References
This page lists RSE-related publications curated by the HiRSE community. It covers research software engineering best practices, FAIR software principles, sustainable software development, and related topics.
You can download the full bibliography as a BibTeX file: Download .bib file
Publications by Year
2025
2024
2023
2022
2021
2020
2019
2018
2017
2016
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2025
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Good practice versus reality: A landscape analysis of Research Software metadata adoption in European Open Science Clusters
Anas El Hounsri, Daniel Garijo
2025 IEEE/ACM 22nd International Conference on Mining Software Repositories (MSR), pp. 116--128, 2025
DOI: 10.1109/MSR66628.2025.00028 -
GI- und DE-RSE Muster-Leitlinie zur effizienten Entwicklung von Forschungssoftware
Andreas Czerniak, Adrian Ehrenhofer, Bernadette Fritzsch, Maximilian Funk, Florian Goth, Reiner Hähnle, Carina Haupt, Marco Konersmann, Jan Linxweiler, Frank Löffler, Alexander Lüpges, Bernhard Rumpe, Ina Schieferdecker, Tobias Schlauch, Robert Speck, Alexander Struck, Jan Philipp Thiele, Matthias Tichy, Inga Ulusoy
2025
DOI: 10.18420/2025-GI_DE-RSE -
Reviewing reproducibility in software engineering research
André F. R. Cordeiro, Jr., Edson Oliveira
Proceedings of the 27th International Conference on Enterprise Information Systems – Volume 2: ICEIS, pp. 364--371, 2025
DOI: 10.5220/0013456000003929 -
Ironies of generative AI: understanding and mitigating productivity loss in human-AI interaction
Auste Simkute, Lev Tankelevitch, Viktor Kewenig, Ava Elizabeth Scott, Abigail Sellen, Sean Rintel
International Journal of Human–Computer Interaction, 41(5), pp. 2898--2919, 2025
DOI: 10.1080/10447318.2024.2405782 -
Decoding research software impact
Deekshitha, Rena Bakhshi, Rob van Nieuwpoort, Slinger Jansen
CEUR Workshop Proceedings, 3921, 2025
https://ceur-ws.org/Vol-3921/ -
Digitale Forschungspraxis und kooperative Informationsinfrastrukturen. Ein Diskussionspapier der Deutschen Forschungsgemeinschaft zu Förderung und Finanzierung wissenschaftlicher Informationsinfrastrukturen
Deutsche Forschungsgemeinschaft. Ausschuss für Wissenschaftliche Bibliotheken und Informationssysteme
2025
DOI: 10.5281/ZENODO.14621979 -
Strategic priorities and challenges in research software funding: Results from an international survey [version 2; peer review: 2 approved, 2 approved with reservations, 1 not approved]
Eric A. Jensen, Daniel S. Katz
F1000Research, 13(1447), 2025
DOI: 10.12688/f1000research.155879.2 -
Teaching research software engineering skills for developing simulation software
Gerasimos Chourdakis, Hasan Ashraf, Santiago Narvaez Rivas, Tobias Neckel, Hans-Joachim Bungartz
Electronic Communications of the EASST, 83, 2025
DOI: 10.14279/eceasst.v83.2615 -
Open Research Tools: Stand und Herausforderungen im Spannungsfeld von Forschungssoftware, Offenheit und digitaler Infrastruktur
Jürgen Streicher, Marlies Schütz, Clemens Blümel, Alexander Schniedermann
2025
DOI: 10.5281/ZENODO.15771943 -
Sharing is caring: the effect of knowledge exchange workshops on community commitment among research software engineers
Katharina Dworatzyk, Tobias Schlauch
Human-Computer Interaction, pp. 157--174, 2025
DOI: 10.1007/978-3-031-93835-1_10 -
