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thpar / diffany

Diffany is an open-source toolbox for calculating and visualizing differential networks.
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[CLOSED] make sample of osmotic use-case data #208

Closed diffany-admin closed 9 years ago

diffany-admin commented 9 years ago

Issue by svlandeg Mon Nov 3 19:16:13 2014

Because Cytoscape can't load too big networks (cf #191)

diffany-admin commented 9 years ago

Comment by svlandeg Tue Nov 18 14:35:10 2014

Loading time is getting better, but the algorithm still takes a while. If this can't be fixed, I'll have to do the sample.

[Edit]

In fact, I am going to make the sample first. Then we can at least submit and have the reviewers view the sample, and I can work on the speed in the meantime still before (full) publication (Milestone V2.1)

diffany-admin commented 9 years ago

Comment by svlandeg Thu Nov 20 09:36:03 2014

"phosphorylation hub" MPK3 could be removed from the network? Same thing for MPK2? MPK6 is also a hub...

diffany-admin commented 9 years ago

Comment by svlandeg Thu Nov 20 13:48:26 2014

idea: 1) better filter on PPI and phosphorylation hubs 2) completely remove single-connected nodes, e.g. a non-DE node that has just one PPI partner

diffany-admin commented 9 years ago

Comment by svlandeg Thu Nov 20 17:21:04 2014

attempt at 1) Gone from 24.868 edges between 3.791 nodes to 3.856 edges between 1.757 nodes. Need to test whether the resulting networks are correct!

diffany-admin commented 9 years ago

Comment by svlandeg Mon Nov 24 09:22:58 2014

Now also filtering for kinase-target hubs (both source and target nodes seperately, which should automatically solve the MPK3 problem

diffany-admin commented 9 years ago

Comment by svlandeg Mon Nov 24 10:48:03 2014

the hub-filtering worked nicely, we now only have 2354 edges between 1393 nodes, though all relevant information is still present in the networks.