Aporras1 Week 9

User Page: Antonio Porras

Assignment Page: Week 9

Electronic Notebook

1. Selected the following files for our test:
   • 21-genes_31-edges_Schade-data_estimation_output.xlsx
   • 21-genes_31-edges_Schade-data_estimation_output.sif
   • 21-genes_31-edges_Schade-data_estimation_output.graphml
2. Opened up GRNsight - beta

Test one

1. Loaded the excel file.
2. Restricted graph to viewport.
3. Passed test one.

Test two

1. Loaded the sif file.
2. Restricted graph to viewport.
3. Passed test two.

Test three

1. Loaded the GraphML file.
2. Restricted graph to viewport
3. Passed test three.

Test four

1. Loaded the excel file.
2. Unchecked restrict graph to viewport.
3. Failed test four by restricting the graph bounding box.

Test five

1. Loaded the sif file.
2. Unchecked restrict graph to viewport.
3. Failed test five by restricting the graph bounding box.

Test six

1. Loaded the GraphML file.
2. Unchecked restrict graph to viewport.
3. Failed test six by restricting the graph bounding box.

Test seven

1. Loaded the excel file.
2. Restricted graph to viewport.
3. Increased zoom level with slider.
4. Graph box was contained within the viewport and the graph zoomed in.
5. Passed test seven.

Test eight

1. Loaded the sif file.
2. Restricted graph to viewport.
3. Increased zoom level with slider.
4. Graph box was contained within the viewport and the graph zoomed in.
5. Passed test eight.

Test nine

1. Loaded the GraphML file.
2. Restricted graph to viewport.
3. Increased zoom level with slider.
4. Graph box was contained within the viewport and the graph zoomed in.
5. Passed test nine.

Test ten

1. Loaded the excel file.
2. Unchecked restrict graph to viewport.
3. Increased zoom level with slider.
4. Graph bounding box was allowed to extend past the viewport and the graph zoomed in.
5. Passed test ten.

Test eleven

1. Loaded the sif file.
2. Unchecked restrict graph to viewport.
3. Increased zoom level with slider.
4. Graph bounding box was allowed to extend past the viewport and the graph zoomed in.
5. Passed test eleven.

Test twelve

1. Loaded the GraphML file.
2. Unchecked restrict graph to viewport.
3. Increased zoom level with slider.
4. Graph bounding box was allowed to extend past the viewport and the graph zoomed in.
5. Passed test twelve.

Test thirteen

1. Loaded the excel file.
2. Restricted graph to viewport.
3. Decreased zoom level with zoom slider,
4. Graph bounding box was contained within the viewport and graph zoomed out.
5. Passed test thirteen.

Test fourteen

1. Loaded the sif file.
2. Restricted graph to viewport.
3. Decreased zoom level with zoom slider,
4. Graph bounding box was contained within the viewport and graph zoomed out.
5. Passed test fourteen.

Test fifteen

1. Loaded the GraphML file.
2. Restricted graph to viewport.
3. Decreased zoom level with zoom slider,
4. Graph bounding box was contained within the viewport and graph zoomed out.
5. Passed test fifteen.

Test sixteen

1. Loaded the excel file.
2. Unchecked restrict graph to viewport.
3. Decreased zoom level with zoom slider.
4. The graph bounding box was allowed to extend past the viewport and graph zoomed out.
5. Passed test sixteen.

Test seventeen

1. Loaded the sif file.
2. Unchecked restrict graph to viewport.
3. Decreased zoom level with zoom slider.
4. The graph bounding box was allowed to extend past the viewport and graph zoomed out.
5. Passed test seventeen.

Test eighteen

1. Loaded the GraphML file.
2. Unchecked restrict graph to viewport.
3. Decreased zoom level with zoom slider.
4. The graph bounding box was allowed to extend past the viewport and graph zoomed out.
5. Passed test eighteen.

Web Service API Exploration

1. Clicked on the first link http://rest.ensembl.org/documentation and went down to "GET lookup/symbol/:species/:symbol
2. Knowing that the "species" had to be "saccharomyces_cerevisiae", I looked through their example requests and tried using bash next to see what came up.
3. First I tried curling http://rest.ensembl.org/lookup/symbol/homo_sapiens/BRCA2?content-type=application/json to see if their example worked.
4. Their example worked and provided the information they said it would.
5. Next, I tried it for the favorite gene we used:CLN1.
6. So, I knew the species "homo_sapiens" had to be replaced by "saccharomyces_cerevisiae" and "BRCA2" with "CLN1".
7. Resulted in putting the following into Bash: curl http://rest.ensembl.org/lookup/symbol/saccharomyces_cerevisiae/CLN1?content-type=application/json
8. Found the id for CLN1 to be "YMR199W".
9. Then, used the resource GET lookup/id/:id to see if the id I found would work.
10. Went to their example and used their format to format the URL: http://rest.ensembl.org/lookup/id/ENSG00000157764?content-type=application/json
11. Instead of using their id, I replaced it with "YMR199W" to ultimately make this URL: http://rest.ensembl.org/lookup/id/YMR199W?content-type=application/json

Deliverable

curl http://rest.ensembl.org/lookup/id/YMR199W?content-type=application/json

Acknowledgements

1. Met outside of class and worked in class with Zach Van Ysseldyk to discuss any questions we had throughout the process of completing the Week 9 assignment.
2. Additionally, worked alongside Arash Lari and Nicole Kalcic to complete the Web Service API Exploration on the Week 9 assignment.
3. Special thanks to Dondi for providing the clues to figure out the rest of the homework and find the URL.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Aporras1 (talk) 15:40, 24 October 2017 (PDT)

References

1. LMU BioDB 2017. (2017). Week 9. Retrieved October 24, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
2. Ensembl Gene Browser 90. (n.d.). Retrieved October 30, 2017, from https://www.ensembl.org/