Hhinsch Week 9

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GRNsight Client Side Testing Document: Normalization + Zoom and Web Service API Exploration

GRNsight Client Side Testing Document: Normalization + Zoom

  • We used the following files for our tests:


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

Test Pass or Fail Additional Explanation
Test 1 Pass There weren't any errors in completing this process.
Test 2 Pass There weren't any errors in completing this process.
Test 3 Pass There weren't any errors in completing this process. The graph showed up completely grey in the other two .graphml files.
Test 4 Pass There weren't any errors. I used the edge weight factor of one and the lines became very thick.
Test 5 Pass I imported the .sif file and changed the weight factor from 1 to 2. It should be noted that the edge weight factor stays the same as when you determined it in the step before, even if you import a new graph.
Test 6 Pass For this .graphml file it uploaded then I changed the edge weight factor to 0.001 and it worked. There isn't any way to set the normative factor for the other two .graphml files.
Test 7 Pass The graph zoomed without a problem.
Test 8 Pass The graph zoomed without a problem.
Test 9 Pass The graph zoomed without a problem.
Test 10 Pass I set the normalization factor to 0.001. The graph zoomed without a problem.
Test 11 Pass I set the normalization factor to 0.001. The graph zoomed without a problem.
Test 12 Pass I set the normalization factor to 0.001. The graph zoomed without a problem.
Test 13 Pass The graph zoomed out without a problem.
Test 14 Pass The graph zoomed out without a problem.
Test 15 Pass The graph zoomed out without a problem.
Test 16 Pass I set the normalization factor to 0.001 and it zoomed out without a problem.
Test 17 Pass I set the normalization factor to 0.001 and it zoomed out without a problem.
Test 18 Pass I set the normalization factor to 0.001 and it zoomed out without a problem.

Web Service API Exploration

  • The URLs to access in order to retrieve the desired data
  • Any portions in these URLs that need to be substituted for specific queries, such as the gene name or ID within that web service
  • Specific instructions on how to interpret the data returned by each URL so that you can extract exactly the information you need in order to proceed to the next step
    • If you copy the URL that is used to access the desired data and hit enter, your computer will download a .json file that can be easily read in a text editor. From here, it is easy to read the data that is provided. You can also use the computer's terminal to invoke the curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1 command in order to retrieve the data in a text form. This is a little bit more difficult to read but it is entirely possible to do so if you have some basic knowledge of reading .json. I however would recommend that an individual retrieving this data should use the method for downloading the .json file of the data so it is a bit easier to read.
    • If you would like to obtain a sole object of the gene's data, you can use the curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1 | grep '"primaryIdentifier":"S' command in the terminal, then copy the text to a code reader such as atom.
    • I however believe that simply using the https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1 url in the browser to download a .json file of the data is the best option. This is because you can open the .json file in a code reader, and it contains additional identifiers that may be useful.

Electronic Notebook

  • In order to complete the tests, I dowloaded the three files noted above onto my computer.
  • In order to download the sif and graphml files, I needed to change the parameters from text files to all files.
  • Once the files were on my desktop, all I had to do was follow the instructions for each test to complete them.

URL Explanation

Acknowledgments

  1. John Lopez, Dina Bashoura, Simon Wroblewski and I worked together in the lab in order to complete the deliverables of this assignment. John Lopez and I worked together in person more than once to complete the deiverables of this assignment.
  2. John David N. Dionisio helped explain the use of curl to complete the deliverables of this assignment.
  3. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.Hhinsch (talk) 23:32, 30 October 2017 (PDT)

References

  1. LMU BioDB 2017. (2017). Week 9. Retrieved October 30, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9.
  2. BRO1 HTML File. (2017). Retrieved October 30,2017, from BRO1 HTML File.
  3. GRNsight Client Side Testing Document: Normalization + Zoom. (2017). Retrieved October 30, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/images/9/9d/GRNsight_Testing-Normalization_and_Zoom.pdf.
  4. GRNsight. (2017) Retrieved October 29, 2017, from http://dondi.github.io/GRNsight/.

Assignments

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Week 9
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Hayden's Individual Journal Entries

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Class Journal Entries

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Electronic Notebook

Hhinsch Electronic Notebook

Hayden's User Page

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