Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg galFiltered.sif) and attributes from text (eg. galGeneNames.csv)
3. Select the Node Attribute Browser tab

B2.1.1

1. Click Select Attributes
2. Check the appropriate attribute boxes eg. cannonicalName

A new column for the attribute should appear in the panel

B2.1.2

Select a node and then select another node while in the Node Attribute Browser

Attributes should change to those for each specific node

B2.1.3

Drag and select multiple nodes

Nodes should be highlighted and their attributes listed

B2.1.4

Click one of the attributes of a node with multiple nodes selected

The selected attribute should get highlighted and the node a new highlight colour

B2.1.5

1. Select a node
2. Double click on the text under one of the attribute columns
3. Edit the text of eg. Species by changing the capitalisation the press enter

The Browser should reflect the text changes and they should persist even if the node is unselected and then reselected

B2.1.6

1. Drag and select several nodes (say 5)
2. Click create a new (string) attribute and call it Names
3. Click on the Attribute batch editor and select the Copy tab, select species from the Copy From menu and Names from the To menu
4. Click GO

The contents of the Copy From cells should now appear in the new attribute column Names

B2.1.7

1. Select the Clear tab from the Attribute batch editor box
2. Choose Names as the attribute column
3. Click GO

The Browser should reflect the changes by showing no entries in the Names column

B2.1.8

1. Select the Operation tab from the Node Attribute Batch Editor
2. Choose Set from the operation menu and choose the Names attribute as the column to edit
3. Type “Galactose Metabolism” into the text field and click GO

The Names attribute column should contain “Galactose Metabolism” for all the selected nodes

B2.1.9

1. Repeat step 1 from B2.1.8
2. Choose Replace from the operation menu and choose the Names attribute as the column to edit
3. Type “Galactose Transport” into the text field and click GO

The Names attribute column should contain “Galactose Transport” for all the selected nodes

B2.1.10

1. Repeat step 1 from B2.1.8
2. Choose To upper-case from the operation menu and choose the Names attribute as the column to edit
3. Click GO

The Names attribute column should contain “GALACTOSE TRANSPORT” or the text in the column should be all capitals

B2.1.11

1. Repeat step 1 from B2.1.8
2. Choose To lower-case from the operation menu and choose the Names attribute as the column to edit

The Names attribute column should contain “galactose transport” or the text in the column should all be lower case

B2.1.12

1. Repeat step 1 from B2.1.8
2. Choose Add Prefix from the operation menu and choose the Names attribute as the column to edit
3. Type “Yeast-“ into the text field and click GO

The Names attribute column should contain “Yeast-galactose transport” or the text in the column should be preceded by “Yeast-“

B2.1.13

1. Repeat step 1 from B2.1.8
2. Choose Add Suffix from the operation menu and choose the Names attribute as the column to edit
3. Type “-intracellular” into the text field and click GO

The Names attribute column should contain “Yeast-galactose transport-intracellular” or the text in the column should be followed by “-intracellular”

B2.1.14

1. Click create a new (Integer) attribute and call it Numbers
2. Repeat step 1 from B2.1.8
3. Choose Set from the operation menu and choose the Numbers attribute as the column to edit
4. Type “2” into the text field and click GO

The Numbers attribute column should contain “2”

B2.1.15

1. Repeat step 1 from B2.1.8
2. Choose Add Number from the operation menu and choose the Numbers attribute as the column to edit
3. Type “2” into the text field and click GO

The Numbers attribute column should contain “4”

B2.1.16

1. Repeat step 1 from B2.1.8
2. Choose Mul from the operation menu and choose the Numbers attribute as the column to edit
3. Type “2” into the text field and click GO

The Numbers attribute column should contain “8”

B2.1.17

1. Repeat step 1 from B2.1.8
2. Choose Div from the operation menu and choose the Numbers attribute as the column to edit
3. Type “4” into the text field and click GO

The Numbers attribute column should contain “2"

