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README.md

pip-db

Build Status

This repository contains the source code for the Protein Isoelectric Point Database, a website which houses data accumulated by members of Aston University's Life and Health Sciences department. The purpose of the website is to provide a powerful and easy-to-use search engine for the mass of biological data which has been acquired, making the valuable research accessible to all.

The project was developed by Chris Cummins (http://chriscummins.cc) as partial fulfillment of the requirements for the degree of MEng Electronic Engineering & Computer Science at Aston University. Read the submission report.

Background

Bioinformatics is a multidisciplinary field which uses computational methods to aid in biological research by creating systems for storing, organising and analysing complex biological data. Within this field there are many online databases categorising biological information at the molecular level, and one such purpose of these is for storing the functional and physical properties of proteins. Currently, no such database exists for one of the most widely-used, important, and useful properties of proteins: the isoelectric point (pI). An isoelectric point is the acidity (pH) at which a molecule carries no net charge; below the isoelectric point, proteins have a net positive charge, above it a net negative charge. Additionally, proteins are at their lowest solubility at their isoelectric point, and this makes the isoelectric point a vitally important property when both characterising and purifying proteins.

The dataset which has been compiled is a collection of entries stored as a non-relational table, and for each entry it records the name of the protein, its identity, origin, experimental conditions, its isoelectric point, and other pertinent data. There are also links to a heterogeneous collection of databases containing associated data, such as amino acid sequence, function, etc. A web-accessible database that warehouses this data and offers a robust and adaptable GUI for searching, viewing and downloading results would greatly increase the accessibility of the dataset. For more detailed information about pip-db, see the documentation.

Installation

Execute:

$ ./bin/build

See ./configure --help for a list of configuration options for building the website.

Requirements

  • Autoconf
  • Automake
  • Java
  • Leiningen
  • PostgreSQL
  • Git (optional, required only to build the extra tools)
  • npm (optional, required only to build the extra tools)
  • node-optimist (optional, required only to build the extra tools)
  • Python (optional, required only to build the extra tools)
  • pdftex (optional, required only to build the extra documentation)
  • pandoc (optional, required only to build the extra documentation)
  • doctoc (optional, required only to build the extra documentation)

Running the website

# First, setup the required environment variables:
$ ./scripts/env.sh
Starting a development shell...
# Start a user database session:
$ postgres -D pg >/dev/null &
# Run the website server:
$ lein run

License

Copyright 2014 Chris Cummins.

pip-db is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

pip-db is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with pip-db. If not, see http://www.gnu.org/licenses/.