Temporal dynamics of microbial mats a network based approach

Logo

Microbial mats from Churince Supplementary Information

View the Project on GitHub valdeanda/Time_series_mats

Supplementary Information

Repository that contain the main data and scripts to recompute the figures from:

De Anda V, Zapata PeƱasco I, Blaz J, Poot-Hernandez AC, Contreras Moreira B, Gonzales Laffite Marcos, Hernandez Rosales M, Gamez Tamariz N, Eguiarte Fruns E, Souza V. Understanding the mechanisms behind the response to environmental perturbations in microbial mats: a metagenomic-network based approach Front. Microbiol. 9:2606. doi: 10.3389/fmicb.2018.02606

Last updated: 11/29/2018

To reproduce the figures first install jupyter notebook and then clone the repository.

git clone https://github.com/valdeanda/Time_series_mats.git
cd scripts 
ipython3 notebook 

Requirements


In order to reproduce all the figures the following libraries and packages must be installed first

Python

R packages

Figures


Taxonomic composition, microbial mat core and rare biosphere

The script is available in notebook format

jupyter notebook  Diversity.ipynb

Presence absence profile with get_homologues

jupyter notebook  Core_bacteria.ipynb

Capturing the dynamics of biogeochemical cycles with MEBS

jupyer notebook MebsInTime.ipynb

Script available in notebook format.

jupyter notebook completeness.ipynb

Networks

Open the following script directly in R

The dynamic networks for each site are available here:

Network motifs

Script available in notebook format.

jupyter notebook  Motifs.ipynb

MORE

For more information about Cuatro Cienegas please visit the documentary film, click the image below

README in html version