Difference between revisions of "Hhinsch Week 9"
From LMU BioDB 2017
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| + | ==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=== | ||
| + | *First, I used Dondi's hint to find the URL that retrieves json from our ajax-starter files. | ||
| + | *To get this, I inspected the loading box on bro1.html and hit the load button. | ||
| + | *I then clicked on the network tab on the inspection section and hovered my mouse over the <code>Gene?id=66043773</code> in order to see the url. | ||
| + | *By right-clicking on <code>Gene?id=66043773</code> I was able to copy and paste the link. I then changed <code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?id=66043773</code> to <code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1</code> in order to have the search parameters be in terms of the Gene's symbol. | ||
| + | *Because this is on yeastmine, we didn't need to set a species parameter in the URL. | ||
| + | *Next I needed to simply type the <code>curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1</code> command into my command prompt to have it retrieve the json data. | ||
| + | *I found that I can type the <code>https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1</code> into a browser and download the data in .json format. | ||
| + | *By opening the download in a text editor, it easily provides the data for a specific gene. | ||
| + | *I found that I can use any gene symbol to find the data for any specific gene simply by using the <code>curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=</code> template. | ||
==Acknowledgments== | ==Acknowledgments== | ||
#[[User:johnllopez616|John Lopez]], [[User:dbashour|Dina Bashoura]], [[User:Simonwro120|Simon Wroblewski]] and I worked together in order to complete the deliverables of this assignment. [[User:johnllopez616|John Lopez]] and I worked together more than once to complete the deiverables of this assignment. | #[[User:johnllopez616|John Lopez]], [[User:dbashour|Dina Bashoura]], [[User:Simonwro120|Simon Wroblewski]] and I worked together in order to complete the deliverables of this assignment. [[User:johnllopez616|John Lopez]] and I worked together more than once to complete the deiverables of this assignment. | ||
Revision as of 23:31, 30 October 2017
Contents
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.
|
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
- First, I used Dondi's hint to find the URL that retrieves json from our ajax-starter files.
- To get this, I inspected the loading box on bro1.html and hit the load button.
- I then clicked on the network tab on the inspection section and hovered my mouse over the
Gene?id=66043773in order to see the url. - By right-clicking on
Gene?id=66043773I was able to copy and paste the link. I then changedhttps://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?id=66043773tohttps://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1in order to have the search parameters be in terms of the Gene's symbol. - Because this is on yeastmine, we didn't need to set a species parameter in the URL.
- Next I needed to simply type the
curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1command into my command prompt to have it retrieve the json data. - I found that I can type the
https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=BRO1into a browser and download the data in .json format. - By opening the download in a text editor, it easily provides the data for a specific gene.
- I found that I can use any gene symbol to find the data for any specific gene simply by using the
curl https://yeastmine.yeastgenome.org/yeastmine/service/data/Gene?symbol=template.
Acknowledgments
- John Lopez, Dina Bashoura, Simon Wroblewski and I worked together in order to complete the deliverables of this assignment. John Lopez and I worked together more than once to complete the deiverables of this assignment.
- John David N. Dionisio helped explain the use of curl to complete the deliverables of this assignment.
- While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
References
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 14
Week 15
Hayden's Individual Journal Entries
hhinsch Week 1
hhinsch Week 2
hhinsch Week 3
hhinsch Week 4
hhinsch Week 5
hhinsch Week 6
hhinsch Week 7
hhinsch Week 8
hhinsch Week 9
hhinsch Week 10
hhinsch Week 11
hhinsch Week 12
hhinsch Week 14
hhinsch Week 15
Page Desiigner Deliverables Page
Class Journal Entries
Class Journal Week 1
Class Journal Week 2
Class Journal Week 3
Class Journal Week 4
Class Journal Week 5
Class Journal Week 6
Class Journal Week 7
Class Journal Week 8
Class Journal Week 9
Class Journal Week 10
Page Desiigner
