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Making Your Code Citable

Software development is often an important part of scientific work at TUHH. Many of you use GitLab or GitHub to collaboratively create and share scientific software. But how can you best cite the software then?

Digital Object Identifiers (DOI) have become the quasi-standard for referencing electronic publications. So what could be more obvious than using DOIs for software as well? Since 2014, this has been possible thanks to the cooperation between GitHub and Zenodo:

LDACS MCSOTDMA Simulator
Lindner, Sebastian | ORCID logo
Fuger, Konrad | ORCID logo
Ahmed, Musab Ahmed Eltayeb | ORCID logo
and 1 other
The central piece of the LDACS MCSOTDMA Simulator, providing an installation script that downloads  the other simulator components, defines simulation scenarios, result evaluation and graph creation.

DOI

Zenodo is an open platform for the permanent archiving of research outputs of almost any kind, operated by CERN and funded by the EU and others: about.zenodo.org

Develop on GitLab (internal)

Put on GitHub (public)

Archive on Zenodo

  • obtain DOI
  • reference DOI in your paper

How to connect GitHub with Zenodo

  1. Navigate to the login page for Zenodo.
  2. Click Sign in with GitHub.
  3. Review the information about access permissions, then click Authorize zenodo.
  4. Navigate to the Zenodo GitHub page.
  5. To the right of the name of the repository you want to archive, toggle the button to On.

Zenodo archives your repository and issues a new DOI each time you create a new GitHub release. Follow the steps at “Managing releases in a repository” to create a new one.

And two more tips:

Header TUHH Community on Zenodo

Use the TUHH community on Zenodo for your publication: https://zenodo.org/communities/tuhh/
Assignment is also possible at a later date.

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Druskat
    given-names: Stephan
    orcid: https://orcid.org/1234-5678-9101-1121
title: "My Research Software"
version: 2.0.4
identifiers:
  - type: doi
    value: 10.5281/zenodo.1234
date-released: 2021-08-11

Put a CITATION.cff in your repository

CITATION.cff files are plain text files with human- and machine-readable citation information for software (and datasets). Code developers can include them in their repositories to let others know how to correctly cite their software.

Zenodo also uses these data.

And worth reading is the practical report from the Institute for Control Systems: Open Access Publishing at TUHH: Exemplary Step-by-step guide for a toolchain with TORE, GitLab, Sherpa Romeo and Zenodo von Patrick Göttsch, Christian Hespe, Adwait Datar, Simon Heinke und Lennart Heeren. tub.torials. 20 May 2022

Journals for research software

There are also journals for scientific research software. Two relevant open access journals are SoftwareX (founded in 2015) by Elsevier and The Journal of Open Source Software – JOSS (founded in 2016) by Open Journals.

The Journal of Open Source Software is a developer friendly, open access journal for research software packages. Committed to publishing quality research software with zero article processing charges or subscription fees.

https://joss.theoj.org

SoftwareX aims to acknowledge the impact of software on today’s research practice, and on new scientific discoveries in almost all research domains. SoftwareX also aims to stress the importance of the software developers who are, in part, responsible for this impact.

https://www.sciencedirect.com/journal/softwarex

Examples of publications from TUHH:

  • M. Dosta und V. Skorych, „MUSEN: An open-source framework for GPU-accelerated DEM simulations“, SoftwareX, Bd. 12, S. 100618, Juli 2020, doi: 10.1016/j.softx.2020.100618.
  • V. Skorych, M. Dosta, und S. Heinrich, „Dyssol—An open-source flowsheet simulation framework for particulate materials“, SoftwareX, Bd. 12, S. 100572, Juli 2020, doi: 10.1016/j.softx.2020.100572.
  • T. Knopp u. a., „MPIFiles.jl: A Julia Package for Magnetic Particle Imaging Files“, JOSS, Bd. 4, Nr. 38, S. 1331, Juni 2019, doi: 10.21105/joss.01331.

Publication in JOSS is free of charge (Diamond Open Access), for publication in SoftwareX a fee of currently 950 $ is charged. And a final reading tip if you are interested in the different models and their implications: Editorial by Ross Mounce for the Open Science Council in January.

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