[Networkit] Biochemical Pathways

Henning Meyerhenke henning.meyerhenke at kit.edu
Fri Jun 12 21:46:35 CEST 2015

If "prime application" or "one application" is debatable. But before 
discarding a whole research area on the basis of a picture, I strongly 
recommend reading the relevant literature, starting from appropriate 
textbooks and surveys.

One way PPI models work (and I would not consider myself an expert, 
either) is to measure the strength of interactions in experiments. The 
crucial thing is which conclusions to draw from this and from analyzing 
the data with our methods (and which not to draw).


Am 12.06.15 um 21:08 schrieb Christian Staudt:
> I came across the following interesting “complex network”:
> http://biochemical-pathways.com/#/map/2
> Is this an instance of the famous and often cited Protein Interaction
> Networks? I’m far from an expert on this, but it has always puzzled
> me that anyone would model the machinery of life as something as
> simple as an undirected graph with one type of node and one type of
> edge. Among the phenomena which can be modelled as graphs, some are
> more like complex machines, others are more like a bunch of linked
> entities, for instance, co-purchase networks ( “people who bought X
> also bought…”). This distinction may be important to decide how much
> we can learn from the application of network analysis methods, which
> are, after all, relatively simple descriptive statistics of dyadic
> data.
> I’d love to be taught otherwise, but this picture is impressive
> enough for me to stop citing "protein interaction networks” as a
> prime application of network analysis for now.
> Best, Chris


Karlsruhe Institute of Technology (KIT)
Institute of Theoretical Informatics (ITI)

Juniorprof. Dr. Henning Meyerhenke
Theoret. Informatics / Parallel Computing

Phone: +49-721-608-41876
Web: http://parco.iti.kit.edu/henningm/

KIT - University of the State of Baden-Wuerttemberg and
National Research Center of the Helmholtz Association

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