GutFeeling Knowledgebase

GutFeeling Knowledgebase (GFKB) is a reference database of the human gut microbiome.

The contents of this repository make up the GutFeeling KnowledgeBase website, as well as some of the available files to download.

The Gut Feeling Knowledgebase (GFKB) is a reference database of human gut microbiomes from both healthy individuals and those diagnosed with a disease or condition. The GFKB is generated by a metagenomic analysis pipeline described in our paper (doi: 10.1371/journal.pone.0206484), and includes three tools which are integrated in the HIVE platform. The aim of this database is to catalog bacterial organisms found within the human digestive tract as the lab continues to conduct metagenomic research on various diseases and conditions (e.g. epilepsy and pre-diabetes). Our hope is to identify key organisms found within the gut as a means to understand how their imbalances may impact human health. Currently, the HIVE lab has documented over 500 bacterial organisms within this database, and we hope to continue adding more organisms as we proceed with our current project in predicting intervention outcomes of pre-diabetic patients using their relative gut microbiome abundances.

GFKB is apart of the Gut Microbiome Analytic System Project of HIVE Lab GW.

Contributing

If you are unfamiliar with Github please start HERE

For those who would like to contribute:

1. Fork this repository

2. Make changes on your fork, then sync with the Upstream Branch

3. Submit a Pull Request (PR)

Updating the webpage with new content from this repo:

Prerequisites: ssh access to the HIVE-Lab servers and sudo.

Test site (REQUIRED before production)

1. ssh into the HIVE LOGIN NODE (hive-login.biochemistry.gwu.edu)
2. ssh into hive1-node1
3. cd /hive/tst/html/gfkb
4. git pull

Production site

1. ssh into the HIVE LOGIN NODE (hive-login.biochemistry.gwu.edu)
2. ssh into hive1-node1
3. cd /hive/prd/html/gfkb
4. git pull