ProteInspector

This repository contains code for the application ProteInspector, which is developed as part of my Master Thesis at Faculty of Math and Physics, Charles University.

ProteInspector is a bioinformatics tool, which contains information about protein transformations, and can be used to analyze and mine data to deepen our understanding of proteins and changes in their conformation. This work loosely follows up the work of Adam Král (see https://github.com/adam-kral/apo-holo-protein-structure-stats).

Quick Start

To start the application, simply run

docker-compose up

to build and run the application using Docker.

Docs

Each part of the software framework is documented. The documentation can be found in the /documentation folder.

Full Installation

Required packages

sudo apt install build-essential
sudo apt install nodejs npm
sudo npm install -g node-gyp
npm install -g @angular/cli
sudo apt-get -y install nlohmann-json3-dev
sudo apt install postgresql

Download sql dump

Download database dump from this link.

Upload SQL dump to Postgres

Relog as postgres and create new user and new database:

su - postgres
createuser apo_holo_db
createdb apo_holo_db
exit

Run psql:

psql -U postgres

Change password for the new user and grant privileges:

alter user apo_holo_db with encrypted password 'YOUR-PASSWORD';
grant all privileges on database apo_holo_db to apo_holo_db;
\q

Load the database from SQL dump:

psql -U apo_holo_db -d apo_holo_db < dump.sql

Download and install library pq

Fedora:

sudo dnf install libpq-devel

Ubuntu:

sudo apt-get install libpq-dev

Download and install library pqxx

1. Download the respective library source code from github (https://github.com/jtv/libpqxx) - we used version 7.7.1. (the most recent version 7.7.4. was not working with the --enable-shared from the step 2.)

wget -O pqxx.zip https://github.com/jtv/libpqxx/archive/refs/tags/7.7.1.zip 

2. unzip the file:

unzip pqxx.zip

3. run:

./configure --enable-shared
make && make install

Download and install library hyrise/sql-parser

Clone the repository and build the library:

git clone https://github.com/hyrise/sql-parser.git
cd sql-parser
make
make install

Launch both services:

1. Go to /api folder and run:

npm run build
npm run start

to build and launch the backend service.

2. Go to /client folder and run:

npm install
ng serve

to build and launch the frontend service.