{"id":21995609,"url":"https://github.com/chriscummins/pip-db","last_synced_at":"2026-04-28T23:04:43.266Z","repository":{"id":11195272,"uuid":"13577005","full_name":"ChrisCummins/pip-db","owner":"ChrisCummins","description":"Bioinformatics search engine for protein isoelectric points","archived":false,"fork":false,"pushed_at":"2014-09-18T11:30:55.000Z","size":69336,"stargazers_count":4,"open_issues_count":39,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-28T10:45:17.276Z","etag":null,"topics":["bioinformatics","blas","clojure","database","protein-isoelectric-points","research-tool"],"latest_commit_sha":null,"homepage":"http://www.pip-db.org/","language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ChrisCummins.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2013-10-15T00:39:46.000Z","updated_at":"2024-07-04T00:34:57.000Z","dependencies_parsed_at":"2022-08-31T05:01:16.187Z","dependency_job_id":null,"html_url":"https://github.com/ChrisCummins/pip-db","commit_stats":null,"previous_names":[],"tags_count":59,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ChrisCummins%2Fpip-db","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ChrisCummins%2Fpip-db/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ChrisCummins%2Fpip-db/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ChrisCummins%2Fpip-db/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ChrisCummins","download_url":"https://codeload.github.com/ChrisCummins/pip-db/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245053691,"owners_count":20553378,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","blas","clojure","database","protein-isoelectric-points","research-tool"],"created_at":"2024-11-29T21:17:07.209Z","updated_at":"2026-04-28T23:04:38.237Z","avatar_url":"https://github.com/ChrisCummins.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"![pip-db](https://raw.github.com/ChrisCummins/pip-db/master/Documentation/assets/logo.png)\n\n[![Build Status](https://api.travis-ci.org/ChrisCummins/pip-db.png)](https://travis-ci.org/ChrisCummins/pip-db)\n\nThis repository contains the source code for the [Protein Isoelectric\nPoint Database](http://www.pip-db.org), a website which houses data\naccumulated by members of Aston University's Life and Health Sciences\ndepartment. The purpose of the website is to provide a powerful and\neasy-to-use search engine for the mass of biological data which has\nbeen acquired, making the valuable research accessible to all.\n\nThe project was developed by Chris Cummins (http://chriscummins.cc) as\npartial fulfillment of the requirements for the degree of MEng\nElectronic Engineering \u0026 Computer Science at Aston University. [Read\nthe submission report](Documentation/Report.pdf?raw=true).\n\n## Background\n\nBioinformatics is a multidisciplinary field which uses computational methods to\naid in biological research by creating systems for storing, organising and\nanalysing complex biological data. Within this field there are many online\ndatabases categorising biological information at the molecular level, and one\nsuch purpose of these is for storing the functional and physical properties of\nproteins. Currently, no such database exists for one of the most widely-used,\nimportant, and useful properties of proteins: the isoelectric point (pI). An\nisoelectric point is the acidity (pH) at which a molecule carries no net charge;\nbelow the isoelectric point, proteins have a net positive charge, above it a net\nnegative charge. Additionally, proteins are at their lowest solubility at their\nisoelectric point, and this makes the isoelectric point a vitally important\nproperty when both characterising and purifying proteins.\n\nThe dataset which has been compiled is a collection of entries stored as a\nnon-relational table, and for each entry it records the name of the protein, its\nidentity, origin, experimental conditions, its isoelectric point, and other\npertinent data. There are also links to a heterogeneous collection of databases\ncontaining associated data, such as amino acid sequence, function, etc. A\nweb-accessible database that warehouses this data and offers a robust and\nadaptable GUI for searching, viewing and downloading results would greatly\nincrease the accessibility of the dataset. For more detailed information about\npip-db, see [the documentation](Documentation/).\n\n## Installation\n\nExecute:\n\n```sh\n$ ./bin/build\n```\n\nSee `./configure --help` for a list of configuration options for building the\nwebsite.\n\n### Requirements\n* [Autoconf](http://www.gnu.org/software/autoconf/)\n* [Automake](http://www.gnu.org/software/automake/)\n* [Java](http://www.java.com/en/)\n* [Leiningen](https://github.com/technomancy/leiningen)\n* [PostgreSQL](http://www.postgresql.org/)\n* [Git](http://git-scm.com/) *(optional, required only to build the extra tools)*\n* [npm](https://npmjs.org/) *(optional, required only to build the extra tools)*\n* [node-optimist](https://github.com/substack/node-optimist) *(optional, required only to build the extra tools)*\n* [Python](http://www.python.org/) *(optional, required only to build the extra tools)*\n* [pdftex](http://www.tug.org/applications/pdftex/) *(optional, required only to build the extra documentation)*\n* [pandoc](http://johnmacfarlane.net/pandoc/) *(optional, required only to build the extra documentation)*\n* [doctoc](https://github.com/thlorenz/doctoc) *(optional, required only to build the extra documentation)*\n\n## Running the website\n\n```sh\n# First, setup the required environment variables:\n$ ./scripts/env.sh\nStarting a development shell...\n# Start a user database session:\n$ postgres -D pg \u003e/dev/null \u0026\n# Run the website server:\n$ lein run\n```\n\n## License\n\nCopyright 2014 Chris Cummins.\n\npip-db is free software: you can redistribute it and/or modify it\nunder the terms of the GNU General Public License as published by the\nFree Software Foundation, either version 3 of the License, or (at your\noption) any later version.\n\npip-db is distributed in the hope that it will be useful, but WITHOUT\nANY WARRANTY; without even the implied warranty of MERCHANTABILITY or\nFITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License\nfor more details.\n\nYou should have received a copy of the GNU General Public License\nalong with pip-db.  If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchriscummins%2Fpip-db","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchriscummins%2Fpip-db","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchriscummins%2Fpip-db/lists"}