Examples¶
φ-evo provides a series of examples of project and already run seeds.
Examples of projects¶
The example of projects are stored in the Example directory of the phievo package:
The function download_example allows to download one of the
following examples:
- adaptation [1]
- somite [2]
- hox [3]
- hox_pareto
- lac_operon
- immune [4]
- minimal_project
import phievo
phievo.download_example("adaptation")
This command creates a project directory example_adaptation at your current path. The project contains all the configuration files required to start an evolution.
Examples of seeds¶
Because some simulation can take some time to run, we provide the result seeds we used to generate the figure of the paper:
- seed_adaptation
- seed_adaptation_pruning
- seed_somite
- seed_somite_pruning
- seed_lacOperon
- seed_lacOperon_pruning
- seed_hox_pareto_light
To download the result of a simulation on your computer, you can use phievo:
import phievo
phievo.download_example("seed_adaptation")
The project downloaded can be analysed using the Analyse Run.ipynb notebook.
Hox pareto¶
The complete simulation for the Hox Genes takes a lot of space, only a portion of the original results is accessible through phievo.
You can manually download the complete simulation here.
References¶
| [1] | François P, Siggia ED. A case study of evolutionary computation of biochemical adaptation. Physical Biology. 2008;5(2):26009. |
| [2] | François P, Hakim V, Siggia ED. Deriving structure from evolution: metazoan segmentation. Molecular Systems Biology. 2007 Dec;3:9. |
| [3] | François P, Siggia ED. Predicting embryonic patterning using mutual entropy fitness and in silico evolution. Development (Cambridge, England). 2010;137(14):2385–2395. |
| [4] | Lalanne JB, François P. Principles of adaptive sorting revealed by in silico evolution. Physical Review Letters. 2013 May;110(21):218102. |