FACILE-RS: archiving and long-term preservation of research software repositories made easy
Marie Houillon, Jochen Klar, Ziad Boutanios, Tomas Stary, Terry Cojean, Hartwig Anzt, Axel Loewe
Journal of Open Source Software, 10(114), pp. 7330, 2025
DOI: 10.21105/joss.07330 -
A 2030 roadmap for software engineering
Mauro Pezzè, Silvia Abrahão, Birgit Penzenstadler, Denys Poshyvanyk, Abhik Roychoudhury, Tao Yue
ACM Transactions on Software Engineering and Methodology, 34(5), 2025
DOI: 10.1145/3731559 -
Investigating Research Software Engineering: Toward RSE Research
Michael Felderer, Michael Goedicke, Lars Grunske, Wilhelm Hasselbring, Anna-Lena Lamprecht, Bernhard Rumpe
Communications of the ACM, 68(2), pp. 20--23, 2025
DOI: 10.1145/3685265 -
Ten Simple Rules for Catalyzing Collaborations and Building Bridges between Research Software Engineers and Software Engineering Researchers
Nasir U. Eisty, Jeffrey C. Carver, Johanna Cohoon, Ian A. Cosden, Carole Goble, Samuel Grayson
Computing in Science & Engineering, pp. 1--7, 2025
DOI: 10.1109/MCSE.2025.3569786 -
The future of research software is the future of research
Neil P. Chue Hong, Selina Aragon, Simon Hettrick, Caroline Jay
Patterns, 6(7), pp. 101322, 2025
DOI: 10.1016/j.patter.2025.101322 -
Stop treating code like an afterthought: record, share and value it
Roberto Di Cosmo, Sabrina Granger, Konrad Hinsen, Nicolas Jullien, Daniel Le Berre, Violaine Louvet, Camille Maumet, Clémentine Maurice, Raphaël Monat, Nicolas P. Rougier
Nature, 646(8084), pp. 284--286, 2025
DOI: 10.1038/d41586-025-03196-0 -
Seek and You Shall Find - Or Not! Why Can't We Find the Research Software We Really Need?
Ronny Gey, Tim Wittenborg, Daniel Mietchen, Alexander Struck, Oliver Karras
2025
DOI: 10.5281/ZENODO.14878607 -
find.software: Foundations for Interdisciplinary Discovery of (Research) Software
Ronny Gey, Daniel Mietchen, Oliver Karras, Tim Wittenborg, Moritz Schubotz, Jan Bumberger
Research Ideas and Outcomes, 11, pp. e179253, 2025
DOI: 10.3897/rio.11.e179253 -
Code for Science: Bessere Forschung durch bessere Forschungssoftwarekompetenzen
Simon Christ, Bernadette Fritzsch, Yves Vincent Grossmann, Dominic Kempf, Jan Linxweiler, Frank Löffler, Lydia Riedl, Jan Philipp Thiele, Adina S. Wagner, Lorenzo Zanon, Cora Assmann, Dirk Brömmel, René Caspart, Mustafa Dogan, Sven Fillinger, Jasmin Frangenberg, Michael Franke, Annalena Frey, Jonas Hagenberg, Carina Haupt, Volodymyr Kushnarenko, Sarah Neuwirth, Tobias Ribizel, Jens Saak, Andreas Schieberle, Kristine Schima-Voigt, Peter Schmidt, Heidi Seibold, Robert Speck, Mathijs Vleugel, Alexander Wellmann, Philipp Wieder, Samantha Wittke
2025
DOI: 10.5281/ZENODO.14273366 -
Better architecture, better software, better research
Stephan Druskat, Nasir U. Eisty, Robert Chisholm, Neil P. Chue Hong, Ryan C. Cocking, Myra B. Cohen, Michael Felderer, Lars Grunske, Sarah A. Harris, Wilhelm Hasselbring, Thomas Krause, Jan Linxweiler, Colin C. Venters
Computing in Science & Engineering, 27(2), pp. 45--57, 2025
DOI: 10.1109/MCSE.2025.3573887 -
Challenges in Designing Research Infrastructure Software in Multi-Stakeholder Contexts
Stephan Druskat, Sabine Theis
Human-Computer Interaction, 15767, pp. 321--343, 2025
DOI: 10.1007/978-3-031-93838-2_21 -
What can computer science educators learn from the failures of top-down pedagogy?
