Cwong34 Week 9 - Revision history

Cwong34: Finished electronic journal, added acknowledgments and references

2017-10-29T00:15:34Z

Finished electronic journal, added acknowledgments and references

Cwong34: Added to electronic notebook

2017-10-28T22:50:59Z

Added to electronic notebook

Cwong34: Added to electronic notebook

2017-10-28T22:47:07Z

Added to electronic notebook

Cwong34: Added research information to electronic notebook

2017-10-28T22:21:02Z

Added research information to electronic notebook

Cwong34: Added uniprot url

2017-10-28T21:50:47Z

Added uniprot url

Cwong34: Edited format

2017-10-28T21:44:04Z

Edited format

Cwong34: Added conclusions to the rest of the tests

2017-10-28T21:42:09Z

Added conclusions to the rest of the tests

Cwong34: Added conclusions for tests 1-3

2017-10-28T21:30:20Z

Added conclusions for tests 1-3

Cwong34: Added tests to page

2017-10-28T21:18:26Z

Added tests to page

Cwong34: Created sections, added links and category

2017-10-28T21:11:51Z

Created sections, added links and category

New page

=GRNsight=

=API Exploration=

=Acknowledgmenets=

=References=

{{cwong34}}

[[Category: Journal Entry]]

@@ Line 154: / Line 154: @@
 *We used the links under the relevant documentation for UniProt on the Week 9 Assignment page, and found UniProt uses xml. We used the [http://www.uniprot.org/uploadlists/ Retrieve/ID mapping] link to run example searches to collect the information we will need to get to the final data profile. We determined that when we put in a gene name, for example ACT 1, we need to select "Gene name" under UniProt in the drop-down menu for the "From" section, "UniProtKB" in the "To" drop-down menu, and we needed to type the Taxon ID for our strain of ''S. cerevisiae'', which is 559292, under the Organism text box. Then the results come up with one gene, and when we click on it, we get to the gene's profile.
 *To specify "Gene name" and "UniProtKB," we looked at [http://www.uniprot.org/help/api_idmapping mapping database identifiers] to identify the abbreviations for the categories. "Gene name" is "GENENAME," and "UniProtKB" is "ACC."
 =Acknowledgmenets=

@@ Line 152: / Line 152: @@
 ==Research==
-We used the links under the relevant documentation for UniProt on the Week 9 Assignment page, and found UniProt uses xml. We used the [http://www.uniprot.org/uploadlists/ Retrieve/ID mapping] link to run example searches to collect the information we will need to get to the final data profile. We determined that when we put in a gene name, for example ACT 1, we need to select "Gene name" under UniProt in the drop-down menu for the "From" section, "UniProtKB" in the "To" drop-down menu, and we needed to type the Taxon ID for our strain of ''S. cerevisiae'', which is 559292, under the Organism text box. Then the results come up with one gene, and when we click on it, we get to the gene's profile.
+*We used the links under the relevant documentation for UniProt on the Week 9 Assignment page, and found UniProt uses xml. We used the [http://www.uniprot.org/uploadlists/ Retrieve/ID mapping] link to run example searches to collect the information we will need to get to the final data profile. We determined that when we put in a gene name, for example ACT 1, we need to select "Gene name" under UniProt in the drop-down menu for the "From" section, "UniProtKB" in the "To" drop-down menu, and we needed to type the Taxon ID for our strain of ''S. cerevisiae'', which is 559292, under the Organism text box. Then the results come up with one gene, and when we click on it, we get to the gene's profile.
 =Acknowledgmenets=

← Older revision		Revision as of 22:21, 28 October 2017
Line 150:		Line 150:

	[http://www.uniprot.org/ UniProt]		[http://www.uniprot.org/ UniProt]
		+
		+	==Research==
		+	We used the links under the relevant documentation for UniProt on the Week 9 Assignment page, and found UniProt uses xml. We used the [http://www.uniprot.org/uploadlists/ Retrieve/ID mapping] link to run example searches to collect the information we will need to get to the final data profile. We determined that when we put in a gene name, for example ACT 1, we need to select "Gene name" under UniProt in the drop-down menu for the "From" section, "UniProtKB" in the "To" drop-down menu, and we needed to type the Taxon ID for our strain of ''S. cerevisiae'', which is 559292, under the Organism text box. Then the results come up with one gene, and when we click on it, we get to the gene's profile.

