Get n-th degree neighbor

[Alexander Pico]

I have a colleague who was surprised that there weren't more "networky"
functions in the API. As a new Cytoscape plugin developer, he wants to do
some basic things like getting the n-th degree neighbors of a node.

In 2.x I think you just have to run getAdjacentIndecies() multiple times (or
something like that). How would you do this in 3.0? Would it be helpful to
come up with a set of these "networky" functions to layer into the API?

- Alex

[Mike Smoot]

Lot's of these sorts of functions have been implemented in the network analyzer plugin.  While these will be available through the user interface in 3.0, they are not (yet) available from a programming API.  It's certainly possible to add a new API to Cytoscape to make these sorts of functions more readily available to programmers.  It's "just" a matter of defining and implementing what should go in there.   It's worth noting that the same can be said for many aspects of Cytoscape's functionality that may be missing or unavailable.   Enterprising volunteers are welcome!

thanks,

Mike

BTW, to get n-th neighbors in 3.0 just call network.getNeighborList() multiple times.

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____________________________________________________________
Michael Smoot, Ph.D.              
UCSD Department of Medicine
tel: 858-822-4756

[giovanni scardoni]

Hi Mike,
all my plugins (CentiScaPe, Interference, Pesca) need some network functions.
Which functions will not available in 3.0? I hope the basic functions
will remain.
If needed I can help on implementing some of them.
thanks
Giovanni

2011/12/15 Mike Smoot <msm...@ucsd.edu>:

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Giovanni Scardoni
The Center for BioMedical Computing (CBMC)
www.cbmc.it
University of Verona
Strada le Grazie, 15 -37134
Verona -Italy

[piet molenaar]

Wouldn't it be an idea to expose some of the network analyzer functionality to the outside world? As an OSGI bundle? This seems a typical case for that...
Cheers,
Piet

Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

[Alexander Pico]

Giovanni,

We are talking about adding new network functions, not taking away any of
the existing functions. Functions like those provided by Network Analyzer,
but made available directly to plugin/app developers through the API.

It would be great to have your suggestions for such functions, since you've
taken advantage of many of the existing one in your plugins. I'll start this
list in a separate thread on this mailing list. Once we put a list together,
then it would also be great to have your help implementing.

Thanks!
- Alex

On 12/16/11 12:18 AM, "giovanni scardoni" <giovanni...@gmail.com>
wrote:

[giovanni scardoni]

Great!
I will be happy to contribute to new network functions!
Please, let me know how to proceed.
thanks!
Giovanni

2011/12/16 Alexander Pico <ap...@gladstone.ucsf.edu>:

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