Difference between revisions of "Cazinge Week 9"

Revision as of 23:04, 24 October 2017

Part 1: GRNsight Testing

XLSX file

SIF file

GRAPHML file

GRNsight Client Side Testing Document: D-Pad Control

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:

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:
  • 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 'http://www.uniport.org?query=this&type=that')
  • 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

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