Mbalducc Week 9

GRNSight Edge Weight + Gray Threshold Test Results

Test 1

• Passed
  • The graph displayed.
  • The edge weights showed only when I moused over them.

Test 2

• Passed
  • The graph displayed.
  • The edge weights showed only when I moused over them.

Test 3

• Passed
  • The file opened and graph displayed.
  • The edge weights showed only when I moused over them.

Test 4

• Passed
  • The graph displayed.
  • The edge weights showed at all times.

Test 5

• Passed
  • The graph displayed.
  • The edge weights showed at all times.

Test 6

• Passed
  • The graph displayed.
  • The edge weights showed at all times.

Test 7

• Passed
  • The graph displayed.
  • The edge weights never showed.

Test 8

• Passed
  • The graph displayed.
  • The edge weights never showed.

Test 9

• Passed
  • The graph displayed.
  • The edge weights never showed.

Test 10

• Passed
  • The graph displayed.
  • The edge weights showed only when moused over.
  • The lines turned gray at the new thresholds I set.

Test 11

• Passed
  • The graph displayed.
  • The edge weights showed only when moused over.
  • The lines turned gray at the new thresholds I set.

Test 12

• Passed
  • The graph displayed.
  • The edge weights showed only when moused over.
  • The lines turned gray at the new thresholds I set.

Test 13

• Passed
  • The graph displayed.
  • The edge weights showed at all times.
  • The lines turned gray at the new thresholds I set.

Test 14

• Passed
  • The graph displayed.
  • The edge weights showed at all times.
  • The lines turned gray at the new thresholds I set.

Test 15

• Passed
  • The graph displayed.
  • The edge weights showed at all times.
  • The lines turned gray at the new thresholds I set.

Test 16

• Passed
  • The graph displayed.
  • The edge weights never showed.
  • The lines turned gray at the new thresholds I set.

Test 17

• Passed
  • The graph displayed.
  • The edge weights never showed.
  • The lines turned gray at the new thresholds I set.

Test 18

• Passed
  • The graph displayed.
  • The edge weights never showed.
  • The lines turned gray at the new thresholds I set.

Notes

Part 1:

• I used the 21-genes_31-edges_Schade-data_estimation_output.graphml, 21-genes_31-edges_Schade-data_estimation_output.sif, and 21-genes_31-edges_Schade-data_estimation_output.xlsx files for the tests.
• I checked with my partner to make sure that he got the same results for each test as I did.

Part 2:

• We started by using this Searching a Database page
• We used the general search link: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=<database>&term=<query>
  • The <database> we were looking in was gene.
  • The <query> is whatever gene you are looking for.
• The example we used first was https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2
  • This gave 539 results, so we had to narrow this down to genes contained within one organism, Saccharomyces cerevisiae.
• To narrow down, we added the organism name, Saccharomyces cerevisiae to the term field, so that the URL became: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2+AND+Saccharomyces+cerivisiae
  • This did narrow the results to 492, but did not get us what we wanted.
• We searched the Searching a Database page again and found that adding bracketed categories to the terms would give us the results we wanted, so the next URL we tried was: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2[gene]+AND+Saccharomyces+cerevisiae[Organism]
  • This gave only one result, with the ID for PBS2 in Saccharomyces cerevisiae, which was 853313.
• We then tried this again replacing the "pbs2" term with other genes.
  • This worked to give their IDs as well.

Acknowledgements

I worked with my homework partner, Quinn Lanners, on this assignment.

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

Mbalducc (talk) 16:36, 29 October 2017 (PDT)

References

LMU BioDB 2017. (2017). Week 9. Retrieved October 24, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9

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