Data

Tools

Indexes

Applications

Experiments

Open Source Science

piqmie

Proteomics Identifications & Quantitations Data Management & Integration Service

https://github.com/arnikz/piqmie

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords

data-analysis data-management data-visualisation mass-spectrometry peptide-identification protein-inference protein-quantification proteomics silac web-application
Last synced: 6 months ago · JSON representation

Repository

Proteomics Identifications & Quantitations Data Management & Integration Service

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 2
  • Releases: 2
Topics
data-analysis data-management data-visualisation mass-spectrometry peptide-identification protein-inference protein-quantification proteomics silac web-application
Created over 10 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License Citation Zenodo

README.md

PIQMIe

DOI Published in NAR CI

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 software (Cox et al., 2008, 2011), with additional biological information from the UniProtKB database, and makes the linked data available in the form of a light-weight relational database (SQLite). 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

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 on your local PIQMIe instance, follow Sample Data tab and click on results.

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 <DATA_DIR>/<jobID> including I/O files will be created.

Owner

  • Name: Arnold Kuzniar
  • Login: arnikz
  • Kind: user
  • Location: Milky Way

GitHub Events

Total
  • Issues event: 1
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 5
  • Pull request event: 1
Last Year
  • Issues event: 1
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 5
  • Pull request event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 91
  • Total Committers: 2
  • Avg Commits per committer: 45.5
  • Development Distribution Score (DDS): 0.451
Past Year
  • Commits: 36
  • Committers: 1
  • Avg Commits per committer: 36.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
arnikz a****r@g****m 50
Arnold Kuzniar a****r@e****l 41
Committer Domains (Top 20 + Academic)
esciencecenter.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 5
  • Total pull requests: 2
  • Average time to close issues: over 1 year
  • Average time to close pull requests: about 4 years
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.2
  • Average comments per pull request: 0.5
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • arnikz (5)
Pull Request Authors
  • dependabot[bot] (2)
Top Labels
Issue Labels
bug (2) enhancement (2)
Pull Request Labels
dependencies (2)

Dependencies

requirements.txt pypi
  • cairosvg ==1.0.22
  • cherrypy >=3.2.2
  • genshi >=0.7
  • python-magic >=0.4.3
.github/workflows/ci.yaml actions
  • docker/login-action v1 composite
.github/workflows/docker-build.yaml actions
  • actions/checkout v2 composite
  • docker/login-action v1 composite
Dockerfile docker
  • node 13-alpine build
package.json npm
  • bootstrap ^3.0.0
  • d3 ^4.0.0
  • jqGrid ^5.3.2
  • jquery ^1.11
  • jquery-form ^4.2.2
  • jquery-ui ^1.14
  • jquery-validation ^1.19.1