Train-the-Trainers -- Week 3

In the third week, we ran through the Cytoscape Automation Workshop. Please answer the questions below to demonstrate your mastery of this week's tasks.

Question Title

1. What are good reasons to automate or script operations in Cytoscape? (Choose one or more)

To document data analysis and visualization steps

To repeat a sequence of steps multiple times

To validate the quality of a published dataset

To interactively explore a network with click'n'drag

To integrate with existing scripts or pipelines

Question Title

2. Which R package is NOT installed for the Automation Workshop?

httr

ggplot2

RColorBrewer

r2cytoscape

XML

Question Title

3. Which Cytoscape app is NOT installed for the Automation Workshop?

STRING

CyREST

Diffusion

CyTCGA

Question Title

4. How many nodes are in first breast cancer network you get from STRING?

Question Title

5. Which function would perform a force-directed layout with a default spring length of 50?

applyLayout("layout force-directed defaultSpringLength=50")

commandHelp("force-directed defaultSpringLength=50")

applyLayout("force-directed defaultSpringLength=5")

applyLayout("force-directed defaultSpringLength=50")

Question Title

6. Which R function would list all available r2cytoscape functions?

help(package=CyR3)

list(r2cytoscape)

help(package=r2cytoscape)

list(package=r2cytoscape)

Question Title

7. How much of this week's material was new to you?

None of it was new

Half of it was new

All of it was new

Clear

i We adjusted the number you entered based on the slider’s scale.

Question Title

8. How much time did you spend with this week's material?

an hour or less

1-2 hours

2-4 hours

more than 4 hours

Question Title

9. Let us know who you are if you plan to complete the program:

Name

Email Address

Question Title

* 1. What are good reasons to automate or script operations in Cytoscape? (Choose one or more)

Question Title

* 2. Which R package is NOT installed for the Automation Workshop?

Question Title

* 3. Which Cytoscape app is NOT installed for the Automation Workshop?

Question Title

* 4. How many nodes are in first breast cancer network you get from STRING?

Question Title

* 5. Which function would perform a force-directed layout with a default spring length of 50?

Question Title

* 6. Which R function would list all available r2cytoscape functions?

Question Title

* 7. How much of this week's material was new to you?

Question Title

* 8. How much time did you spend with this week's material?

Question Title

* 9. Let us know who you are if you plan to complete the program:

1. What are good reasons to automate or script operations in Cytoscape? (Choose one or more)

2. Which R package is NOT installed for the Automation Workshop?

3. Which Cytoscape app is NOT installed for the Automation Workshop?

4. How many nodes are in first breast cancer network you get from STRING?

5. Which function would perform a force-directed layout with a default spring length of 50?

6. Which R function would list all available r2cytoscape functions?

7. How much of this week's material was new to you?

8. How much time did you spend with this week's material?

9. Let us know who you are if you plan to complete the program: