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