Sverrir Thorgeirsson, Tracy Ewen, Zhendong Su
Proceedings of the 56th ACM technical symposium on computer science education (SIGCSETS 2025), volume 1, pp. 1127--1133, 2025
DOI: 10.1145/3641554.3701873 -
Enabling new pathways for Research Software Engineers: three years of the UNIVERSE-HPC project
Weronika Filinger, Neil Chue Hong, Stephen Crouch, Martin Robinson, Jeremy Cohen, David Henty
Practice and Experience in Advanced Research Computing 2025 (PEARC '25), 2025
DOI: 10.1145/3708035.3736008 -
Multidimensional Research Software Categorization
Wilhelm Hasselbring, Stephan Druskat, Jan Bernoth, Philine Betker, Michael Felderer, Stephan Ferenz, Ben Hermann, Anna-Lena Lamprecht, Jan Linxweiler, Arnau Prat, Bernhard Rumpe, Katrin Schöning-Stierand, Shinhyung Yang
Computing in Science & Engineering, 27(2), pp. 59--68, 2025
DOI: 10.1109/MCSE.2025.3555023
2024
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Requirements Engineering for Research Software: A Vision
Adrian Bajraktari, Michelle Binder, Andreas Vogelsang
2024
DOI: 10.48550/ARXIV.2405.07781 -
Reproducible Workflows and Compute Environments for Reusable Datasets, Simulations and Research Software
Alan Correa, Anil Yildiz, Julia Kowalski
2024
DOI: 10.5194/egusphere-egu24-18724 -
RepoFromPaper: An Approach to Extract Software Code Implementations from Scientific Publications
Aleksandar Stankovski, Daniel Garijo
2024 -
Software in science is ubiquitous yet overlooked
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, Stefan Böschen
Nature Computational Science, 2024
DOI: https://doi.org/10.1038/s43588-024-00651-2 -
Automated Extraction of Research Software Installation Instructions from README files: An Initial Analysis
Carlos Utrilla Guerrero, Oscar Corcho, Daniel Garijo
2024 -
Clarifying Dual Use Research of Concern
Christopher Bobier, Daniel J. Hurst
Philosophy & Technology, 37(4), pp. 139, 2024
DOI: 10.1007/s13347-024-00827-8 -
Building RSE Communities
Claire Wyatt
2024
https://juser.fz-juelich.de/record/1034677 -
Navigating the complexity of generative AI adoption in software engineering
Daniel Russo
ACM Transactions on Software Engineering and Methodology, 33(5), 2024
DOI: 10.1145/3652154 -
Special issue on software citation, indexing, and discoverability
Daniel S. Katz, Neil P. Chue Hong
PeerJ Computer Science, 10, pp. e1951, 2024
DOI: 10.7717/peerj-cs.1951 -
RSMM: A Framework to Assess Maturity of Research Software Project
Deekshitha, Rena Bakhshi, Jason Maassen, Carlos Martinez Ortiz, Rob van Nieuwpoort, Slinger Jansen
2024 -
A Vision on Open Science for the Evolution of Software Engineering Research and Practice
Edson OliveiraJr, Fernanda Madeiral, Alcemir Rodrigues Santos, Christina von Flach, Sergio Soares
Companion proceedings of the 32nd ACM international conference on the Foundations of Software Engineering (FSE 2024), pp. 512--516, 2024
DOI: 10.1145/3663529.3663788 -
Foundational Competencies and Responsibilities of a Research Software Engineer [version 1; peer review: 2 approved]
Florian Goth, Renato Alves, Matthias Braun, Leyla Jael Castro, Gerasimos Chourdakis, Simon Christ, Jeremy Cohen, Stephan Druskat, Fredo Erxleben, Jean-Noël Grad, Magnus Hagdorn, Toby Hodges, Guido Juckeland, Dominic Kempf, Anna-Lena Lamprecht, Jan Linxweiler, Frank Löffler, Michele Martone, Moritz Schwarzmeier, Heidi Seibold, Jan Philipp Thiele, Harald von Waldow, Samantha Wittke
F1000Research, 13(1429), 2024
DOI: 10.12688/f1000research.157778.1 -
A coherent curriculum track of RSE skills for simulation software
Gerasimos Chourdakis
deRSE24, 2024
https://events.hifis.net/event/994/contributions/7961/ -
A choice, not an obligation: Releasing scientific software as open source should be the responsibility of the authors
I Kappas, VJ Promponas, CA Ouzounis
EMBO Reports, 25(2), pp. 464--466, 2024
DOI: 10.1038/s44319-023-00039-9 -
A large-scale survey on the usability of AI programming assistants: Successes and challenges
Jenny T. Liang, Chenyang Yang, Brad A. Myers
