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https://github.com/chriscummins/pip-db

Bioinformatics search engine for protein isoelectric points
https://github.com/chriscummins/pip-db

bioinformatics blas clojure database protein-isoelectric-points research-tool

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Bioinformatics search engine for protein isoelectric points

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README 

        
![pip-db](https://raw.github.com/ChrisCummins/pip-db/master/Documentation/assets/logo.png)



[![Build Status](https://api.travis-ci.org/ChrisCummins/pip-db.png)](https://travis-ci.org/ChrisCummins/pip-db)



This repository contains the source code for the [Protein Isoelectric

Point Database](http://www.pip-db.org), 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](Documentation/Report.pdf?raw=true).



## 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](Documentation/).



## Installation



Execute:



```sh

$ ./bin/build

```



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

website.



### Requirements

* [Autoconf](http://www.gnu.org/software/autoconf/)

* [Automake](http://www.gnu.org/software/automake/)

* [Java](http://www.java.com/en/)

* [Leiningen](https://github.com/technomancy/leiningen)

* [PostgreSQL](http://www.postgresql.org/)

* [Git](http://git-scm.com/) *(optional, required only to build the extra tools)*

* [npm](https://npmjs.org/) *(optional, required only to build the extra tools)*

* [node-optimist](https://github.com/substack/node-optimist) *(optional, required only to build the extra tools)*

* [Python](http://www.python.org/) *(optional, required only to build the extra tools)*

* [pdftex](http://www.tug.org/applications/pdftex/) *(optional, required only to build the extra documentation)*

* [pandoc](http://johnmacfarlane.net/pandoc/) *(optional, required only to build the extra documentation)*

* [doctoc](https://github.com/thlorenz/doctoc) *(optional, required only to build the extra documentation)*



## Running the website



```sh

# 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 .