deeenes

Cambridge, United Kingdom

ebi.ac.uk/~denes

I am a biologist, doing bioinformatics, working with networks of signaling pathways, using primarily python with igraph. Sometimes I code in R, PHP, javascript and bash. I love MySQL, especially 100+ lines long queries. I use LaTeX often, with beamer and TikZ, I love typography and graphic design.

Apr
11
awarded Nice Question
Apr
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awarded Supporter
Mar
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awarded Autobiographer
Mar
13
awarded Tumbleweed
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Mar
6
asked POST request in browser and pycurl: what is the difference?
Feb
18
accepted Public dataset without license: what is allowed?
Feb
16
awarded Nice Question
Feb
12
answered Set up nginx to serve files from subdirectories
Feb
10
asked Public dataset without license: what is allowed?
Jan
25
comment igraph invalid vertex Id
It depends on your data if it makes sense to take the average/minimum/maximum weight of 2 edges of the opposite directections, and then run fastgreedy. I can imagine it does not make sense at all, and then you should not use fastgreedy, but only other methods.
Jan
25
comment igraph invalid vertex Id
If you build a graph with directed = True, then you can add 1 -> 2 and/or 2 -> 1 edge separately. If you build an undirected graph, it does not matter if you add 1 -> 2 or 2 -> 1, the two endpoints are equal, and it is only matter of chance which will be the "source" or "target", because undirected edges don't have source and target, just 2 endpoints, it is really random. You should not assume in case of undirected graph that source will be 1 if you added the edge 1 -> 2, because it can be 2 with equal chance. That's why it is undirected.
Jan
25
comment igraph invalid vertex Id
You can not run fastgreedy on undirected graph, igraph simply throws an error if you try.
Jan
24
awarded Scholar
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24
accepted How to visit an institute when looking for job?
Jan
23
revised igraph invalid vertex Id
adding info about igraph's reindexing
Jan
23
revised igraph invalid vertex Id
adding info about directed/undirected graphs
Jan
23
comment igraph invalid vertex Id
You can still use fastgreedy, but it does not consider directionality, so you loose that additional information. Once you initialize the igraph.Graph() object, you decide if it will be a directed or undirected network. Here we initialized it to be undirected, exactly because fastgreedy needs an undirected graph. If you use other methods, like spinglass, which are able to consider directions, you should create a directed network: igraph.Graph.TupleList(L, directed = True, ...). You can also convert between directed and undirected graphs with as_directed() and as_undirected() methods.
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