Simonwro120 Week 9

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Homework Instructions

Hands-On with GRNsight

Each homework pair has been assigned one subset of the GRNsight client-side testing protocol for the current beta version of GRNsight. Follow this protocol and report the results of your tests in the electronic journal. Homework partners have one testing subset each so that you can talk to each other about the requested tests, but the testing itself should still be done and reported individually, in the spirit of seeking reproducible results.

  1. Each feature is to be tested in combination will all three formats that GRNsight can read (Excel workbook, SIF, GraphML). This is already specified in the testing document. Choose one file for each of these formats from this web page for use in your tests and specify them in your electronic notebook. In order to have a basis for comparison, homework partners should use the same test files for their individual test sequences.
    • For the Excel workbooks (.xlsx) in the linked collection above, click on the file then click Download to save the file to your computer.
    • For the SIF (.sif) and GraphML (.graphml) files, click on the file, click on the Raw button, then either copy-paste or save the resulting file to your computer.
  2. Each test specifies a sequence of actions to perform, followed by their expected results. Use the latter to determine whether GRNsight passed a particular test. Report the result of each test in your electronic notebook.
    • The version of GRNsight that you are testing is a beta version, so results that diverge from the expected ones are certainly possible.
    • If the observed result is the same as the expected result, indicate that GRNsight passed that particular test.
    • If the observed result is not the same as the expected result, indicate that GRNsight failed that particular test and document what was different. For many tests, a screenshot will be the most effective way to document this difference, so do not hesitate to supply one.
  3. If you see any other behavior that appears incorrect, erroneous, or confusing, please report those observations in a section of your electronic notebook as well.
  4. As always, make sure to document and acknowledge your interactions with your homework partner in the Acknowledgments section of your individual journal.

Web Service API Exploration

Each homework pair has been assigned one of the four gene-related web services that we have used for the “favorite gene page” assignments (Ensembl, NCBI, UniProt, SGD/YeastMine). Because there are only four such services, two homework pairs will be working on the same service, so if you wish, you may join “fources” (sorry) to explore the same web service together. Still, you must write up your findings individually in your own respective words.

Your Mission

For the web service that has been assigned to you, use the information given on this page to discover how to take a gene name/symbol (e.g., ACT1, BRO1, SPT15, etc.) and find your way to its full “data profile” within that service. This process may require multiple web service calls and will involve “reading” web service data formats such as JSON or XML.

Your foundational knowledge for this exercise begins with what you have learned from working with “your favorite gene” and from using the services’ corresponding websites. Furthermore, the final URLs that lead to the full gene data are already known to you: they are in the ajax-starter files from the Week 7 assignment. You will want to use a combination of a web browser and curl, with a code-savvy editor like Atom or Visual Studio Code to help make any received data more readable to you.

The Deliverable

Upon determining how to go from a gene name/symbol to that gene’s individual data record (as shown in the Week 7 ajax-starter files), write up this process as a reproducible “recipe” in your electronic journal. In general, this recipe will consist of:

  • 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

This exercise is somewhat unusual in that the work lies in the process of figuring out how to use the web service. Once the steps are known, actually performing these steps is quite straightforward. Thus, although the prospect of doing this may be quite intimidating to those who are new to it, please rest assured that the journey itself is the reward here and it is the very open-endedness of this exploration that we’d like you to experience in this exercise.

That said, it is again imperative that you take good notes about the things you try, and their results, so that you don’t go around in circles and eventually narrow down your exploration the the desired set of steps.

GRNsight Lab Notebook

Beta Testing GRNsight

  1. To begin, I downloaded three different files from the GRNsight repository. One in .sif format, .xlsx format, and .graphml format.
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
  1. Next, I performed each test on the .xlsx file, .sif file, and .graphml file in GRNsight.
    • Test 1: Passed
    • Test 2: Passed
    • Test 3: Passed
    • Test 4: Passed.
    • Test 5: Passed
    • Test 6: Passed
    • Test 7: Passed
    • Test 8: Passed
    • Test 9: Passed
    • Test 10: Passed
    • Test 11: Passed
    • Test 12: Passed
    • Test 13: Passed.
    • Test 14: Passed
    • Test 15: Passed
    • Test 16: Passed
    • Test 17: Passed
    • Test 18: Passed

Observations

  • All tests passed which is excellent!
  • When performing tests in reference to normalization, Dina and I noticed that the changes made to the thickness of the lines were only noticeable when the change in the Edge Weight Normalization Factor had a large difference in value.

Web Service API Exploration Notes

  • The URL my group use in order to retrieve the desired data was:
https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene


-Which returned all the genes in the database.
  • We added ?symbol=BRO1 to the end of thus URL, which then allowed us to specify a gene.
    • The last part of this URL ?symbol=BRO1 is what specificies what we are looking for: 1: a symbol, and 2: a symbol with the characters "BRO1"
  • What happens if you enter this query request in your address bar?

Notebook Step-by-Step

  • Downloaded the three necessary files
  • Beta-tested and observed/reported any unexpected behavior
  • Played around with the curl command until I was able to return all the data of a gene via the request of a specific URL

Acknowledgements

  • I met with Dina on Sunday 10/29 to start working on the tests for GRNsight. We met in the biological database lab in person to collaborate on this section.
  • On Monday 10/30 I met with Dina, John, and Hayden in the lab to work on the API exploration of the assignment.
  • Special thanks to Dondi for his helpful hints and generous responses to our lifeline.
  • While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
  • Signature: Simonwro120 (talk) 18:58, 30 October 2017 (PDT)

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 Week 13 Week 14 Week 15

List of Journal Entries

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

List of Shared Journals

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15

References

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