Publications

Leyla Jael Castro, Stephan Ferenz, Hamideh Hajiabadi, Patrick Kuckertz, Matthias Löbe, Christian Schmidt, Alexander Struck, and Florian Thiery. Results on a Survey on Research Software Metadata in the NFDI Consortia. Zenodo, August 2024. [PUMA: forschungsdaten metadata nfdi software survey] URL

Mario David, Miguel Colom, Daniel Garijo, Leyla Jael Castro, Violaine Louvet, Elisabetta Ronchieri, Massimo Torquati, Laura del Caño, Leong Cerlane, Maxime Van den Bossche, Isabel Campos, and Roberto Di Cosmo. Ensure Software Quality. Zenodo, February 2024. [PUMA: forschungsdaten metadata qualitry software] URL

Alexandre Hocquet, Frédéric Wieber, Gabriele Gramelsberger, Konrad Hinsen, Markus Diesmann, Fernando Pasquini Santos, Catharina Landström, Benjamin Peters, Dawid Kasprowicz, Arianna Borrelli, Phillip Roth, Clarissa Ai Ling Lee, Alin Olteanu, and Stefan Böschen. Software in science is ubiquitous yet overlooked. Nature Computational Science, 2024. [PUMA: RSE licensing maintenance research software] URL

Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, and Peter W. Rose. Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. PLOS Computational Biology, (15)7:1-8, Public Library of Science, July 2019. [PUMA: bestPractice jupyter software workflows] URL

Sheeba Samuel, and Daniel Mietchen. FAIR Jupyter: a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset. 2024. [PUMA: jupyter knowledgegraph reproducibility software]

Michael Selzer. Kadi4Mat - Karlsruhe Data Infrastructure for Materials Science. Zenodo, 2023. [PUMA: eln forschungsdaten software tools] URL

Michael Felderer, Michael Goedicke, Lars Grunske, Wilhelm Hasselbring, Anna-Lena Lamprecht, and Bernhard Rumpe. Toward Research Software Engineering Research. Zenodo, 2023. [PUMA: classification forschungsdaten metadata software] URL

Stefan Bieliauskas, and Andreas Schreiber. DLR-SC/prov-comics: QS PROV Comics Prototype - Big fixes. Zenodo, April 2017. [PUMA: comics forschungsdaten javascript metadata provenance software tools] URL

Morane Gruenpeter, Sabrina Granger, Alain Monteil, Neil Chue Hong, Elena Breitmoser, Mario Antonioletti, Daniel Garijo, Esteban González Guardia, Alejandra Gonzalez Beltran, Carole Goble, Stian Soiland-Reyes, Nick Juty, and Gabriela Mejias. D4.4 - Guidelines for recommended metadata standard for research software within EOSC. Zenodo, June 2023. [PUMA: eosc forschungsdaten metadata software standards] URL

Sheeba Samuel, and Daniel Mietchen. Computational reproducibility of Jupyter notebooks from biomedical publications. 2022. [PUMA: forschungsdaten jupyter reproducibility review software]

Carlos Martinez-Ortiz, Paula Martinez Lavanchy, Laurents Sesink, Brett G. Olivier, James Meakin, Maaike de Jong, and Maria Cruz. Practical guide to Software Management Plans. Zenodo, October 2022. [PUMA: datenmänagementplan dmp forschungsdaten software] URL

Morane Gruenpeter, Daniel S. Katz, Anna-Lena Lamprecht, Tom Honeyman, Daniel Garijo, Alexander Struck, Anna Niehues, Paula Andrea Martinez, Leyla Jael Castro, Tovo Rabemanantsoa, Neil P. Chue Hong, Carlos Martinez-Ortiz, Laurents Sesink, Matthias Liffers, Anne Claire Fouilloux, Chris Erdmann, Silvio Peroni, Paula Martinez Lavanchy, Ilian Todorov, and Manodeep Sinha. Defining Research Software: a controversial discussion. Zenodo, 2021. [PUMA: definition forschungsdaten software] URL

European Commission, Directorate-General for Research, and Innovation. Scholarly infrastructures for research software : report from the EOSC Executive Board Working Group (WG) Architecture Task Force (TF) SIRS. Publications Office, 2020. [PUMA: eosc forschungsdaten infrastruktur software]

Roberto Di Cosmo, Morane Gruenpeter, Bruno Marmol, Alain Monteil, Laurent Romary, and Jozefina Sadowska. Curated Archiving of Research Software Artifacts: Lessons Learned from the French Open Archive (HAL). International Journal of Digital Curation, (15)1:16, Edinburgh University Library, August 2020. [PUMA: curation forschungsdaten quality repository software] URL

Philipp Cimiano, Christian Pietsch, and Cord Wiljes. Studies in Analytical Reproducibility: the Conquaire Project. 8057464 bytes, 2021. [PUMA: analyticalreproducibility forschungsdaten psychology reproducibility software] URL

Timo Koch, Dennis Gläser, Anett Seeland, Sarbani Roy, Katharina Schulze, Kilian Weishaupt, David Boehringer, Sibylle Hermann, and Bernd Flemisch. A sustainable infrastructure concept for improved accessibility, reusability, and archival of research software. 2023. [PUMA: forschungsdaten repository software tools]

Stephan Druskat, Oliver Bertuch, Guido Juckeland, Oliver Knodel, and Tobias Schlauch. Software publications with rich metadata: state of the art, automated workflows and HERMES concept. 2022. [PUMA: forschungsdaten metadata project software]

Neil P. Chue Hong, Daniel S. Katz, Michelle Barker, Anna-Lena Lamprecht, Carlos Martinez, Fotis E. Psomopoulos, Jen Harrow, Leyla Jael Castro, Morane Gruenpeter, Paula Andrea Martinez, and Tom Honeyman. FAIR Principles for Research Software (FAIR4RS Principles). Research Data Alliance, 2021. [PUMA: fairPrinciples forschungsdaten software] URL

Bernd Flemisch, Sibylle Hermann, Christian Holm, Miriam Mehl, Guido Reina, Benjamin Uekermann, David Boehringer, Thomas Ertl, Jean-Noël Grad, Dorothea Iglezakis, Alexander Jaust, Timo Koch, Anett Seeland, Rudolf Weeber, Florian Weik, and Kilian Weishaupt. Umgang mit Forschungssoftware an der Universität Stuttgart. Universität Stuttgart, 2020. [PUMA: forschungsdaten myown software] URL

Graham Lee, Sebastian Bacon, Ian Bush, Laura Fortunato, David Gavaghan, Thibault Lestang, Caroline Morton, Martin Robinson, Philippe Rocca-Serra, Susanna-Assunta Sansone, and Helena Webb. Barely sufficient practices in scientific computing. Patterns, (2)2:100206, 2021. [PUMA: forschungsdaten motivation software] URL