Beta Version Test: Edge Weights + Normalization: syntax fix

@@ Line 100: / Line 100: @@
 == Acknowledgements ==
 I met with [[User: Simonwro120 | Simon]] on Sunday 10/29 to start working on the tests for GRNsight. We met in the biodatabases lab in person in order to collaborate on this section. On Monday 10/30 I met with [[User: Simonwro120 | Simon]], [[User:Johnllopez616 | John]], and [[User:Hhinsch | Hayden]] in the lab to work on the API exploration of the assignment.
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

@@ Line 105: / Line 105: @@
 ==References==
-LMU BioDB 2017. (2017). Week 9. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
+LMU BioDB 2017. (2017). Week 9. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9 <br>
 {{template:dbashour}}

@@ Line 101: / Line 101: @@
 I met with [[User: Simonwro120 | Simon]] on Sunday 10/29 to start working on the tests for GRNsight. We met in the biodatabases lab in person in order to collaborate on this section. On Monday 10/30 I met with [[User: Simonwro120 | Simon]], [[User:Johnllopez616 | John]], and [[User:Hhinsch | Hayden]] in the lab to work on the API exploration of the assignment.
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
 ==References==

@@ Line 89: / Line 89: @@
 === Web Service API Exploration ===
 *We used the link listed below to retrieve the desired data:
-<code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene <code>
+<code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene </code>
 *We added <code>?symbol=BRO1</code> to the end of the URL in order to specify that we were looking for the specific gene symbol, BRO1.
 <code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1</code>
 * By simply copy and pasting that said URL into a web browser, a .json file will automatically be downloaded containing all the data on the gene BRO1. This file can be opened in a simple text editor and read by anyone who understands .json. You can repeat this action with any gene you might inquire by simply replacing the added code in the second step with any gene symbol that YeastMine has.
 <br>
-*In order to figure out the process listed above, my partners and I used the hints that Dondi provided us in order to get the json from ajax.starter. We started off by using the inspect function on the page and locating the gene ID. Once this was located, we then were able to use the link attached to that gene ID to retrieve the URL. Once we had the URL we were looking for, <code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?id=66043773</code> , we replaced the Gene ID in that URL with the gene symbol, BRO1 since we could have used either one.
+In order to figure out the process listed above, my partners and I used the hints that Dondi provided us in order to get the json from ajax.starter. We started off by using the inspect function on the page and locating the gene ID. Once this was located, we then were able to use the link attached to that gene ID to retrieve the URL. Once we had the URL we were looking for, <code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?id=66043773</code> , we replaced the gene ID in that URL with the gene symbol, BRO1 since we could have used either one.
-to <code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1</code>
+<code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1</code>
 We then figured out you can simply copy and past that URL into a web browser and a .json file would automatically download. We then repeated this for other genes like ADH1 and ACT1 and retrieved the .json file for those genes as well, leading us to conclude that you simply switch out the gene symbol with any other gene and retrieve the data.

@@ Line 89: / Line 89: @@
 === Web Service API Exploration ===
 *We used the link listed below to retrieve the desired data:
-<code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene
+<code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene <code>
 *We added <code>?symbol=BRO1</code> to the end of the URL in order to specify that we were looking for the specific gene symbol, BRO1.
 <code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1</code>

@@ Line 83: / Line 83: @@
 Test 18: '''passed'''
-Notices: When performing tests having to do with normalization, I noticed that because the graph reloads every time you set the normalization factor, it's hard to distinctly see what changes were made when the normalization factor was set as something similar to what the edge weights already were. But if you made them extreme and set the factors to extreme levels, you can clearly see the changes made with the edge weight thickness.
+Notices: When performing tests having to do with normalization, I noticed that because the graph reloads every time you set the normalization factor, it's hard to distinctly see what changes were made when the normalization factor was set as something similar to what the edge weights already were. But if you made them extreme and set the factors to extreme levels, you can clearly see the changes made with the edge weight thickness. My partner acknowledged this as well when he performed his own tests.
 === Web Service API Exploration ===
-#"recipe" -- how do you get the gene symbol to the specific ID that that gene symbol uses. stick the ID into ajax starter.
+*We used the link listed below to retrieve the desired data:
 == Acknowledgements ==

← Older revision		Revision as of 23:43, 30 October 2017
Line 87:		Line 87:
	=== Web Service API Exploration ===		=== Web Service API Exploration ===
	#"recipe" -- how do you get the gene symbol to the specific ID that that gene symbol uses. stick the ID into ajax starter.		#"recipe" -- how do you get the gene symbol to the specific ID that that gene symbol uses. stick the ID into ajax starter.
		+
		+	== Acknowledgements ==
		+	I met with [[User: Simonwro120 \| Simon]] on Sunday 10/29 to start working on the tests for GRNsight. We met in the biodatabases lab in person in order to collaborate on this section. On Monday 10/30 I met with [[User: Simonwro120 \| Simon]], [[User:Johnllopez616 \| John]], and [[User:Hhinsch \| Hayden]] in the lab to work on the API exploration of the assignment.
		+
		+	'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
		+
		+	==References==
		+	LMU BioDB 2017. (2017). Week 9. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
		+
		+	{{template:dbashour}}

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 ==Electronic Journal==
 === GRNsight Beta Version Test: Edge Weights + Normalization ===
 Test 1: '''passed'''
@@ Line 75: / Line 83: @@
 Test 18: '''passed'''
-Notices: When performing tests 10 and beyond, I noticed that because the graph reloads every time you set the normalization factor, it's hard to distinctly see what changes were made when the normalization factor was set as something similar to what the edge weights already were. But if you made them extreme and set the factors to extreme levels, you can clearly see the changes made with the edgeweight thickness.
+Notices: When performing tests having to do with normalization, I noticed that because the graph reloads every time you set the normalization factor, it's hard to distinctly see what changes were made when the normalization factor was set as something similar to what the edge weights already were. But if you made them extreme and set the factors to extreme levels, you can clearly see the changes made with the edge weight thickness.
 Web Service API Exploration
 #"recipe" -- how do you get the gene symbol to the specific ID that that gene symbol uses. stick the ID into ajax starter.

@@ Line 40: / Line 40: @@
 Test 1: '''passed'''
 Test 2: '''passed'''
 Test 3: '''passed'''
 Test 4: '''passed'''
 Test 5: '''passed'''
 Test 6: '''passed'''
 Test 7: '''passed'''
 Test 8: '''passed'''
 Test 9: '''passed'''
 Test 10: '''passed'''
 Test 11: '''passed'''
 Test 12: '''passed'''
 Test 13: '''passed'''
 Test 14: '''passed'''
 Test 15: '''passed'''
 Test 16: '''passed'''
 Test 17: '''passed'''
 Test 18: '''passed'''