Predictive Behavior Within Microbial Genetic Networks
Ilias Tagkopoulos*, Yir-Chung Liu*, and Saeed Tavazoie (*IL and YL contributed equally)
To contact us: {iliast@ucdavis.edu, yliu@princeton.edu, st2744@columbia.edu}
Science (2008) 320:1313-1317, Epub 2008 May 8. PDF and supplementary material.
EVE: Evolution in Variable Environments
The EVE software is a simulation framework for microbial populations in complex dynamic environments. The simulator allows the study of microbial evolution in multiple scales, ranging from network to meta-population level.
Installation instructions
You can download the source code (C++) of EVE by clicking here. In the package a README.txt file is included with installation and running instructions.
Briefly, to run EVE you have to compile it either by executing the Makefile or by running the following commands:
- g++ -c -o eve23.o eve23.cpp
- g++ -c ilibrary.cpp
- g++ -c import_export.cpp
- g++ -c lineage.cpp
- g++ -c rtclassv3.cpp
- g++ -c list.cpp
- g++ -c value_calculation.cpp
- g++ -o eve23 eve23.o ilibrary.o import_export.o lineage.o rtclassv3.o list.o value_calculation.o
where instead of g++ you may choose any compatible C++ compiler. Then the executable may run by any valid definition of its 13 parameters, for example:
./eve23 0 0 0 1 18000000 200 4500 1 1 0 0 0 /temp/test/
Note that the last parameter is the path where the output files will be stored. More information in the README.txt file of the package (also available here).
Datasets
The final populations (200 organisms per population) that have evolved in AND, OR, XOR, NOR, NAND environments are available for download. Files has been compressed in multiple zip files. For each environment, simulations under very low mutation (vlm), low mutation (lm), medium mutation (mm) rates are included. Due to file size (several GB), simulations for the high mutation rate environments are not available online. For information on what organism parameters represent, please consult the supplementary material.
- AND
- andvlm
- andlm
- andmm
- OR
- orvlm
- orlm
- ormm
- XOR
- xorvlm
- xorlm
- xormm
- NOR
- norvlm
- norlm
- normm
- NAND
- nandvlm
- nandlm
- nandmm