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Open Source Science

https://github.com/compomics/denovogui

Graphical user interface for de novo sequencing of tandem mass spectra

https://github.com/compomics/denovogui

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.7%) to scientific vocabulary

Keywords

de-novo-sequencing denovo graphical-user-interface proteomics
Last synced: 5 months ago · JSON representation

Repository

Graphical user interface for de novo sequencing of tandem mass spectra

Basic Info
Statistics
  • Stars: 14
  • Watchers: 14
  • Forks: 7
  • Open Issues: 6
  • Releases: 0
Topics
de-novo-sequencing denovo graphical-user-interface proteomics
Created over 10 years ago · Last pushed almost 2 years ago
Metadata Files
Readme

README.md

DeNovoGUI

DeNovoGUI Publication:

  • Muth T, Weilnböck L, Rapp E, Huber CG, Martens L, Vaudel M, Barsnes H: DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra. PMID 24295440.
  • If you use DeNovoGUI as part of a publication, please include this reference.

| | | | | :------------------------- | :--------------- | :--: | | download | v1.16.8 - Windows | ReleaseNotes | | download | v1.16.8 - Mac and Linux |ReleaseNotes |

| | | | :--: | :--: | | | |

Introduction

DeNovoGUI provides a user-friendly open-source graphical user interface for running the de novo sequencing algorithms Novor, DirecTag, PepNovo+ and pNovo+ (beta) on Windows, Mac and Linux.

To start using DeNovoGUI, unzip the downloaded file, and double-click the DeNovoGUI-X.Y.Z.jar file. No additional installation required!

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Command Line

DeNovoGUI can also be used via the command line, see DeNovoCLI for details.

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Issues, Questions and Bug Reports

Code of Conduct

As part of our efforts toward delivering open and inclusive science, we follow the Contributor Convenant Code of Conduct for Open Source Projects.

Issue Tracker

Despite our efforts at enforcing good practices in our work, like every software, DeNovoGUI might crash, fail to cover specific use cases, not perform as well as expected. We apologize for any inconvenience and will try to fix things to the best of our capabilities. We welcome bug reports, suggestions of improvements, and contributions via our issue tracker.

Troubleshooting

Note that PepNovo+ is not supported on Linux 32 bit, pNovo+ is only supported on Windows, and that DirectTag is currently not supported on Mac (support is in development).

If you get problems running PepNovo+ on Linux (or OSX), please try the following: (1) install dos2unix, (2) run the following two commands inside the resources/PepNovo folder: dos2unix Models/*.* and dos2unix Models/*/*.*.

For problems related to Java, memory or startup issues, please see: Java Troubleshooting.

For other questions or suggestions please contact the developers of DeNovoGUI by setting up an Issue with your comment, or by sending an e-mail to the DeNovoGUI Google Group.

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Owner

  • Name: Computational Omics and Systems Biology Group
  • Login: CompOmics
  • Kind: organization
  • Email: compomics.list@gmail.com

The CompOmics group, headed by Prof. Dr. Lennart Martens, specializes in the management, analysis and integration of high-throughput Omics data.

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
Last Year
  • Issues event: 1
  • Watch event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: about 18 hours
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: about 18 hours
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • prk888 (1)
  • erikeiko (1)
  • JannikSchneider12 (1)
Pull Request Authors
Top Labels
Issue Labels
help wanted (2)
Pull Request Labels

Dependencies

pom.xml maven
  • com.compomics:utilities 4.12.15
  • jfree:jfreechart 1.0.13
  • net.jimmc:jshortcut 0.4-oberzalek
  • no.uib:jsparklines 1.0.12
  • junit:junit 4.13.1 test