Emmatyrnauer Week 9

Electronic Notebook

Hands on with GRNsight

I tested the gray threshold and zoom functions on GRNsight beta version. Files were chosen from this web page to perform tests: 21-genes_31-edges_Schade-data_input.xlsx, 21-genes_31-edges_Schade-data_estimation_output.sif, and 21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml.

Test 1

• Instructions: Load Graph - File Menu -> Open
• Expected results: GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
• Results: Passed

Test 2

• Instructions: Load Graph - File Menu -> Import SIF
• Expected results: GRNsight should lay out a network graph from the SIF file if there are no errors in the file
• Results: 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
• Results: Passed

Test 4

• Instructions: Load Graph - File Menu -> Open. Gray Threshold Slider - Change the Grey Threshold Value
• Expected 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
• Results: Failed; gray threshold function not visible

Test 4: Zoom function missing in bottom left corner of display for Excel workbook

Test 5

• Instructions: Load Graph - File Menu -> Import SIF. Gray Threshold Slider - Change the Grey Threshold Value
• Expected 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
• Results: Passed

Test 6

• Instructions: Load Graph - File Menu -> Import GraphML. Gray Threshold Slider - Change the Grey Threshold Value
• Expected 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
• Results: Failed; gray threshold function not visible

Test 6: Zoom function missing in bottom left corner of display for GraphML

Test 7

• Instructions: Load Graph - File Menu -> Open. Zoom Slider - Increase Zoom Level
• Expected 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)
• Results: Passed

Test 8

• Instructions: Load Graph - File Menu -> Import SIF. Zoom Slider - Increase Zoom Level
• Expected 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)
• Results: Passed

Test 9

• Instructions: Load Graph - File Menu -> Import GraphML. Zoom Slider - Increase Zoom Level
• Expected 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)
• Results: Passed

Test 10

• Instructions: Load Graph - File Menu -> Open. Gray Threshold Slider - Change the Grey Threshold Value Zoom Slider - Increase Zoom Level
• Expected 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)
• Results: Failed; gray threshold function not visible

Test 11

• Instructions: Load Graph - File Menu -> Import SIF. Gray Threshold Slider - Change the Grey Threshold Value Zoom Slider - Increase Zoom Level
• Expected 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)
• Results: Passed

Test 12

• Instructions: Load Graph - File Menu -> Import GraphML. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Increase Zoom Level
• Expected 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).
• Results: Failed; gray threshold function not visible

Test 13

• Instructions:
• Load Graph - File Menu -> Open. Zoom Slider - Decrease Zoom Level
• Expected 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)
• Results: Passed

Test 14

• Instructions: Load Graph - File Menu -> Import SIF. Zoom Slider - Decrease Zoom Level
• Expected 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)
• Results: Passed

Test 15

• Instructions: Load Graph - File Menu -> Import GraphML. Zoom Slider - Decrease Zoom Level
• Expected 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)
• Results: Passed

Test 16

• Instructions: Load Graph - File Menu -> Open. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Decrease Zoom Level
• Expected 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)
• Results: Failed; gray threshold function not visible

Test 17

• Instructions: Load Graph - File Menu -> Import SIF. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Decrease Zoom Level
• Expected 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)
• Results: Passed

Test 18

• Instructions: Load Graph - File Menu -> Import GraphML. Gray Threshold Slider - Change the Grey Threshold Value. Zoom Slider - Decrease Zoom Level
• Expected 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)
• Results: Failed; gray threshold function not visible

Web service API exploration for NCBI

Process

1. We referenced Searching a Database from the Relevant Documentation section in the Week 9 assignment page as well as the hints Dondi provided for syntax.
2. https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ was used because this service requires performing an E-utility call.
3. We replaced <database> with gene and <query> with ADA2 (a 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. This was determined through the performance of different specific searches in the database (ie. in a search for a scientific journal one would put scientific[journal] to indicate the category).
5. +AND+Saccharomyces+cerevisiae[Organism] allowed us to reach the final product by specifying the organism (Saccharomyces cerevisiae) where + replaced all the spaces and [Organism] indicated that organism data was wanted.
6. The URL was tested with other specific genes and it worked!

Final URL

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

Acknowledgements

1. I worked with Blair Hamilton for this assignment. We texted while performing the testing portion of the assignment and then met up in person to work on the web service API portion of the assignment.
2. Blair and I also met up in person with Quinn Lanners who also was assigned the NCBI database.
3. User:Dondi for helping walk through the process and basics of this assignment during class
4. Files from this web page
   • 21-genes_31-edges_Schade-data_input.xlsx used for beta version of GRNsight testing
   • 21-genes_31-edges_Schade-data_estimation_output.sif used for beta version of GRNsight testing
   • 21-genes_31-edges_Schade-data_estimation_output_unweighted.graphml used for beta version of GRNsight testing
5. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Emmatyrnauer (talk) 18:00, 30 October 2017 (PDT)

References

1. LMU BioDB 2017. (2017). Gray Threshold + Zoom. Retrieved October 30, 2017, from Media:GRNsight_Testing-Gray_Threshold_and_Zoom.pdf
2. LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9

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)