Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

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

AL1

The graph should take on one of the Cytoscape Automatic Layouts (in this case a grid)

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Click File → New → Network → Create network using cPath…

C1

1. Click the Help button

A window entitled Quick Reference Manual should appear describing the basics of using cPath searches

C2

Click the About button

A widow containing details on the cPath plugin should appear

C3

1. Select All Organisms and type “p53” into the search field
2. Set the limit to 10 and click search

cPath should generate a network containing genes related to p53 for all organisms in the list

C4

1. Select C. elegans and type “rpl-12” into the search field
2. Set the limit to 20 and click search

cPath should generate a network containing the genes related to rpl-12 in C. elegans

C5

1. Select D. melanogaster and type “DPP” into the search field
2. Set the limit to 50 and click search

cPath should generate a network containing the genes related to DPP in D. melanogaster

C6

1. Select E. coli and type “LacI” into the search field
2. Set the limit to 100 and click search

cPath should generate a network containing the genes related to LacI in E. coli

C7

1. Select H. Sapiens and type “CD4” into the search field
2. Set the limit to 500 and click search

cPath should generate a network containing the genes related to CD4 in H. sapiens

C8

1. Select H. pylori 26695 and type “” into the search field
2. Set the limit to 1000 and click search

This appears to be broken at the moment since no search is returning any results

C9

1. Select M. musculus and type “CLCA” into the text field
2. Set the limit to 5000 and click search

cPath should generate a network containing genes related to CLCA in M. musculus

C10

1. Select S. cerevisiae and type “STE7” into the search field
2. Set the limit to 10 and click search

cPath should generate a network containing genes related to STE7 in S. cerevisiae

C11

1. Select R. norvegicus and type “BKCa” into the search field
2. Set the limit to 20 and click search

cPath should generate a network containing the genes related to BKCa in R. norvegicus

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.sif)
3. Select the Editor tab from the Control Panel

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 a network file (eg. galFiltered.sif)
3. Click Create new (Integer) Attribute from the Node Attribute Browser and call it Numbers
4. Drag and select a group of nodes and click on the Attribute Batch Editor
5. Choose Set from the Operation tab and Numbers from the Attribute menu and type “3” into the text field then click GO, repeat using “2” and “4”
6. Click Select → Use Old Filters

OF1

1. Click Create new filter from the Manage Filters box and select Numeric Filter
2. Leave the default settings in the Numeric Attribute Filter box but type “3” into the text field, click Apply selected filter

The nodes highlighted should contain “3” in the Numbers attribute column (since the default operation is “=”)

OF2

1. Change the operation to “<” from the menu in the Numeric Attribute Filter box and type “3” into the text field
2. Click Apply selected filter

All the nodes with “2” in the Numbers attribute column (or any number less than 3) should be highlighted

OF3

1. Change the operation to “>” from the menu in the Numeric Attribute Filter box and type “3” into the text field
2. Click Apply selected Filter

All the nodes with “4” in the Numbers attribute column (or any number greater than 3) should be highlighted

OF4

Click Remove selected filter with the Numbers>3 filter selected

The filter should no longer be listed in the Available Filters box

OF5

1. Click Create new filter from the Manage Filters box and select String Filter
2. Select canonicalName from the text attribute menu in the String Pattern Filter box
3. Type “?” into the text field and click Apply selected Filter

The node whose canonicalName value is “?” should be highlighted

OF6

1. Click Create new filter from the Manage Filters box and select Topology Filter
2. Change the “Select nodes with at least” text field to “2” and click Apply selected filter

Only nodes that are the source or target of at least two edges should be highlighted

OF7

1. Click Create new filter from the Manage Filters box and select Boolean Meta-Filter
2. Select the Topology and String filters and click the Negate check box
3. Chose ALL, ONLY ONE or AT LEAST ONE from the “Select objects that pass” menu and click Apply selected filter in each case

With the ALL parameter every node apart from “?” should be highlighted, with the AT LEAST ONE parameter every node apart from “?” with at least two interactions should be highlighted and with the ONLY ONE parameter only nodes with one interaction should be highlighted

OF8

1. Click Create new filter from the Manage Filters box and select Edge Interaction
2. Choose “source or target” from the “Select edges with a node” menu and the Topology Filter from the “which passes the filter” menu
3. Click Apply selected filter