	=Acknowledgmenets=		=Acknowledgmenets=

← Older revision		Revision as of 21:50, 28 October 2017
Line 148:		Line 148:

	=API Exploration=		=API Exploration=
		+
		+	[http://www.uniprot.org/ UniProt]

	=Acknowledgmenets=		=Acknowledgmenets=

@@ Line 14: / Line 14: @@
 :* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
 : '''Conclusions:''' I loaded the xlsx file, and the graph appeared on the page with no problems.
 ; Test 2
 : Instructions:
@@ Line 21: / Line 20: @@
 :* GRNsight should lay out a network graph from the SIF file if there are no errors in the file
 : '''Conclusions:''' I imported the SIF file to the page, and the map showed up with no problems.
 ; Test 3
 : Instructions:
@@ Line 28: / Line 26: @@
 :* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
 : '''Conclusions:''' I imported the GraphML file to the page, and the map showed up with no problems.
 ; Test 4
 : Instructions:
@@ Line 37: / Line 34: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
 : '''Conclusions:''' I opened the Excel workbook, clicked the right arrow, and it correctly moved to the right.
 ; Test 5
 : Instructions:
@@ Line 46: / Line 42: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
 : '''Conclusions:''' I imported the SIF file, clicked the right arrow, and the map correctly moved to the right.
 ; Test 6
 : Instructions:
@@ Line 55: / Line 50: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
 : '''Conclusions:''' I imported the GraphML file, clicked the right arrow, and the map correctly moved to the right.
 ; Test 7
 : Instructions:
@@ Line 64: / Line 58: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
 : '''Conclusions:''' I opened the Excel workbook, clicked the left arrow, and the the map correctly moved to the left.
 ; Test 8
 : Instructions:
@@ Line 73: / Line 66: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
 : '''Conclusions:''' I imported the SIF file, clicked the left arrow, and the map correctly moved to the left.
 ; Test 9
 : Instructions:
@@ Line 82: / Line 74: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
 : '''Conclusions:''' I imported the GraphML file, clicked the left arrow, and the map correctly moved to the left.
 ; Test 10
 : Instructions:
@@ Line 91: / Line 82: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
 : '''Conclusions:''' I opened the Excel workbook, clicked the up arrow, and the map correctly moved up.
 ; Test 11
 : Instructions:
@@ Line 100: / Line 90: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
 : '''Conclusions:''' I imported the SIF file, clicked the up arrow, and the file correctly moved up.
 ; Test 12
 : Instructions:
@@ Line 109: / Line 98: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
 : '''Conclusions:''' I imported the GraphML file, clicked the up arrow, and the map correctly moved up.
 ; Test 13
 : Instructions:
@@ Line 118: / Line 106: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
 : '''Conclusions:''' I opened the Excel workbook, clicked the down arrow, and the map correctly moved down.
 ; Test 14
 : Instructions:
@@ Line 127: / Line 114: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
 : '''Conclusions:''' I imported the SIF file, clicked the down arrow, and the map correctly moved down.
 ; Test 15
 : Instructions:
@@ Line 136: / Line 122: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
 : '''Conclusions:''' I imported the GraphML file, clicked the down arrow, and the map correctly moved down.
 ; Test 16
 : Instructions:
@@ Line 145: / Line 130: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
 : '''Conclusions:''' I opened the Excel workbook, clicked the center button, and the map correctly moved to the center.
 ; Test 17
 : Instructions:
@@ Line 154: / Line 138: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
 : '''Conclusions:''' I imported the SIF file, clicked the center button, and the map correctly moved to the center.
 ; Test 18
 : Instructions:
@@ Line 163: / Line 146: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
 : '''Conclusions:''' I imported the GraphML file, clicked the center button, and the map correctly moved to the center.
 =API Exploration=

