Cytoscape_3/Cy3TestPlan/misc

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.sif)

CE1

Click and drag a new node from the Editor tab and drop into an empty space on the graph

A new node should appear number sequentially according to the number of times a new node has been added

CE2

1. Click and drag a new directed edge and drop it on top of the new node created in the previous case
2. Click on an already existing node as the target for the interaction

A directed edge between the new node and the existing node should appear

CE3

1. Select the new node and edge alone by dragging a box around them
2. Right-click on the node and then click Delete selected nodes and edges

The selected edge and node should be deleted and no longer appear on the graph

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import two network files: (eg. galFiltered.sif and BINDyeast.sif)
3. Click on Plugins and select Advanced Network Merge
4. Select each network from the available networks box and then click the right arrow to move them to the selected networks box.
5. Click OK to merge the selected networks (Note: with large networks Cytoscape may not automatically create a graphical view, so click on the Edit menu with the network highlighted and click on Create View)

GM1

Before precondition step 5 select the Union operation

A new graph should be created displaying the merged networks (If this does not happen see preconditions Note)

GM2

Before precondition step 5 select the Intersection operation

A new graph should be created displaying the common nodes from the two networks

GM3

Before precondition step 5 select the Difference operation (order matters)

A new graph should be created displaying the parts of the first network that are not in the second network

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.sif)

LO1

1. Right click on a node and select LinkOut from the right-click menu
2. Select Reactome → ReactomeID

The link should open the web page www.reactome.org

LO2

1. Right click on a node and select LinkOut from the right-click menu
2. Select Entrez → Protein

The link should open the web page www.ncbi.nlm.nih.gov

LO3

1. Right click on a node and select LinkOut from the right-click menu
2. Select iHOP → yeast

The link should open the web page www.ihop-net.org

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. Sample1.xml++)

P1

The graph produced should contain only 6 nodes and 8 edges

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.sif)

QF1.1

Enter text into the search field on the Tool bar and press Enter

If the search term is found it should be highlighted and zoomed the view panel should zoom in

QF1.2

With text in the search field click on the triangle tab at the end of the field

A list of similar terms to the text entered in the search field should appear

QF1.3

Enter irrelevant text into the search field

The field should be highlighted red and the drop down menu should display the search term followed by 0 hits

QF2.1

Select the Configure search options and then click cancel

The dialog box should disappear and settings should remain the same

QF2.2

1. Select the Configure search options, then click on the Node or Edge radio buttons and change the Selected attribute and click Apply
2. Enter text appropriate for the new search parameters

The search configuration box should disappear and the drop down menu should contain the corresponding style of suggestions to the search parameters. The term entered should highlight the object in the graph

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. File → Import network from Table (eg. SampleHumanNetwork.xlsx Note: This file can also be found in the testData directory.)

TI1

1.Before pressing Import, select the Show Text File Import Options (under the Advanced heading)
2. Ensure that the preview options are working by changing the radio button to Show First and then enter 5 entries
3. Press the refresh preview button

The preview box should reflect the changes made to the Preview Options and should now show only the first 5 entries in the file

TI2

1. Repeat step 1 from TI1
2. Click on the Transfer first line as attribute names check box

The bolded cells at the top of each column that were labeled Column 1, Column 2 etc should now contain the contents of the 1st row of the table (eg. Gene, Interaction)

TI3

1. In the Interaction Definition box select column 1 from the drop down menu for Source Interaction and select Column three from the menu for Target Interaction
2. Click Import taking note of the contents of the Default interaction field
3. Select the newly created network from the network tab and click the Edge Attribute Browser
4. Select an edge

Every edge selected should display the Default interaction type between the two nodes (eg. pp). Repeat steps 1-4, but change the Default interaction (eg. cc)

TI4

1. Repeat step 1 from TI1 bit do not designate a file to upload yet
2. Click the Show all entries radio button under Preview Options
3. Select a file to upload

This should work normally, but if the known bug is still present a message appears: File is broken or empty!

TI5

1. In the Interaction definition box select column 1 from the drop down menu for Source Interaction
2. Repeat step 1 from TI1

A graph containing only the genes listed in the Source Interaction column should appear (with no edges)

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg.EcoliSBML.sbml)

SR1

A network should appear in the viewing panel and the results panel should contain a visual legend of the features in the graph