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MDPbiomeGEM

Description

MDPbiomeGEM is a combination of the published system MDPbiome and Genome-scale Metabolic models (GEMs). Multiple microbial community dynamics under perturbations timeseries are simulated by MMODES, followed by prediction of the interventions required to direct the engineering of such a microbial community into a desirable state with MDPbiome.

MDPbiomeGEM identifies different microbial community states arising in the simulated data, and the perturbation-caused transitions between states. It then computes a recommendation consisting of directed interventions that will move microbial communities from a disease or low-performance state to a more desirable state.


Installation

MDPbiome is a combination of different technologies that can be run in three docker containers (recommended). Alternatively, you could download and install the pre-requisites individual software by yourself.

Docker container (recommended):

Once you have the docker daemon running, download the different docker images from the cloud:

docker pull carrascomj/mmodes
docker pull beatrizgj/mmodes-to-mdpbiome
docker pull beatrizgj/mdpbiome

Running MDPbiomeGEM

Step 0

Before run the docker images, you need to create a folder in the host (for example, $HOME/DockerOutputMDPbiomeGEM), to exchange the data between different docker images, where the output/input data will be copied. If you do not create the folder before run the docker, it would be created automatically with NO permissions to write them.

1.- MMODES

Step 1.1

To design and code your simulations in a run_MyCommunity_simulations.py, following the MMODES documentation (https://mmodes.readthedocs.io/) and/or the examples of run_BifFae_simulations.py and run_Atrazine_simulations.py, saving in the host folder to share (for example: $HOME/DockerOutputMDPbiomeGEM)

Step 1.2

Run simulations:

You can install MMODES locally in your host, following the instructions at https://github.com/carrascomj/mmodes or you can run the MMODES docker image:

sudo docker run -it --volume "$HOME/DockerOutputMDPbiomeGEM":/home/cleanapp carrascomj/mmodes

Copy your designed simulation file (run_MyCommunity_simulations.py) in "$HOME/DockerOutputMDPbiomeGEM" and your GEMs in the right pathway (ex. "$HOME/DockerOutputMDPbiomeGEM/draft/ModelsInput/").

As an example, you could copy the files from https://github.com/beatrizgj/MDPbiomeGEM/tree/master/Src/DockerMMODES, or inside the docker container from /app directory.

Inside the docker (or in the bash terminal), run the simulations with:

python3 run_Atrazine_simulations.py <num_processors> <num_simulations>

For example, running in background, for example:

nohup python3 run_Atrazine_simulations.py 6 10 >& output_runMMODES.txt &

Step 1.3

To run the complementary scripts to collect all the simulations:

python3 to_results.py <directory_with_outputfiles>

Step 1.4

To move the biomass*.tsv files to a folder that should be accesible for the next steps. Following with the example '$HOME/DockerOutputMDPbiomeGEM/CommunityExample/'


2.- MMODEStoMDPbiome

Step 2.1

sudo docker run -it --rm -p 8888:8888 -v "$HOME/DockerOutputMDPbiomeGEM":/home/jovyan/work beatrizgj/mmodes-to-mdpbiome

Click or copy the last URL to open jupyter in the web browser

Step 2.2

Inside jupyter:

a.- Go to MMODEStoMDPbiome folder, open and run step by step runMMODEStoMDPbiome.ipynb, personalized the steps requiring USER-INTERACTION

b.- Then, you need to move the folder with the results (for example 'CommunityExample') to /work folder, that is the folder shared with your host

Step 2.3

Close the mmodes-to-mdpbiome docker container (because the next one runs in the same port)


3.- MDPbiome

Step 3.1

sudo docker run -it --rm -p 8888:8888 -v "$HOME/DockerOutputMDPbiomeGEM":/home/jovyan/work beatrizgj/mdpbiome

Click or copy the last URL to open jupyter in the web browser

Step 3.2

Inside jupyter:

a.- Go to work/ (that is the folder shared with your host) and to move the folder with the results from the previous step (for example 'CommunityExample') to /MDPbiome folder. If there are a folder with the same name in MDPbiome/, you should remove or rename it before

b.- Go to MDPbiome folder, open and run step by step config_MDPbiome_template.ipynb, personalized the steps requiring USER-INTERACTION

c.- Then, you need to move the folder with the results (for example 'CommunityExample') to /work folder, to preserve the result files when you close the docker


Datasets

The input and output data files used in the current MDPbiomeGEM case studies are available at Zenodo: http://doi.org/10.5281/zenodo.3667601


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Modeling microbiome individualized treatments, by simulating dynamics under perturbations

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