Welcome to backend interface and import build script for FluPRINT database

Technology

FluPRINT uses a number of open source projects to work properly ¯_(ツ)_/¯ You can find more info on fluprint.com website that is also avaliable as open-source project here

Installation process

To install and configure FluPRINT first you need to satisfy following requirements: PHP > 7, MySQL, Linux or Mac OS.

Please make sure to install those basic dependencies and start the MySQL server before proceeding to installation.

Installation Quickstart

1. Install composer

	php -r "copy('https://getcomposer.org/installer', 'composer-setup.php');"
	php -r "if (hash_file('sha384', 'composer-setup.php') === '93b54496392c062774670ac18b134c3b3a95e5a5e5c8f1a9f115f203b75bf9a129d5daa8ba6a13e2cc8a1da0806388a8') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;"
	php composer-setup.php
	php -r "unlink('composer-setup.php');"

2. Install PHP dependencies by running following command from project root directory:

	composer install

3. Create new MySQL database and configure MySQL user

4. Now when dependencies are set please import database schema into MySQL database you created

	mysql -u username -p database_name < ./documentation/fluprint_schema.sql

5. Adjust database user credentials by editing following file:

	./config/configuration.json

6. Download raw data from the here, make new directory ./data/upload place your data inside in following format

	./data/upload/{STUDY_ID}/*.csv

STUDY_ID must be a number that is already mapped inside this file ./config/configuration.json Currently supported ones are: 30, 29, 28, 24, 21, 22, 18, 17, 15

7. Start the import and import all data into database!

	php bin/import.php -t import

Submitting Bugs and Enhancements

GitHub Issues is for suggesting enhancements and reporting bugs. We appreciate all enhancements ideas and bug reports. Additionally if you think you can help us with suggesting new useful features we will gladly accept it.

How to use this dataset

One of the examples how to use this dataset is described in our publication Publication code with some examples can also be found as an open source project here

Other useful resources

You may also find helpful our other open source projects

• mulset - Multi-set intersection R package
• simon - Automated knowledge discovery platform

Reaching Out

If you'd like to start a conversation feel free to e-mail me at info@adrianatomic.com We would also gladly like to hear from you if you find this project useful and helpful.

License

Please check LICENSE file for more information. The Software is provided "as is", without warranty of any kind.

Citation

If you use our code for research, please cite following publications:

Adriana Tomic, Ivan Tomic, Cornelia L Dekker, Holden T Maecker, Mark M Davis
bioRxiv 564062; doi: https://doi.org/10.1101/564062

Tomic, Adriana, & Tomic, Ivan. (2019). The FluPRINT database [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3222451

Any questions? Please contact us at info@adrianatomic.com