SpongeEMP

Web + REST-API server for the SpongeEMP project.

SpongeEMP is a comprehensive datatset of sea sponge microbiome samples, which is a part of the Earth Microbiome Project. See Paper.

The server enables retrieving statistics regarding a given 16S V4 sequence (or set of sequences), identifying significant sponge taxa / geographic locations and sample types where this sequences is enriched in the SpongeEMP dataset.

Uses

A running SpongeEMP server is available at: spongeemp.com/.

SpongeEMP can be used as a database for bacterial identification in the Calour analysis program.

Installation

The server can also be installed locally by the following commands:

Install miniconda if not installed yet.
Create a new environment for the server:

conda create --name SpongeEMP python=3 scipy numpy pandas flask h5py nose matplotlib

Activate the environment:

source activate SpongeEMP

Install additional required packages:

pip install biom-format
pip install flask-autodoc

Install SpongeEMP server (or alternatively clone the repository):

pip install git+git://github.com/amnona/SpongeEMP

Locally running a server

Activate the SpongeEMP environment:

source activate SpongeEMP

cd to SpongeEMP/sponge_emp directory
Prepare the flask server:

export FLASK_APP=Server_Main.py
export FLASK_DEBUG=1

and run the server:

flask run

Open the web-browser to: 127.0.0.1:5000/main

Data files

The repository contains two biom tables used by the SpongeEMP server (both located in sponge_emp/data/):

final.withtax.biom : a deblurred biom table of all the SpongeEMP samples. Taxonomy has been added using the qiime assign_taxonomy.py using RDP and GreenGenes.
spongeemp.sub5k.biom : similar to final.withtax.biom, but rarified to 5000 reads/sample. This is what is used by the SpongeEMP server.