@@ Line 155: / Line 155: @@
 *To specify "Gene name" and "UniProtKB," we looked at [http://www.uniprot.org/help/api_idmapping mapping database identifiers] to identify the abbreviations for the categories. "Gene name" is "GENENAME," and "UniProtKB" is "ACC."
 *To specify the taxon ID for our strain of ''S. cerevisiae,'' we inspected the web browser, to see what they called the field where we enter the ID, which they called "taxon."
 =Acknowledgmenets=
 =References=
 {{cwong34}}
 [[Category: Journal Entry]]

← Older revision		Revision as of 21:18, 28 October 2017
Line 1:		Line 1:
	=GRNsight=		=GRNsight=
		+
		+	[https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_50-edges_Dahlquist-data_estimation_output.xlsx XLSX file]
		+
		+	[https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_input.sif SIF file]
		+
		+	[https://github.com/dondi/GRNsight/blob/beta/test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml GRAPHML file]
		+
		+	Last Updated: 2017-10-23
		+	; Test 1
		+	: Instructions:
		+	:* Load Graph - File Menu -> Open
		+	: Results:
		+	:* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
		+	: '''Conclusions:'''
		+	:*
		+	; Test 2
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import SIF
		+	: Results:
		+	:* GRNsight should lay out a network graph from the SIF file if there are no errors in the file
		+	: '''Conclusions:'''
		+	:*
		+	; Test 3
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import GraphML
		+	: Results:
		+	:* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
		+	: '''Conclusions:'''
		+	:*
		+	; Test 4
		+	: Instructions:
		+	:* Load Graph - File Menu -> Open
		+	:* D-Pad Control - Click Right Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
		+	: '''Conclusions:'''
		+	:*
		+	; Test 5
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import SIF
		+	:* D-Pad Control - Click Right Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the SIF file if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
		+	: '''Conclusions:'''
		+	:*
		+	; Test 6
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import GraphML
		+	:* D-Pad Control - Click Right Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
		+	: '''Conclusions:'''
		+	:*
		+	; Test 7
		+	: Instructions:
		+	:* Load Graph - File Menu -> Open
		+	:* D-Pad Control - Click Left Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
		+	: '''Conclusions:'''
		+	:*
		+	; Test 8
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import SIF
		+	:* D-Pad Control - Click Left Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the SIF file if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
		+	: '''Conclusions:'''
		+	:*
		+	; Test 9
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import GraphML
		+	:* D-Pad Control - Click Left Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
		+	: '''Conclusions:'''
		+	:*
		+	; Test 10
		+	: Instructions:
		+	:* Load Graph - File Menu -> Open
		+	:* D-Pad Control - Click Up Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
		+	: '''Conclusions:'''
		+	:*
		+	; Test 11
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import SIF
		+	:* D-Pad Control - Click Up Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the SIF file if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
		+	: '''Conclusions:'''
		+	:*
		+	; Test 12
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import GraphML
		+	:* D-Pad Control - Click Up Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
		+	: '''Conclusions:'''
		+	:*
		+	; Test 13
		+	: Instructions:
		+	:* Load Graph - File Menu -> Open
		+	:* D-Pad Control - Click Down Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
		+	: '''Conclusions:'''
		+	:*
		+	; Test 14
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import SIF
		+	:* D-Pad Control - Click Down Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the SIF file if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
		+	: '''Conclusions:'''
		+	:*
		+	; Test 15
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import GraphML
		+	:* D-Pad Control - Click Down Arrow
		+	: Results:
		+	:* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
		+	: '''Conclusions:'''
		+	:*
		+	; Test 16
		+	: Instructions:
		+	:* Load Graph - File Menu -> Open
		+	:* D-Pad Control - Click Center Button
		+	: Results:
		+	:* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
		+	: '''Conclusions:'''
		+	:*
		+	; Test 17
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import SIF
		+	:* D-Pad Control - Click Center Button
		+	: Results:
		+	:* GRNsight should lay out a network graph from the SIF file if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
		+	: '''Conclusions:'''
		+	:*
		+	; Test 18
		+	: Instructions:
		+	:* Load Graph - File Menu -> Import GraphML
		+	:* D-Pad Control - Click Center Button
		+	: Results:
		+	:* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
		+	:* if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport
		+	: '''Conclusions:'''
		+	:*

	=API Exploration=		=API Exploration=