B2.1.18

1. Click the Import attributes from file icon in the Browser
2. Choose a node attribute file to import (eg. galFiltered.nodeAttrs1) and click Open
3. Click Select Attributes and click on the check box for the name of the newly imported attribute (eg. TestNodeAttribute1)

Each node selected should display either a 1, 2 or 3 in the TestNodeAttribute1 column

B2.1.19

1. Click the Import Expression Matrix icon in the Browser
2. Choose an expression matrix file (eg. galExpData.pvals) and click Open (leave the default setting of Apply nodes using ID)
3. Click Select Attributes and click on the check boxes

Each node selected should display expression values in the Xexp columns and p values in the Xsig columns (where X is the name of the experiment)

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 Edge Attribute Browser tab

B2.2.1

1. Click Select Attributes
2. Check the appropriate attribute boxes eg. cannonicalName, interaction

A new column for each attribute should appear in the panel

B2.2.2

Select an edge and then select another edge while in the Edge Attribute Browser

Attributes should change to those for each specific edge

B2.2.3

Drag and select multiple edges

Edges should be highlighted and their attributes listed

B2.2.4

1. Select an edge
2. Double click on the text under one of the attribute columns
3. Edit the text of eg. interaction by changing the capitalisation the press enter

The Browser should reflect the text changes and they should persist even if the node is unselected and then reselected

B2.2.5

1. Drag and select several edges (say 5)
2. Click create a new (string) attribute and call it Names
3. Click on the Attribute batch editor and select the Copy tab, select interation from the Copy From menu and Names from the To menu
4. Click GO

The contents of the Copy From cells should now appear in the new attribute column Names

B2.2.6

1. Select the Clear tab from the Attribute batch editor box
2. Choose Names as the attribute column
3. Click GO

The Browser should reflect the changes by showing no entries in the Names column

B2.2.7

1. Select the Operation tab from the edge Attribute Batch Editor
2. Choose Set from the operation menu and choose the Names attribute as the column to edit
3. Type “Anabolic Activation” into the text field and click GO

The Names attribute column should contain “Anabolic Activation” for all the selected nodes

B2.2.8

1. Repeat step 1 from B2.2.7
2. Choose Replace from the operation menu and choose the Names attribute as the column to edit
3. Type “Phosphorylates” into the text field and click GO

The Names attribute column should contain “Phosphorylates” for all the selected nodes

B2.2.9

1. Repeat step 1 from B2.2.7
2. Choose To upper-case from the operation menu and choose the Names attribute as the column to edit
3. Click GO

The Names attribute column should contain “PHOSPHORYLATES” or the text in the column should be all capitals

B2.2.10

1. Repeat step 1 from B2.2.7
2. Choose To lower-case from the operation menu and choose the Names attribute as the column to edit
3. Click GO

The Names attribute column should contain “phosphorylates” or the text in the column should all be lower case

B2.2.11

1. Repeat step 1 from B2.2.7
2. Choose Add Prefix from the operation menu and choose the Names attribute as the column to edit
3. Type “De-“ into the text field and click GO

The Names attribute column should contain “De-phosphorylates” or the text in the column should be preceded by “De-“

B2.2.12

1. Repeat step 1 from B2.2.7
2. Choose Add Suffix from the operation menu and choose the Names attribute as the column to edit
3. Type “-serine residues” into the text field and click GO

The Names attribute column should contain “De-phosphorylates-serine residues” or the text in the column should be followed by “-serine residues”

B2.2.13

1. Click create a new (Integer) attribute and call it Numbers
2. Repeat step 1 from B2.2.7
3. Choose Set from the operation menu and choose the Numbers attribute as the column to edit
4. Type “2” into the text field and click GO

The Numbers attribute column should contain “2”

B2.2.14

1. Repeat step 1 from B2.2.7
2. Choose Add Number from the operation menu and choose the Numbers attribute as the column to edit
3. Type “2” into the text field and click GO

The Numbers attribute column should contain “4”