Proceedings of the IEEE/ACM 46th International Conference on Software Engineering, pp. 1--13, 2024
DOI: 10.1145/3597503.3608128 -
Sustaining Scientific Open-Source Software Ecosystems: Challenges, Practices, and Opportunities
Jiayi Sun
Proceedings of the 2024 IEEE/ACM 46th International Conference on Software Engineering: Companion Proceedings, 2024
DOI: 10.1145/3639478.3639805 -
How to Sustain a Scientific Open-Source Software Ecosystem: Learning from the Astropy Project
Jiayi Sun, Aarya Patil, Youhai Li, Jin L. C. Guo, Shurui Zhou
2024
DOI: 10.48550/ARXIV.2402.15081 -
Six tips for going public with your lab's software
Julian Nowogrodzki
Nature, 634(8034), pp. 742--743, 2024
DOI: 10.1038/d41586-024-03344-y -
Ten simple rules for teaching sustainable software engineering
Kit Gallagher, Richard Creswell, Ben Lambert, Martin Robinson, Chon Lok Lei, Gary R. Mirams, David J. Gavaghan
2024
DOI: 10.48550/ARXIV.2402.04722 -
Research Software Engineering-Forschungssoftware effizient erstellen und dauerhaft erhalten
Lars Grunske, Anna-Lena Lamprecht, Wilhelm Hasselbring, Bernhard Rumpe
Forschung & Lehre, 24(3), pp. 186--188, 2024 -
Open Software Catalogue – Supporting the Management of Research Software
Marcin Wolski, Jan Todek, Maciej Łabędzki, Bartosz Walter
Good Practices and New Perspectives in Information Systems and Technologies, pp. 165--171, 2024
DOI: 10.1007/978-3-031-60227-6_14 -
nfdi.software - Initialisation Phase
Martin Hammitzsch, Beate Hetenyi, Björn Grüning, Aleksander Marcic, Matthias Löbe, Layla-Jael Castro, Felix Engel, Konrad Höfner, Michael Zacharias, Oliver Werth, Vasiliy Seibert, Andreas Rausch
2024
DOI: 10.5281/ZENODO.14507302 -
Research Software Engineering: A Guide to the Open Source Ecosystem
Matthias Bannert
2024
DOI: 10.1201/9781003286899 -
No Free Lunch: Research Software Testing in Teaching
Michael Dorner, Andreas Bauer, Florian Angermeir
2024
DOI: 10.48550/ARXIV.2405.11965 -
Non-expert programmers in the generative AI future
Molly Q Feldman, Carolyn Jane Anderson
Proceedings of the 3rd Annual Meeting of the Symposium on Human-Computer Interaction for Work (CHIWORK '24), pp. 1--19, 2024
DOI: 10.1145/3663384.3663393 -
Teaching ethics in computing: A systematic literature review of ACM computer science education publications
Noelle Brown, Benjamin Xie, Ella Sarder, Casey Fiesler, Eliane S. Wiese
ACM Transactions on Computing Education, 24(1), 2024
DOI: 10.1145/3634685 -
DataDesc: A framework for creating and sharing technical metadata for research software interfaces
Patrick Kuckertz, Jan Göpfert, Oliver Karras, David Neuroth, Julian Schönau, Rodrigo Pueblas, Stephan Ferenz, Felix Engel, Noah Pflugradt, Jann M. Weinand, Astrid Nieße, Sören Auer, Detlef Stolten
Patterns, pp. 101064, 2024
DOI: 10.1016/j.patter.2024.101064 -
Open geospatial research software in 2024: Assessing service quality with technology readiness levels
Peter Löwe
2024
DOI: 10.5194/egusphere-egu24-6254 -
FAIR-USE4OS: Guidelines for creating impactful open-source software
Raphael Sonabend, Hugo Gruson, Leo Wolansky, Agnes Kiragga, Daniel S. Katz
PLOS Computational Biology, 20(5), pp. e1012045, 2024
DOI: 10.1371/journal.pcbi.1012045 -
FAIR-USE4OS: Guidelines for Creating Impactful Open-Source Software
Raphael Sonabend, Hugo Gruson, Leo Wolansky, Agnes Kiragga, Daniel S. Katz
2024
DOI: 10.48550/ARXIV.2402.02824 -
FAIR Workflows and Methods for Scaling
Sean R. Wilkinson
2024
DOI: 10.5194/egusphere-egu24-19486 -
State of the practice for lattice Boltzmann method software
Spencer Smith, Peter Michalski, Jacques Carette, Zahra Keshavarz-Motamed
Archives of Computational Methods in Engineering, 31(1), pp. 313--350, 2024
DOI: 10.1007/s11831-023-09981-2 -
Software engineering, research software and requirements engineering
Stephan Druskat, Michael Felderer, Carina Haupt
Softwaretechnik-Trends, 44(1), 2024
https://dl.gi.de/items/1b96d440-bd4d-48c4-8eb6-1b368206addd -
Research Software Requirements Engineering?
