Kwrigh35 Week 9
Contents
Electronic Notebook
Viewport Size Testing Instructions
- We were tasked with testing the viewport on the GRNsight Beta.
- The files we used for testing were titled
- 21-genes_31-edges_Schade-data_input.graphml,
- 21-genes_31-edges_Schade-data_input.sif
- 21-genes_31-edges_Schade-data_input.xlsx.
- The files were downloaded from this website.
- We followed the testing instructions on this PDF.
Viewport Size Testing Results
Test numbers refer to tests found on this PDF
| Test Number | Results |
|---|---|
| Test 1 | PASS |
| Test 2 | PASS |
| Test 3 | PASS |
| Test 4 | PASS |
| Test 5 | PASS |
| Test 6 | PASS |
| Test 7 | PASS |
| Test 8 | PASS |
| Test 9 | PASS |
| Test 10 | PASS |
| Test 11 | PASS |
| Test 12 | PASS |
| Test 13 | FAIL |
| Test 14 | FAIL |
| Test 15 | FAIL |
Failed Test Explanation
Tests 13, 14, and 15 were designed to test the "Fit to Window" functionality of the viewport. We noticed that when the browser window was small (less than 1317 pixels wide) the viewport extended further than the scope of the browser. Figure 1 highlights the scroll bar that appears at the bottom of the browser window (which appears when the viewport extends beyond the width of the browser window.)
API
The database my partner and I worked with was UniProt. By executing the first two commands given below, one can successfully find the gene ID number for any Saccharomyces Cerevisiae gene if the gene name is known. Simply replace <gene name> with the name of the gene you are looking for (e.g. ASP1, ACT1, etc.)
gene_name=<gene name> gene_id=$(curl -L "http://www.uniprot.org/uniprot/?query=559292+$gene_name&sort=score" | grep -o -P '(?<=tbody><tr id=").*(?=\" class=" entry s)') curl -L "http://uniprot.org/uniprot/$gene_id.xml"
We used this URL http://www.uniprot.org/uniprot/?query=559292+$gene_name&sort=score as part of the command. The number 559292 refers to the Taxon ID that represents Saccharomyces Cerevisiae in UniProt.
In order to find the raw data about the gene, you then simply execute the third command given above. UniProt returns this information in XML format.
Acknowledgements
- I'd like to thank my homework partner, Eddie Bachoura, for meeting with me on Monday afternoon (10/30). We worked on the assignment together and were able to finish in a couple of hours.
- While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Kwrigh35 (talk) 23:19, 30 October 2017 (PDT)
References
- LMU BioDB 2017. (2017). Week 9. Retrieved October 24, 2017, from Week 9
- LMU BioDB 2017. (2017). GRNsight Client Side Testing Document: Viewport Size. Retrieved October 24, 2017, from media:GRNsight_Testing-Viewport_Size.pdf
Useful Links
| Category | Links |
|---|---|
| Interwiki | Main Page Katie Wright Course schedule Lights, Camera, InterACTION! |
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