Cazinge Week 9

Part 1: GRNsight Testing

GRNsight Client Side Testing Document: D-Pad Control

Last Updated: 2017-10-23

Test 1

Instructions:

Load Graph - File Menu -> Open

Results:

GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file

Conclusions:

GRNsight appears to successfully lay out the mentioned network graph as specified from the Excel workbook.

Test 2

Instructions:

Load Graph - File Menu -> Import SIF

Results:

GRNsight should lay out a network graph from the SIF file if there are no errors in the file

Conclusions:

GRNsight appears to successfully lay out the mentioned network graph as specified from the SIF file.

Test 3

Instructions:

Load Graph - File Menu -> Import GraphML

Results:

GRNsight should lay out a network graph from the GraphML file if there are no errors in the file

Conclusions:

GRNsight appears to successfully lay out the mentioned network graph as specified from the GraphML file.

Test 4

Instructions:

Load Graph - File Menu -> Open
D-Pad Control - Click Right Arrow

Results:

GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left

Conclusions:

GRNsight appears to successfully shift to the left when the Excel workbook is loaded and restrict graph to viewport is unchecked.

Test 5

Instructions:

Load Graph - File Menu -> Import SIF
D-Pad Control - Click Right Arrow

Results:

GRNsight should lay out a network graph from the SIF file if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left

Conclusions:

GRNsight appears to successfully shift to the left when the SIF file is loaded and restrict graph to viewport is unchecked.

Test 6

Instructions:

Load Graph - File Menu -> Import GraphML
D-Pad Control - Click Right Arrow

Results:

GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the left

Conclusions:

GRNsight appears to successfully shift to the left when the GraphML file is loaded and restrict graph to viewport is unchecked.

Test 7

Instructions:

Load Graph - File Menu -> Open
D-Pad Control - Click Left Arrow

Results:

GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right

Conclusions:

GRNsight appears to successfully shift to the right when the Excel workbook is loaded and restrict graph to viewport is unchecked.

Test 8

Instructions:

Load Graph - File Menu -> Import SIF
D-Pad Control - Click Left Arrow

Results:

GRNsight should lay out a network graph from the SIF file if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right

Conclusions:

GRNsight appears to successfully shift to the right when the SIF file is loaded and restrict graph to viewport is unchecked.

Test 9

Instructions:

Load Graph - File Menu -> Import GraphML
D-Pad Control - Click Left Arrow

Results:

GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift to the right

Conclusions:

GRNsight appears to successfully shift to the right when the GraphML file is loaded and restrict graph to viewport is unchecked.

Test 10

Instructions:

Load Graph - File Menu -> Open
D-Pad Control - Click Up Arrow

Results:

GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift down

Conclusions:

GRNsight appears to successfully shift down when the Excel workbook is loaded and restrict graph to viewport is unchecked.

Test 11

Instructions:

Load Graph - File Menu -> Import SIF
D-Pad Control - Click Up Arrow

Results:

GRNsight should lay out a network graph from the SIF file if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift down

Conclusions:

GRNsight appears to successfully shift down when the SIF file is loaded and restrict graph to viewport is unchecked.

Test 12

Instructions:

Load Graph - File Menu -> Import GraphML
D-Pad Control - Click Up Arrow

Results:

GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift down

Conclusions:

GRNsight appears to successfully shift down when the GraphML file is loaded and restrict graph to viewport is unchecked.

Test 13

Instructions:

Load Graph - File Menu -> Open
D-Pad Control - Click Down Arrow

Results:

GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift up

Conclusions:

GRNsight appears to successfully shift up when the Excel workbook is loaded and restrict graph to viewport is unchecked.

Test 14

Instructions:

Load Graph - File Menu -> Import SIF
D-Pad Control - Click Down Arrow

Results:

GRNsight should lay out a network graph from the SIF file if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift up

Conclusions:

GRNsight appears to successfully shift up when the SIF file is loaded and restrict graph to viewport is unchecked.

Test 15

Instructions:

Load Graph - File Menu -> Import GraphML
D-Pad Control - Click Down Arrow

Results:

GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should shift up

Conclusions:

GRNsight appears to successfully shift up when the GraphML file is loaded and restrict graph to viewport is unchecked.

Test 16

Instructions:

Load Graph - File Menu -> Open
D-Pad Control - Click Center Button

Results:

GRNsight should lay out a network graph from the Excel workbook if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport

Conclusions:

GRNsight appears to successfully shift to the center of the bounding box when the Excel workbook is loaded and restrict graph to viewport is unchecked.

Test 17

Instructions:

Load Graph - File Menu -> Import SIF
D-Pad Control - Click Center Button

Results:

GRNsight should lay out a network graph from the SIF file if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport

Conclusions:

GRNsight appears to successfully shift to the center of the bounding box when the SIF file is loaded and restrict graph to viewport is unchecked.

Test 18

Instructions:

Load Graph - File Menu -> Import GraphML
D-Pad Control - Click Center Button

Results:

GRNsight should lay out a network graph from the GraphML file if there are no errors in the file
if "Restrict Graph to Viewport" is Unchecked., The graph should move to the center of the bounding box (note that it is not the same thing as the viewport

Conclusions:

GRNsight appears to successfully shift to the center of the bounding box when the GraphML file is loaded and restrict graph to viewport is unchecked.

Part 2: Web Service Exploration

UniProt

Relevant documentation:
Supplementary websites:
- Retrieve/ID mapping web page
Technical information:
- You will encounter redirects in these web services; web browsers handle this automatically, but if using curl make sure to add the -L switch (i.e., curl -L …)
- Your URLs will include ampersands (&), which will need special handling with curl: in these cases, enclose the URL in apostrophes (e.g., curl -L 'http://www.uniport.org?query=this&type=that')
- UniProt primarily provides results in XML format; in one relevant step, the data can be provided in tab-delimited format, which might be easier to work with
Miscellaneous information:
- You will encounter the need for a taxon ID, which identifies a specific organism; the taxon ID for our strain of S. cerevisiae is 559292

Solution

This is a bash function that we made to display the results from today's exercise

NOTE: We are assuming that you are using bash for the purposes of running this command.
put this code into a file named getInfoForGene
run chmod +x ./getInfoForGene
use the function like so: ./getInfoForGene "GENE_NAME"
- ex: ./getInfoForGene PBS2

#!/bin/bash

gene_id=$(curl -L "http://www.uniprot.org/uploadlists/?from=GENENAME&to=ACC&format=tab&taxon=559292&query=$1" | grep $1 | sed "s/$1[[:space:]]*\([A-Za-z0-9]*\).*/\1/g")

curl -L "http://uniprot.org/uniprot/$gene_id.xml"

Notebook

When doing this assignment, we first made a point of identifying and outlining the endpoints that we'd need to go from the gene name to the gene description; of which there were 2: turning the gene name into the matching uniprot id; then turning the uniprot id into the gene's information page. It was pretty clear how to do the latter part, which had been provided to us in an earlier assignment, but to do the former, we needed to use Uniprot's format conversion endpoint. First we found what parameters we'd need to provide to the endpoint, inspecting the elements to find the names of the specific parameters, and we promptly became stuck on the taxon id because our answers weren't being restricted solely to the genes that we wanted. Luckily, however, Dondi's notes provided us with the taxon id we needed, speeding up our process of getting to the answer. After we were able to get the uploadlists endpoint to work, we just needed to extract the id from the tab delimited output. we ran into a problem regarding POSIX-based whitespace, but we resolved it using the sed command you see provided. Finally, we assigned that output to a variable and fed it into the gene description endpoint.