FluTypeDB

Janek Grzegorzewski and Matthias König

Overview

The FluTypeDB project is a web application for the data management of binding assays for the classification of influenza subtypes.

FluTypeDB consists of a database and web interface with focus on various binding assays for the classification of influenza viruses and contains experimental data based on

• ELISA antibody binding assays
• Peptid binding assays on microwell plates
• Peptid bindings assays on peptide microarrays

FluTypeDB is developed for the data management and data analysis within the FluType project by Janek Grzegorzewski (Universität Potsdam) and Matthias König (Humboldt Universität Berlin).

The production version is available at http://www.flutype.de.

License

• Source Code: LGPLv3
• Documentation: CC BY-SA 4.0
• Data: Copyright and ownership FluType.

Funding

FluTypeDB is funded via the German FluType project.

Changelog

v0.1.5 [2017-11-23]

• bug fixes and small improvements

v0.1.4 [2017-11-17]

In this release a multitude of bug fixes and improvements in the FluTypeDB interface have been implemented. In addition new features are available with this release

New features

• Gal file generator from database
• New table design
• Create/edit ligands (virus, peptides, antibodies), buffers and the respective batches
• Simplified user interface and improved forms with validation
• Admin interface & superuser administration via edit/delete
• Improved URL schema
• Better documentation
• Improved Database Backup

v0.1.3

• bug fixes and small improvements
• reusable macros
• improved UI

v0.1.2

• new grid system for layout
• more intuitive layout
• tutorial and about pages updated
• bug fixes

v0.1.0 [2017-10-15]

• updated web interface
• data models updated

Technical Documentation

In this section technical information for setup and testing with FluTypeDB is provided.

Setup

To test the webapp with the sqlite3 backend clone the repository and run the django development server in a virtual environment

git clone https://github.com/janekg89/flutype_webapp.git
mkvirtualenv flutype_webapp
(flutype_webapp) pip install -r requirements.txt
(flutype_webapp) python manage.py runserver

Necessary to create core database with

create_db.sh

To fill the database with test data run the following script. This applies all migrations and writes the database content.

(flutype_webapp) ./create_db.sh

Testing

Tests are run via

(flutype_webapp) python manage.py test

Running the unittests requires phantomjs which can be installed via the following the instructions on https://www.vultr.com/docs/how-to-install-phantomjs-on-ubuntu-16-04

sudo apt-get install build-essential chrpath libssl-dev libxft-dev libfreetype6-dev libfreetype6 libfontconfig1-dev libfontconfig1 -y
sudo wget https://bitbucket.org/ariya/phantomjs/downloads/phantomjs-2.1.1-linux-x86_64.tar.bz2
sudo tar xvjf phantomjs-2.1.1-linux-x86_64.tar.bz2 -C /usr/local/share/
sudo ln -s /usr/local/share/phantomjs-2.1.1-linux-x86_64/bin/phantomjs /usr/local/bin/
phantomjs --version

Coverage

Coverage of Test are run via

coverage run --source='.' manage.py test

a report is displayed via:

coverage report

a html report is saved via:

coverage html

© 2017-2018 FluType