Difference between revisions of "Cazinge Week 9"
From LMU BioDB 2017
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:* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file | :* GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook. |
; Test 2 | ; Test 2 | ||
: Instructions: | : Instructions: | ||
| Line 23: | Line 23: | ||
:* GRNsight should lay out a network graph from the SIF file if there are no errors in the file | :* GRNsight should lay out a network graph from the SIF file if there are no errors in the file | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook. |
; Test 3 | ; Test 3 | ||
: Instructions: | : Instructions: | ||
| Line 30: | Line 30: | ||
:* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file | :* GRNsight should lay out a network graph from the GraphML file if there are no errors in the file | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook. |
; Test 4 | ; Test 4 | ||
: Instructions: | : Instructions: | ||
| Line 39: | Line 39: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift to the left when the excel workbook is loaded and restrict graph to viewport is unchecked. |
; Test 5 | ; Test 5 | ||
: Instructions: | : Instructions: | ||
| Line 48: | Line 48: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift to the left when the SIF file is loaded and restrict graph to viewport is unchecked. |
; Test 6 | ; Test 6 | ||
: Instructions: | : Instructions: | ||
| Line 57: | Line 57: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift to the left when the GraphML file is loaded and restrict graph to viewport is unchecked. |
; Test 7 | ; Test 7 | ||
: Instructions: | : Instructions: | ||
| Line 66: | Line 66: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift to the right when the excel workbook is loaded and restrict graph to viewport is unchecked. |
; Test 8 | ; Test 8 | ||
: Instructions: | : Instructions: | ||
| Line 75: | Line 75: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift to the right when the SIF file is loaded and restrict graph to viewport is unchecked. |
; Test 9 | ; Test 9 | ||
: Instructions: | : Instructions: | ||
| Line 84: | Line 84: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift to the right when the GraphML file is loaded and restrict graph to viewport is unchecked. |
; Test 10 | ; Test 10 | ||
: Instructions: | : Instructions: | ||
| Line 93: | Line 93: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift down when the excel workbook is loaded and restrict graph to viewport is unchecked. |
; Test 11 | ; Test 11 | ||
: Instructions: | : Instructions: | ||
| Line 102: | Line 102: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift down when the SIF file is loaded and restrict graph to viewport is unchecked. |
; Test 12 | ; Test 12 | ||
: Instructions: | : Instructions: | ||
| Line 111: | Line 111: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift down | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift down when the GraphML file is loaded and restrict graph to viewport is unchecked. |
; Test 13 | ; Test 13 | ||
: Instructions: | : Instructions: | ||
| Line 120: | Line 120: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift up when the excel workbook is loaded and restrict graph to viewport is unchecked. |
; Test 14 | ; Test 14 | ||
: Instructions: | : Instructions: | ||
| Line 129: | Line 129: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift up when the SIF file is loaded and restrict graph to viewport is unchecked. |
; Test 15 | ; Test 15 | ||
: Instructions: | : Instructions: | ||
| Line 138: | Line 138: | ||
:* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up | :* if "Restrict Graph to Viewport" is Unchecked., The graph should shift up | ||
: '''Conclusions:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift up when the GraphML file is loaded and restrict graph to viewport is unchecked. |
; Test 16 | ; Test 16 | ||
: Instructions: | : 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 | :* 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:''' | : '''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. |
; Test 17 | ; Test 17 | ||
: Instructions: | : Instructions: | ||
| Line 156: | Line 156: | ||
:* 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 | :* 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:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift to the center of the bounding box when the SIF file is loaded and restrict graph to viewport is unchecked. |
; Test 18 | ; Test 18 | ||
: Instructions: | : Instructions: | ||
| Line 165: | Line 165: | ||
:* 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 | :* 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:''' | : '''Conclusions:''' | ||
| − | :* | + | :* GRNsight appears to successfully shift to the center of the bounding box when the GraphML file is loaded and restrict graph to viewport is unchecked. |
==Part 2: Web Service Exploration== | ==Part 2: Web Service Exploration== | ||
Revision as of 21:33, 28 October 2017
Contents
Part 1: GRNsight Testing
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:
- GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook.
- 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:
- GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook.
- 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:
- GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook.
- 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:
- GRNsight appears to successfully shift to the left when the excel workbook is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift to the left when the SIF file is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift to the left when the GraphML file is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift to the right when the excel workbook is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift to the right when the SIF file is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift to the right when the GraphML file is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift down when the excel workbook is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift down when the SIF file is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift down when the GraphML file is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift up when the excel workbook is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift up when the SIF file is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift up when the GraphML file is loaded and restrict graph to viewport is unchecked.
- 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:
- 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:
- 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:
- GRNsight appears to successfully shift to the center of the bounding box when the SIF file is loaded and restrict graph to viewport is unchecked.
- 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:
- GRNsight appears to successfully shift to the center of the bounding box when the GraphML file is loaded and restrict graph to viewport is unchecked.
Part 2: Web Service Exploration
UniProt
- Relevant documentation:
- 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
