https://github.com/midnighter/rfn-generation
Generation of flow networks robust against damages.
https://github.com/midnighter/rfn-generation
Last synced: 3 months ago
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Generation of flow networks robust against damages.
- Host: GitHub
- URL: https://github.com/midnighter/rfn-generation
- Owner: Midnighter
- License: other
- Created: 2013-01-20T14:38:14.000Z (over 13 years ago)
- Default Branch: master
- Last Pushed: 2013-01-21T03:35:55.000Z (over 13 years ago)
- Last Synced: 2025-02-23T09:30:28.572Z (over 1 year ago)
- Size: 160 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE.rst
Awesome Lists containing this project
README
=======================
Flow Network Generation
=======================
Flow networks robust against damages are simple model networks described in a
series of publications by Kaluza *et al*.[\ 1_, 2_, 3_]. The C++ code
presented in this repository allows for the generation of such networks via a
simulated evolution.
Although the code was programmed with a single core in mind, the compiled binary
can easily be (and has been) run multiple times in parallel.
Installation
------------
In the main directory, you need to edit the ``CMakeLists.txt`` file. If your
libraries are installed in non-standard locations, please adapt lines 8 to 11.
Then run the following commands::
cmake init .
make
If everything went smoothly there should now be a ``bin`` and ``lib`` subdirectory.
Add the path to your environment variable ``LD_LIBRARY_PATH`` if you want to run
things from here. In bash this can be done by::
export LD_LIBRARY_PATH="$HOME/path/to/rfn-generation/lib:$LD_LIBRARY_PATH"
You can now run the ``simulation`` binary in the ``bin`` subdirectory which will
print some info to stdout.
If you want to install the ``bin`` and ``lib`` subdirectories in a different
location, either edit line 17 of the ``CMakeLists.txt`` file or invoke::
make install -DDESTDIR=/your/favourite/path
When you are ready to move from testing to large-scale computation you should
rebuild the project without debugging and text output, follow these commands::
cmake -DDEBUG=OFF .
make
Enjoy!
Note
----
The output files are binary and their exact structure depends on your system's architecture (32 or 64 bit).
Requirements
------------
C++:
~~~~
*NB*: If you install these libraries from system packages, please make sure to also
install the ``dev`` packages as the headers are needed for compilation.
* Boost_/ namely: algorithm, random, graph, filesystem V3, accumulators,
pending/queue, program_options
* `GNU Scientific Library`__
Others:
~~~~~~~
* cmake_
.. _Boost: http://www.boost.org/
__ gsl_
.. _gsl: http://www.gnu.org/software/gsl/
.. _cmake: http://www.cmake.org/
References
----------
.. [1] Kaluza, P., Ipsen, M., Vingron, M. & Mikhailov, A. S. Design and statistical properties of robust functional networks: A model study of biological signal transduction. Physical Review E 75, 15101 (2007).
.. [2] Kaluza, P. & Mikhailov, A. S. Evolutionary design of functional networks robust against noise. Europhysics Letters 79, 48001 (2007).
.. [3] Kaluza, P., Vingron, M. & Mikhailov, A. S. Self-correcting networks: function, robustness, and motif distributions in biological signal processing. Chaos 18, 026113 (2008).