Reengineering Network Models Out Of Images Files - Use Cytoscape?

Question

[Markus Krupp]

Hi all together,

our group is interested in building up a major network graph out of a compendium of multiple network image files in jpeg format.

Image extraction is not applicable, because images did not follow any standards :-/

At the moment my best idea is to use Cytoscape to copy the network - network image on desktop1 and cytoscape on desktop2 - and redraw each node and edge manually.

Changing the default background of Cytoscape to those network jpeg files would speed up those 'mission' by just overprinting the nodes and edges - is such a plugin available for Cytoscape? - Did not find one.

Any brilliant ideas how to minimize this effort/busywork?! ...perhaps using other software?

Solution so far:

• Use Cytoscape
• Set window to be transparent 30%
• Apply tons of coffee into mouth
• Analyze multiple donuts by eating them
• Stop multiple brain functions by hearing loud music
• Fight for each drop of motivation!

Other Solution: - Use a node&edge drawing program which save document e.g. in XML foramt - parse XML for node and edges - import into Cytoscape

[Michael Schubert]

Which OS, or are you a bit flexible?

[Michael Schubert]

On a side note: once it's published, do it better and add the machine-readable raw network data as supplement ;-)

Answer 1

[Istvan Albert]

I don't know about changing the background but what you could also do is create a simple edge list with a fast "low tech" process like so:

Relabel nodes to 1, 2 etc and one person reads the connection out loud and uses a highlighter to mark each edge they've read out: "100 to 390" , the other enters this into a tab delimited file 100 to 399

Cytoscape can read in this tab delimited file, and later you can add node labels back. You could be done in a half an hour.

As someone that had to manually enter network information I will recommend the two person approach, networks are very tricky on the eye and mind (at least on they were on mine), doing this as single individual task switching between finding edges and entering them was very error prone when I did it on my own.

[Markus Krupp]

Thanks, this is was also one of our first solutions. However, copying the network from the background images seem less error prone than the tab separated file. ...but if there is no chance to get the network images to the background we will start shouting at each other ;-)

Answer 2

[Michael Schubert]

You could use a window manager that supports compositing, overlay the image with Cytoscape, making Cytoscape e.g. 30% opaque and then just copy what you see.

Well, that would speed up the process a little. Unfortunately not too much.

[Markus Krupp]

Thanks Michael, that's an excellent idea! I will start with this approach ;-)

Answer 3

[Qdjm]

How about using a service like Mechanical Turk to get the networks into Cytoscape? Doesn't solve your Cytoscape background problem but may solve your "fight for motivation problem".

[Markus Krupp]

Mechanical Turk was new to me - thanks for that tip.

But the data should not reach other people ...not yet :-)

[Michael Schubert]

There might be an NDA option?