B2.2.15

1. Repeat step 1 from B2.2.7
2. Choose Mul from the operation menu and choose the Numbers attribute as the column to edit
3. Type “2” into the text field and click GO

The Numbers attribute column should contain “8”

B2.2.16

1. Repeat step 1 from B2.2.7
2. Choose Div from the operation menu and choose the Numbers attribute as the column to edit
3. Type “4” into the text field and click GO

The Numbers attribute column should contain “2"

B2.2.17

1. Click the Import attributes from file icon in the Browser
2. Choose an edge attribute file to import (eg. galFiltered.edgeAttrs1) and click Open
3. Click Select Attributes and click on the check box for the name of the newly imported attribute (eg. TestEdgeAttribute1)

Each edge selected should display either a 1, 2 or 3 in the TestEdgeAttribute1 column

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a file (eg. galFiltered.sif)
3. Select the Network Attribute Browser tab

B2.3.1

1. Click create a new (string) attribute and call it Names
2. Click on the Attribute batch editor and select the Copy tab, select Value from the Copy From menu and Names from the To menu
3. Click GO

The contents of the Copy From cells should now appear in the new attribute column Names

B2.3.2

1. Select the Clear tab from the Attribute batch editor box
2. Choose Names as the attribute column
3. Click GO

The Browser should reflect the changes by showing no entries in the Names column

B2.3.3

1. Select the Operation tab from the network Attribute Batch Editor
2. Choose Set from the operation menu and choose the Names attribute as the column to edit
3. Type “Metabolic” into the text field and click GO

The Names attribute column should contain “Metabolic Function” for all the selected nodes

B2.3.4

1. Repeat step 1 from B2.3.3
2. Choose Replace from the operation menu and choose the Names attribute as the column to edit
3. Type “Galactose Metabolism” into the text field and click GO

The Names attribute column should contain “Galactose Metabolism” for all the selected nodes

B2.3.5

1. Repeat step 1 from B2.3.3
2. Choose To upper-case from the operation menu and choose the Names attribute as the column to edit
3. Click GO

The Names attribute column should contain “GALACTOSE METABOLISM” or the text in the column should be all capitals

B2.3.6

1. Repeat step 1 from B2.3.3
2. Choose To lower-case from the operation menu and choose the Names attribute as the column to edit
3. Click GO

The Names attribute column should contain “galactose metabolism” or the text in the column should all be lower case

B2.3.7

1. Repeat step 1 from B2.3.3
2. Choose Add Prefix from the operation menu and choose the Names attribute as the column to edit
3. Type “Yeast-“ into the text field and click GO

The Names attribute column should contain “Yeast-galactose metabolism” or the text in the column should be preceded by “Yeast-“

B2.3.8

1. Repeat step 1 from B2.3.3
2. Choose Add Suffix from the operation menu and choose the Names attribute as the column to edit
3. Type “-genes” into the text field and click GO

The Names attribute column should contain “Yeast-galactose metabolism-genes” or the text in the column should be followed by “-genes”

B2.3.9

1. Click create a new (Integer) attribute and call it Numbers
2. Repeat step 1 from B2.3.3
3. Choose Set from the operation menu and choose the Numbers attribute as the column to edit
4. Type “2” into the text field and click GO

The Numbers attribute column should contain “2”

B2.3.10

1. Repeat step 1 from B2.3.3
2. Choose Add Number from the operation menu and choose the Numbers attribute as the column to edit
3. Type “2” into the text field and click GO

The Numbers attribute column should contain “4”

B2.3.11

1. Repeat step 1 from B2.3.3
2. Choose Mul from the operation menu and choose the Numbers attribute as the column to edit
3. Type “2” into the text field and click GO

The Numbers attribute column should contain “8”

B2.3.12

1. Repeat step 1 from B2.3.3
2. Choose Div from the operation menu and choose the Numbers attribute as the column to edit
3. Type “4” into the text field and click GO

The Numbers attribute column should contain “2”