Institution address

Folkhälsan Inst of Genetics, Folkhälsan Research Center; Haartmaninkatu 8, Biomedicum 1; P.O. Box 63, FI-00014; Univ of Helsinki, Finland

Helsinki Univ Central Hospital, Dept of Medicine, Division of Nephrology; PL 263, FI-00029; Helsinki, Finland

Himmeli

A general graph constitutes a multi-dimensional object so to draw it on a flat surface involves a coarse simplification of its nature. An equivalent would be to describe a human life by just two words. Sometimes this can be quite effective, sometimes there really is no hope of a meaningful description. In any case, a drawing of an interesting network - be it accurate or not - gives a researcher a glimpse into the abstract mathematical world of complex graphs.

A graph Himmeli is designed for the most difficult cases of weighted and densely connected graphs were no regularities can be exploited. Consequently, large graphs take a long time to process and the textbook examples of exact combinatorial constructs might not be visualized optimally. The core algorithm is a mix of simulated annealing and molecular dynamics and employs a cell grid memory structure to reduce unnecessary computing.

This work started out as a student project, but it has since taken a life of its own. "Himmeli" is a Finnish word for a decorative handicraft made of straws that are tied together to form a regular lattice. The structure is visually striking, yet very light and portable, a perfect model for a drawing software. Himmeli is an effort to make a scientist's life easier, not harder. Thus special care has been taken to reduce the number of unnecessary formatting of input files and to ensure consistent and reliable behavior. There is no graphical user interface, but an online facility is provided for those who are not familiar with the command prompt. Finally, the source code is available under the GNU license so any enthusiastic mind can create his or her own version on any platform.

Ville-Petteri Mäkinen
FinnDiane Study Group
Folkhälsan Research Center

Links

Online version
Documentation
Source code

Publications

Mäkinen et al. (2009) Network of clinical and biochemical characteristics in a set of 4,197 patients with type 1 diabetes. Cardiovasc Diabetol 8:54

Version history

Current code is compatible with gcc 4.3.3 compiler (tested on Ubuntu 9.04).

2009-06-21 Himmeli v3.3
Edges and vertices were incorrectly normalized, which produced too thick or too thin automatic line decorations. Also, a bug in the simulated annealing algorithm caused unfinished layouts. Both problems are fixed in v3.3.7.
2009-01-29 Himmeli v3.3
The non-standard random number generator drand48() is no longer used. The code should therefore be portable to e.g. Windows systems.
2008-12-12 Himmeli v3.3
Compilation problem with the sort() call is now fixed, along with a few other runtime problems that caused segmentation faults. Tree mode was replaced with a more general chassis mode.

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Updated 2010-01-14 by vpmakine.