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PrimBrainLnc

A database of brain lncRNAs from human and non-human primates multiple brain regions.
Link: http://primbrainlnc.bio.uni-mainz.de/
Publication: Navandar, M., Vennin, C., Lutz, B., and Gerber, S. Long non-coding RNAs expression and regulation across different brain regions in primates. Sci Data 11, 545 (2024). (https://doi.org/10.1038/s41597-024-03380-3)

How to get the database?

git clone [email protected]:NavandarM/PrimBrainLnc.git
or
git clone https://github.com/NavandarM/PrimBrainLnc.git

Prerequisite

sudo apt-get update
sudo apt install python3-virtualenv
python3 -m venv myvirtual
source myvirtual/bin/activate
pip install django
pip install -r requirements.txt  #[ "requirements.txt" is given along with the database and contains dependencies. ]
sudo apt-get install python3-tk

How to run the server?

python manage.py runserver 0.0.0.0:8000

Details of the directories and files:

Project Directory (PrimeOrthoLnc):

  • This is the main directory containing the entire Django project.

subdirectories:

  • manage.py: A command-line utility allows to interact with Django project. Use it to run and update the database server.
  • settings.py: This file contains configuration settings of PrimOrthoLnc
  • urls.py: This file contains URL patterns of this project. this file allows to mapping URL paths to views.
  • wsgi.py and asgi.py: These files are entry points for WSGI (Web Server Gateway Interface) and ASGI (Asynchronous Server Gateway Interface) servers respectively.

App Directory (Application):

  • Provides separate files for different task i.e. encapsulate specific functionality.

Files and directories:

  • models.py: This file defines the data models/schema for the application.
  • views.py: This file contains view functions or classes that handle HTTP requests and return HTTP responses.
  • urls.py: This file informs the application how to respond to different web page requests and connect them to specific views or functions.
  • forms.py: It allows to desigb the custom forms of the web page.
  • admin.py: This file is used to register models with the Django admin interface for managing data via the admin site.
  • tests.py: This file contains unit tests for testing the functionality of the app.
  • migrations/: This directory contains database migrations created for the app. Migrations are used to propagate changes made to models into the database schema.

static/:

  • This directory is used to store static files (e.g., CSS, JavaScript, images, software, temporary files generated ).

templates/:

  • This directory contains HTML templates used to render views for the app.

population_script.py

  • To populate the PrimOrthoLnc database with the dataset.
  • Dataset file:Input_for_database_GeneralInfo_sequenceupdated.txt