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.

Jun
25
answered Graph analysis: Identify loop paths
Jun
25
answered igraph plotting: vertices too close in Kamada-Kawai layout
Jun
22
revised Getting vertex list from python-igraph
i think the op primarily needs g.vs
Jun
19
accepted Seaborn barplot with x_order: AttributeError: 'bool' object has no attribute 'sum'
Jun
19
comment Seaborn barplot with x_order: AttributeError: 'bool' object has no attribute 'sum'
Wonderful, it works! Thanks! It's a pity this is not documented.
Jun
19
asked Seaborn barplot with x_order: AttributeError: 'bool' object has no attribute 'sum'
Jun
18
awarded Yearling
Jun
5
answered How to get the vertices from an edge using igraph in python?
Jun
5
answered Using geo-coordinates as vertex coordinates in the igraph r-package
Jun
4
comment Using geo-coordinates as vertex coordinates in the igraph r-package
You need to call here igraph::plot() with rescale=FALSE parameter, otherwise it rescales the coordinates along both dimensions into a [-1; 1] interval.
Jun
4
answered python easy_install fails with SSL certificate error for all packages
Jun
2
comment A similarity measure with binary data: does this one have a name?
Thanks, this is exactly what I was looking for. Also this brief compendium is very nice, thanks for that too.
Jun
2
awarded Scholar
Jun
2
awarded Supporter
Jun
2
accepted A similarity measure with binary data: does this one have a name?
Jun
2
awarded Student
Jun
2
asked A similarity measure with binary data: does this one have a name?
Jun
2
awarded Autobiographer
May
31
awarded Autobiographer
May
30
comment Performance issue when the number of Edges are large
I don't see where you initialize the new_color variable, and I don't know why is it necessary. As v1 is an adjacent vertex of v, it's color should be set to 'red', because in this step it gets infected. However, if you want to set it infected only if it was healthy, then simply do if(vertex.attributes(G)[[sprintf("step%d", step-1)]][v1] == 'blue'){vertex.attributes(G)[[sprintf('step%d', step)]][v1] <- "red"}.
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