https://github.com/arnikz/piqmie
Proteomics Identifications & Quantitations Data Management & Integration Service
https://github.com/arnikz/piqmie
data-analysis data-management data-visualisation mass-spectrometry peptide-identification protein-inference protein-quantification proteomics silac web-application
Last synced: 5 months ago
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Proteomics Identifications & Quantitations Data Management & Integration Service
- Host: GitHub
- URL: https://github.com/arnikz/piqmie
- Owner: arnikz
- License: apache-2.0
- Created: 2015-09-13T17:57:03.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2025-01-31T15:52:25.000Z (over 1 year ago)
- Last Synced: 2025-09-04T22:44:24.653Z (10 months ago)
- Topics: data-analysis, data-management, data-visualisation, mass-spectrometry, peptide-identification, protein-inference, protein-quantification, proteomics, silac, web-application
- Language: HTML
- Homepage: https://www.research-software.nl/software/piqmie
- Size: 93.8 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Citation: CITATION.cff
- Zenodo: .zenodo.json
Awesome Lists containing this project
README
# PIQMIe
[](https://doi.org/10.5281/zenodo.594144)
[](https://doi.org/10.1093/nar/gku478)
[](https://github.com/arnikz/PIQMIe/actions/workflows/ci.yaml)
## Description
_PIQMIe_ is a web-based tool for reliable analysis and visualization of semi-quantitative mass spectrometry (MS)-based proteomics data. _PIQMIe_ readily integrates peptide and (non-redundant) protein identifications and quantitations, as obtained by the [MaxQuant/Andromeda](http://maxquant.org/) software ([Cox _et al._, 2008](https://doi.org/10.1038/nbt.1511), [2011](https://doi.org/10.1021/pr101065j)), with additional biological information from the [UniProtKB](http://www.uniprot.org/) database, and makes the linked data available in the form of a light-weight relational database ([SQLite](http://sqlite.org/)). Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. _PIQMIe_ provides data access via a web interface and programmatic RESTful API.
## Prerequisites
- [Docker CE](https://docs.docker.com/install/)
## Software stack
- perl
- python
- cherrypy
- genshi
- cairo
- sqlite
- javascript/css
- jquery
- d3.js
- bootstrap
## Install
**1. Clone this repository.**
```bash
git clone https://github.com/arnikz/PIQMIe.git
```
**2. Build and deploy web app.**
```bash
cd PIQMIe
docker build -t piqmie .
docker run -d -p 8080:8080 piqmie
```
## Usage
To view the [sample data](/data) on your local PIQMIe instance, follow _Sample Data_ tab and click on [results](http://localhost:8080/results/a000000000000000000000000000000000000001).
Alternatively, upload your own data files, i.e., MaxQuant peptide (`evidence.txt`) and protein (`proteinGroups.txt`) lists including the sequence library in FASTA (`.fa|fasta`), to the web server and click on the _Submit_ button to process the input files. After processing, click on the generated link to view the results. Note: For each session, a new (sub)directory `/` including I/O files will be created.