Difference between revisions of "Emmatyrnauer Week 9"

Revision as of 19:17, 30 October 2017

Electronic Notebook

Hands on with GRNsight

I tested the gray threshold and zoom functions on GRNsight beta version.

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
• Passed

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
• Passed

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
• Passed

Test 4

• Instructions: Load Graph - File Menu -> Open. Gray Threshold Slider - Change the Grey Threshold Value
• Results: GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray
• Did not pass; the zoom function was not visible

Test 5

• Instructions: Load Graph - File Menu -> Import SIF. Gray Threshold Slider - Change the Grey Threshold Value
• Results: GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray
• Passed

Test 6

• Instructions: Load Graph - File Menu -> Import GraphML. Gray Threshold Slider - Change the Grey Threshold Value
• Results: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray
• Did not pass; the zoom function was not visible

Test 7

• Instructions: Load Graph - File Menu -> Open. Zoom Slider - Increase Zoom Level
• Results: GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should zoom in (get larger)
• Passed

Test 8

• Instructions: Load Graph - File Menu -> Import SIF. Zoom Slider - Increase Zoom Level
• Results: GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should zoom in (get larger)
• Passed

Test 9

• Instructions: Load Graph - File Menu -> Import GraphML. Zoom Slider - Increase Zoom Level
• Results: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should zoom in (get larger)
• Passed

Test 10

• Instructions: Load Graph - File Menu -> Open. Gray Threshold Slider - Change the Grey Threshold Value Zoom Slider - Increase Zoom Level
• Results: GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom in (get larger)
• Passed

Test 11

• Instructions: Load Graph - File Menu -> Import SIF. Gray Threshold Slider - Change the Grey Threshold Value Zoom Slider - Increase Zoom Level
• Results: GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom in (get larger)
• Passed

Test 12

• Instructions: Load Graph - File Menu -> Import GraphML. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Increase Zoom Level
• Results: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom in (get larger).
• Passed

Test 13

• Instructions:
• Load Graph - File Menu -> Open. Zoom Slider - Decrease Zoom Level
• Results: GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should zoom out (get smaller)
• Passed

Test 14

• Instructions: Load Graph - File Menu -> Import SIF. Zoom Slider - Decrease Zoom Level
• Results: GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should zoom out (get smaller)
• Passed

Test 15

• Instructions: Load Graph - File Menu -> Import GraphML. Zoom Slider - Decrease Zoom Level
• Results: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should zoom out (get smaller)
• Passed

Test 16

• Instructions: Load Graph - File Menu -> Open. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Decrease Zoom Level
• Results: GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom out (get smaller)
• Passed

Test 17

• Instructions: Load Graph - File Menu -> Import SIF. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Decrease Zoom Level
• Results: GRNsight should lay out a network graph from the SIF file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom out (get smaller)
• Passed

Test 18

• Instructions: Load Graph - File Menu -> Import GraphML. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Decrease Zoom Level
• Results: GRNsight should lay out a network graph from the GraphML file if there are no errors in the file. The graph should reload, with edges that fall below the threshold value colored gray. The graph should zoom out (get smaller)
• Passed

Web service API exploration

1. We referenced [1].
2. https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ was used because this url requires performing an E-utility call.
3. We replaced <database> with gene and <query> with ADA2 (specific gene) in esearch.fcgi?db=<database>&term=<query> and added this to the growing URL to narrow the results to the gene database and a specific gene from NCBI.
4. [gene] was added to narrow the results further to gene specific data
5. +AND+Saccharomyces+20cerevisiae[Organism] allows us to reach the final product by specifying the organism (Saccharomyces cerevisiae) where + replaces the spaces and Organism indicates that organism data is wanted.

Final URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=ada2[gene]+AND+Saccharomyces+20cerevisiae[Organism]

Acknowledgements

References

Links

1. My User Page
2. List of Assignments
   • Week 1
   • Week 2
   • Week 3
   • Week 4
   • Week 5
   • Week 6
   • Week 7
   • Week 8
   • Week 9
   • Week 10
   • Week 11
   • Week 12
   • no Week 13
   • Week 14
   • Week 15
3. List of Journal Entries
   • Emmatyrnauer Week 1
   • Emmatyrnauer Week 2
   • Emmatyrnauer Week 3
   • Emmatyrnauer Week 4
   • Emmatyrnauer Week 5
   • Emmatyrnauer Week 6
   • Emmatyrnauer Week 7
   • Emmatyrnauer Week 8
   • Emmatyrnauer Week 9
   • Emmatyrnauer Week 10
   • Emmatyrnauer Week 11
   • Emmatyrnauer Week 12
   • no Week 13
   • Emmatyrnauer Week 14
   • Emmatyrnauer Week 15
4. List of Shared Journal Entries
   • Class Journal Week 1
   • Class Journal Week 2
   • Class Journal Week 3
   • Class Journal Week 4
   • Class Journal Week 5
   • Class Journal Week 6
   • Class Journal Week 7
   • Class Journal Week 8
   • Class Journal Week 9
   • Class Journal Week 10
   • Group Journal Week 11
   • Group Journal Week 12
   • no week 13
   • Group Journal Week 14 (executive summary)
   • Group Journal Week 14 (executive summary)
   • Group Journal Week 15 (executive summary)