Our R package MCQR is published!
#PAPPSO #Rpackage #statistics #SoftwarePublication #proteomics
http://pappso.inrae.fr/news/2025/06/our-r-package-mcqr-is-published/
MCQR is an R package R package for the in-depth exploration, processing, and analysis of quantitative proteomics data generated from either data-dependent or data-independent acquisition methods. It has been recently accepted for publication in Journal of Proteome research
#introductions I'm Stephan, originally an English Philologist and Linguist, now a #SoftwareEngineering researcher at the German Aerospace Center's (https://social.bund.de/@dlr) Institute of Software Technology in #Berlin.
I'm a 2018 Fellow of the Software Sustainability Institute (https://mastodon.social/@SoftwareSaved), founder and lead of the #CitationFileFormat (https://citation-file-format.github.io/) and co-founder of de-RSE (https://mastodon.social/@de_rse).
I work on #ResearchSoftware, #SoftwareCitation, #SoftwarePublication, #SoftwareIntelligence, #SoftwareSustainability, #EmpiricalSoftwareEngineering.
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New preprint: "Extending and Applying Automated HERMES #SoftwarePublication Workflows" by Sophie Kernchen, @led02, me, Michael Fritzsche and colleagues.
https://arxiv.org/abs/2410.17614
Came out of a #deRSE24 workshop and was really fun, especially as one of the co-authors is an intern from a local high school 🏫 who extended the 'hermes' Python package with a plugin to harvest metadata from Python manifests.
It took him ≪ fortnight. 🤯
I wish I was this talented. 🙌
Research software is an important output of research and must be published according to the FAIR Principles for Research Software. This can be achieved by publishing software with metadata under a persistent identifier. HERMES is a tool that leverages continuous integration to automate the publication of software with rich metadata. In this work, we describe the HERMES workflow itself, and how to extend it to meet the needs of specific research software metadata or infrastructure. We introduce the HERMES plugin architecture and provide the example of creating a new HERMES plugin that harvests metadata from a metadata source in source code repositories. We show how to use HERMES as an end user, both via the command line interface, and as a step in a continuous integration pipeline. Finally, we report three informal case studies whose results provide a preliminary evaluation of the feasibility and applicability of HERMES workflows, and the extensibility of the hermes software package.
📢 Out now:
"Towards Research Software-ready Libraries", a paper by me, @astruck and O. Bertuch discussing what libraries can do to support research software in their respective spheres.
https://doi.org/10.1515/abitech-2023-0031
#ResearchSoftware #SoftwarePublication #SoftwareCitation #AcademicLibraries
Software is increasingly acknowledged as valid research output. Academic libraries adapt to this change to become research software-ready. Software publication and citation are key areas in this endeavor. We present and discuss the current state of the practice of software publication and software citation, and discuss four areas of activity that libraries engage in: (1) technical infrastructure, (2) training and support, (3) software management and curation, (4) policies.
#StackOverflow announce Labs ("improving the developer experience across products" or similar), arguing: "Accuracy is fundamental. That comes from attributed, peer-reviewed sources that provide transparency."
Sounds like they're facing similar issues like us academics/#ResearchSoftwareEngineers do with #SoftwarePublication and #SoftwareCitation, software authorship, #Reproducibility and the like.
Perhaps there's something to learn from them along the way...
Excited to be on my way to an @NSF funded workshop on community-led data & software publishing in Pismo Beach, CA.
I'll be wearing my #CitationFileFormat and #HERMES hats, and am looking forward to meet lots of people from great initiatives and projects for the first time, to discuss aims, ideas and collaborations to improve 💻 #SoftwarePublication.
(Unfortunately, the weather doesn't look like I can sneak in a 🏄 session.)
PAPPSO
Stephan Druskat
Stephan Druskat
Stephan Druskat