Cazinge Week 9 - Revision history

Cazinge: /* Acknowledgements */ adding signiture

2017-11-06T23:44:11Z

‎Acknowledgements: adding signiture

Cazinge: adding Acknowledgements and references

2017-11-02T22:04:30Z

adding Acknowledgements and references

Cazinge: /* Part 2: Web Service Exploration */ Adding notebook

2017-10-31T03:28:12Z

‎Part 2: Web Service Exploration: Adding notebook

Cazinge: /* Solution */

2017-10-28T23:41:51Z

‎Solution

Cazinge: /* Part 2: Web Service Exploration */ added function

2017-10-28T23:37:05Z

‎Part 2: Web Service Exploration: added function

Cazinge: /* GRNsight Client Side Testing Document: D-Pad Control */ updated excel instances

2017-10-28T21:36:34Z

‎GRNsight Client Side Testing Document: D-Pad Control: updated excel instances

Cazinge: /* GRNsight Client Side Testing Document: D-Pad Control */ formatting

2017-10-28T21:34:48Z

‎GRNsight Client Side Testing Document: D-Pad Control: formatting

Cazinge: Added responses to part 1

2017-10-28T21:33:49Z

Added responses to part 1

Cazinge: adding section

2017-10-24T23:05:14Z

adding section

Cazinge: templating part 2

2017-10-24T23:04:29Z

templating part 2

← Older revision		Revision as of 23:44, 6 November 2017
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	'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''		'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

		+	[[User:Cazinge\|Cazinge]] ([[User talk:Cazinge\|talk]]) 15:44, 6 November 2017 (PST)

	===References===		===References===

← Older revision		Revision as of 22:04, 2 November 2017
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	==Links and References==		==Links and References==
		+
		+	===Acknowledgements===
		+
		+	#Met outside of class with [[User:Cwong34\|Corinne Wong]] to discuss any questions we had prior to meeting and throughout the process of completing the Week 9 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 October 17, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
		+
	{{Template:Cazinge}}		{{Template:Cazinge}}

@@ Line 181: / Line 181: @@
 * Miscellaneous information:
 ** You will encounter the need for a ''taxon ID'', which identifies a specific organism; the taxon ID for our strain of ''S. cerevisiae'' is '''559292'''
 ===== Solution =====
@@ Line 195: / Line 196: @@
 curl -L "http://uniprot.org/uniprot/$gene_id.xml"</pre>
 ==Links and References==
 {{Template:Cazinge}}

@@ Line 182: / Line 182: @@
 ** You will encounter the need for a ''taxon ID'', which identifies a specific organism; the taxon ID for our strain of ''S. cerevisiae'' is '''559292'''
 ===== Solution =====
 <pre>#!/bin/bash

@@ Line 181: / Line 181: @@
 * Miscellaneous information:
 ** You will encounter the need for a ''taxon ID'', which identifies a specific organism; the taxon ID for our strain of ''S. cerevisiae'' is '''559292'''
 ==Links and References==
 {{Template:Cazinge}}

@@ Line 39: / Line 39: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left
 : '''Conclusions:'''
-:* GRNsight appears to successfully shift to the left when the excel workbook is loaded and restrict graph to viewport is unchecked.
+:* GRNsight appears to successfully shift to the left when the Excel workbook is loaded and restrict graph to viewport is unchecked.
 ; Test 5
 : Instructions:
@@ Line 66: / Line 66: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right
 : '''Conclusions:'''
-:* GRNsight appears to successfully shift to the right when the excel workbook is loaded and restrict graph to viewport is unchecked.
+:* GRNsight appears to successfully shift to the right when the Excel workbook is loaded and restrict graph to viewport is unchecked.
 ; Test 8
 : Instructions:
@@ Line 93: / Line 93: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down
 : '''Conclusions:'''
-:* GRNsight appears to successfully shift down when the excel workbook is loaded and restrict graph to viewport is unchecked.
+:* GRNsight appears to successfully shift down when the Excel workbook is loaded and restrict graph to viewport is unchecked.
 ; Test 11
 : Instructions:
@@ Line 120: / Line 120: @@
 :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up
 : '''Conclusions:'''
-:* GRNsight appears to successfully shift up when the excel workbook is loaded and restrict graph to viewport is unchecked.
+:* GRNsight appears to successfully shift up when the Excel workbook is loaded and restrict graph to viewport is unchecked.
 ; Test 14
 : Instructions:
@@ Line 147: / Line 147: @@
 :* 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:'''
-:* GRNsight appears to successfully shift to the center of the bounding box when the excel workbook is loaded and restrict graph to viewport is unchecked.
+:* GRNsight appears to successfully shift to the center of the bounding box when the Excel workbook is loaded and restrict graph to viewport is unchecked.
 ; Test 17
 : Instructions:

@@ Line 23: / Line 23: @@
 :* GRNsight should lay out a network graph from the SIF file if there are no errors in the file
 : '''Conclusions:'''
-:* GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook.
+:* GRNsight appears to successfully lay out the mentioned network graph as specified from the SIF file.
 ; Test 3
 : Instructions:
@@ Line 30: / Line 30: @@
 :* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
 : '''Conclusions:'''
-:* GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook.
+:* GRNsight appears to successfully lay out the mentioned network graph as specified from the GraphML file.
 ; Test 4
 : Instructions:

← Older revision		Revision as of 23:05, 24 October 2017
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	** You will encounter the need for a ''taxon ID'', which identifies a specific organism; the taxon ID for our strain of ''S. cerevisiae'' is '''559292'''		** You will encounter the need for a ''taxon ID'', which identifies a specific organism; the taxon ID for our strain of ''S. cerevisiae'' is '''559292'''

		+	==Links and References==
	{{Template:Cazinge}}		{{Template:Cazinge}}

← Older revision		Revision as of 23:04, 24 October 2017
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	==Part 2: Web Service Exploration==		==Part 2: Web Service Exploration==
		+	===== UniProt =====
		+	* Relevant documentation:
		+	** http://www.uniprot.org/help/api
		+	** http://www.uniprot.org/help/api_idmapping
		+	** http://www.uniprot.org/help/api_retrieve_entries
		+	* Supplementary websites:
		+	** [http://www.uniprot.org/uploadlists/ Retrieve/ID mapping] web page
		+	* Technical information:
		+	** You will encounter ''redirects'' in these web services; web browsers handle this automatically, but if using '''curl''' make sure to add the '''-L''' switch (i.e., '''curl -L '''…)
		+	** Your URLs will include ampersands ('''&'''), which will need special handling with '''curl''': in these cases, enclose the URL in apostrophes (e.g., '''curl -L '<nowiki>http://www.uniport.org?query=this&type=that</nowiki>'''')
		+	** UniProt primarily provides results in XML format; in one relevant step, the data can be provided in tab-delimited format, which might be easier to work with
		+	* Miscellaneous information:
		+	** You will encounter the need for a ''taxon ID'', which identifies a specific organism; the taxon ID for our strain of ''S. cerevisiae'' is '''559292'''

	{{Template:Cazinge}}		{{Template:Cazinge}}