Database for Polyphenol Utilized Proteins from gut microbiota (dbPUP)

DOI: 10.1128/AEM.01851-21 Deploymeny: bcb.unl.edu/dbpup/

Introduction

This website is developed for Yin's Lab located at the University of Nebraska - Lincoln and founded by NSF.

This website was written in python3, web framework is Flask and template engine is Jinja2.

This website also use Blast(https://blast.ncbi.nlm.nih.gov/Blast.cgi) to comparing primary biological sequence information and sequence analysis software Hmmer(http://hmmer.org/).

Installation

1. Make sure you have python3, python3-pip and hmmer installed.
2. Make sure you have clone the website and ready to deploy.
3. run pip3 install -r requirements.txt to install all the requirement.
4. Put TrEMBL.tar.gz, Swiss-Prot.tar.gz, Sequence_Similarity_Network.tar.gz and Characterization.tar.gz into static/Download/
5. put fam-A database to pfam/ then run hmmpress Pfam-A.hmm
6. We recommand to serve pn Nginx, but here is the instruction: Instruction to serve on nginx ; If serve on Apache we recommand to run it with gunicorn then use apache to forward the port instead of Nginx(Note a copy of gunicorn configurations is in gunicorn.conf.py.example).

Testing and Contributing

1. run make if you are contributing; run make production if you are deploying.
2. open your browser and go to localhost:5000 or the domain you bind with.

Configurations

If you decide to host your own website, you will need to change the config.json.example to config.json and change configurations accordingly. Remember that if you are developing the application, you should nevercommit sensitive informations in the config.json in the version control system.

If you host it on Apache, you will need to change gunicorn.conf.py.example to gunicorn.conf.pyand change configurations accordingly.

Changing or Adding Content

When adding/modify sequences, add it directly to the database that you connected to. Note: Please make sure the following file contains the family or subfamily you added /static/materials/family.txt and /static/materials/subfamily.txt.

When adding/modify content, add it to /content/. Note: If you are adding subfamily make sure the following file contain the subfamily you added /static/materials/subfamily_charactorized.txt.

When change number Subfamily:

1. open app.py.
2. Change Line257-276 accordingly.

The title of Class, Family and Subfamily will be reading from the first line of the content file. If a new page does not have a markdown file, it may display the default title name or return 404. Having a content page for each page is highly recommended.

Update Dependencies

DO NOT directly run pip install or pip freeze. Instead, add the library to requirements.in then run pip-compile for better dependency management (need to run pip install pip-tools first)