The edges that connect the nodes which pass the Topology filter should be highlighted (similar results for just target or source)

OF9

1. Click the Create new filter from the Manage Filters box and select String Filter
2. Choose Edge from the “select graph objects of type” menu and interaction from the text attribute menu and type “pp” into the text field
3. Click create new filter from the Manage Filters box and select Node Interactions
4. Choose “source or target” from the “Select nodes that are” menu and the String Filter created in step 1 in the “at least one edge that passes the filter” menu
5. Click Apply selected filter

The nodes that are connected by edges that represents pp interactions should be highlighted

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.sif)
3. Click Create New Attribute in the Node Attribute Browser and select Integer from the menu
4. Drag and select some nodes
5. Select Attribute Batch Editor and choose Set from the operation tab
6. Type an integer and click GO
7. Repeat steps 5-7 for two other groups of nodes (with different integers)
8. Click Select → Use Filters (F7) (Alternatively, click on the Filters tab in the Control Panel)

F1

1. Click on the Options button and select Create new filter… from the menu
2. Call the new Filter Numbers
3. In the Filter Definition section select node.Numbers from the menu
4. Click Add, double click the range bar and set the Low and High Bound to 5, click Apply

All the nodes with “5” in their Numbers attribute column should be highlighted

F2

1. (Repeat steps 1-4 from F1)
2. Click the Not check box next to the range bar (then click Apply)

All the nodes that do not have “5” in their Numbers attribute column should be highlighted

F3

1. (Repeat steps 1-4 from F1)
2. Click the Advanced “+” symbol in the Filter Definition area and click on the Negation check box

All the nodes that do not have “5” in their Numbers attribute column should be highlighted

F4

1. (Repeat steps 1-4)
2. Select node.Numbers from the Attribute/Filter menu again and click Add
3. Set the Low and High bounds to 1 and click Apply (ensuring that AND appears between the two range bars)

There should be no selected nodes on the graph because the Numbers attribute only contains one integer

F5

1. (Repeat steps 1-3 from F4)
2. Ensure that OR appears between the two range bars by selecting the OR radio button from the Filter Definition area

All the nodes that have either a 1 or a 5 in their Numbers attribute column should be highlighted

F6

1. (Repeat steps 1-4 from F1)
2. Click the garbage can icon beside the range bar

The parameter should be deleted and no longer appear in the Filter Definition area

F7

1. Select edge.interaction from the Attribute/Filter menu and click Add
2. Type “pp” into the text field and click Apply

All the edges in the graph that represent pp interactions should be highlighted

F8

1. Click the Options button and select Rename Filter
2. Type “Filter 1” into the text field and click OK

The Current Filter menu should reflect the name change to “Filter 1”

F9

1. Click the Options button and select Create new topology filter
2. Type “Topology” into the text field and click OK
3. Under Toplogy Filter Definition type “1” into the first and second text fields and leave the menu on none for additional Filters to pass

All the nodes that have 1 neighbour within 1 edge interaction should be highlighted (eg. All the nodes in galFiltered.sif)

F10

Select Filter 1 from the Topology Filter Definition and click Apply

Only those nodes that pass Filter 1 as well as the Topology Filter should be highlighted

F11

1. Click the Options button and select Create new NodeInteraction Filter
2. Type “Node” into the text field and press OK
3. Leave the default settings in the Interaction Filter Definition area and click Apply

All the nodes that are either the source or the target of at least one edge that passes Filter 1 (eg. Is a pp interaction edge)

F12

1. Click the Options button and select Create new EdgeInteraction Filter
2. Type “Edge” into the text field and press OK
3. Select Node from the Filter menu in the Interaction Filter Definition area

All the edges whose source or target node pass the NodeInteraction filter Node should be highlighted

F13

1. Select Edge from the Current Filter menu
2. Click the Options button and select Delete Filter, click YES when the Warning box appears

The Edge Filter should be deleted and should no longer appear in the Current Filter menu

F14

1. Select Filter 1 from the Current Filter menu
2. Click on the Global check box under Advanced in the Filter Definition area
3. Import another network file (eg. galFiltered.gml)
4. Type “pp” into the text filed next to interaction in the Filter Definition area
5. Click Apply

All of the edges that represent pp interactions in both graphs should be highlighted