cepdnaclk / e17-6sp-host-pathogen-interaction

Building the software for analyzing the microbiome data using machine learning technics. the application provides the GUI for the user they can easily analyze the data without any other programming knowledge developed by @piriyaraj @varnaraj @thanujan @rilwan292

Title	Host Pathogen Interaction
Repository-name	GitHub
Project page	BioWeb
Frontend	BioWeb

Inference of host-microbe associations based on metagenomic data

overview

Finding the diesecs is very challenginig matter. There are many methods available in the filed but the problem these methods are not flow the same procedure. So that we like to develop the software that help to identify the problem using the microbiome samples. The software worked based on the machine learning techniques. It can give more suitable discussion for the user.

problem

When considering the problems in this field we found some of the major things. -imited to testing for differential abundance of microbial taxa between group of sample -They do not allow users to evaluate their predictivity. -the software resulting from these studies is generally not easily modified or transferred to other classification tasks or data types -Some tools have identified these many issues -Specific programming language based -its give poor user experience

solutions

we are suggesting a web application integrated with a machine learning framework and statistical methods.it can help user they can analyze their microbiome data without any machine learning knowledge because our software proving the GUI for doing such things

Prerequist Tecgnolgies To Run this Application

• Docker
• Docker-Compose

Installation

Development level

//Build the new image and spin up the two containers.(only after content changed in requirments.txt or docker-relatedfiles)
//creating new containers.
docker-compose up -d --build

//Run an existing containers
docker-compose up 

//now app will be run on https://localhost:8000

Production level

//spin down the development containers
docker-compose down -v


//Build the new image and spin up the two containers.(only after content changed in requirments.txt or docker-relatedfiles)
//creating new containers.
docker-compose -f docker-compose.prod.yml up -d --build

//Eun migration
docker-compose exec web python manage.py migrate --noinput

//regenerate staticfiles:
docker-compose exec web python manage.py collectstatic --no-input --clear

//Run an existing containers
docker-compose -f docker-compose.prod.yml up 

//now app will be run on https://localhost:1337

Team

• E/17/292, Rilwan M, [email protected]
• E/17/256, Piriyaraj S, [email protected]
• E/17/352, Thanujan T, [email protected]
• E/17/358, Varnaraj N, [email protected]

Links

• Project Repository
• Project Page
• Department of Computer Engineering
• University of Peradeniya

How to run.

• step 01- clone repo

git clone https://github.com/cepdnaclk/e17-co328-Host-Pathogen-Interaction.git

• step 02 - activate virtual environment
  run active file in the software/frontend/script
  A. On Windows(open CMD on script folder)

  activate.bat
  

  B. On linux(open terminal on script folder)

  source activate
  

• step 03 - install modules
  move to folder Fronted in terminal

  pip install -r requirements.txt
  

• step 04 - database migrations move to folder Host_Pathogen_Interaction

  python manage.py makemigrations
  python manage.py migrate
  

• step 05 - run server

  python manage.py runserver
  

Thank you

e17-6sp-host-pathogen-interaction's Issues

design UI of login and register

• task1
• task2
• task3