Stephan Druskat
2024
DOI: 10.5281/ZENODO.10696026 -
Software engineering, research software and requirements engineering
Stephan Druskat, Michael Felderer, Carina Haupt
Softwaretechnik-Trends Band 44, Heft 1, 2024 -
Byte-sized RSE: Season 2, Session 5 - Citation File Format (CFF) / cffinit
Stephan Druskat, Abel Soares Siqueira, Reggie Cushing, Olga Lyashevska, Martinez Carlos
2024
DOI: 10.5281/ZENODO.10838021 -
Don't mention it: An approach to assess challenges to using software mentions for citation and discoverability research
Stephan Druskat, Neil P. Chue Hong, Sammie Buzzard, Olexandr Konovalov, Patrick Kornek
2024
DOI: 10.48550/ARXIV.2402.14602 -
Differenzierbare Forschungssoftware
Uwe Naumann
Softwaretechnik-Trends Band 44, Heft 1, 2024 -
Betty's (Re) Search Engine: A client-based search engine for research software stored in repositories.
Vasiliy Seibert, Andreas Rausch, Stefan Wittek
ing. grid, 1(2), 2024 -
Software engineering education must adapt and evolve for an LLM environment
Vassilka D. Kirova, Cyril S. Ku, Joseph R. Laracy, Thomas J. Marlowe
Proceedings of the 55th ACM technical symposium on computer science education (SIGCSE 2024), volume 1, pp. 666--672, 2024
DOI: 10.1145/3626252.3630927 -
Toward Research Software Categories
Wilhelm Hasselbring, Stephan Druskat, Jan Bernoth, Philine Betker, Michael Felderer, Stephan Ferenz, Anna-Lena Lamprecht, Jan Linxweiler, Bernhard Rumpe
2024
DOI: 10.48550/ARXIV.2404.14364 -
Towards a Quality Indicator for Research Data publications and Research Software publications – A vision from the Helmholtz Association
Wolfgang zu Castell, Doris Dransch, Guido Juckeland, Marcel Meistring, Bernadette Fritzsch, Ronny Gey, Britta Höpfner, Martin Köhler, Christian Meeßen, Hela Mehrtens, Felix Mühlbauer, Sirko Schindler, Thomas Schnicke, Roland Bertelmann
2024
DOI: 10.48550/ARXIV.2401.08804 -
Software Management Plans – Current Concepts, Tools, and Application
Yves Vincent Grossmann, Giacomo Lanza, Katarzyna Biernacka, Tim Hasler, Kerstin Helbig
Data Science Journal, 23, pp. 43, 2024
DOI: 10.5334/dsj-2024-043
2023
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Hiring, Managing, and Retaining Data Scientists and Research Software Engineers in Academia: A Career Guidebook from ADSA and US-RSE
2023
DOI: 10.5281/zenodo.8264152 -
Towards Assessing FAIR Research Software Best Practices in an Organization Using RDF-star.
Ana Iglesias-Molina, Daniel Garijo
SEMANTiCS (Posters & Demos), 2023 -
The digital competence of academics in higher education: is the glass half empty or half full?
Andreia Inamorato dos Santos, Ernesto Chinkes, Marco A. G. Carvalho, Claudia M. V. Solórzano, Lilian S. Marroni
International Journal of Educational Technology in Higher Education, 20(1), 2023
DOI: 10.1186/s41239-022-00376-0 -
Neue Fachgruppe „Research Software Engineering`` gegründet
Anna-Lena Lamprecht, Wilhelm Hasselbring, Jan Philipp Dietrich, Bernadette Fritzsch, Michael Goedicke, Lars Grunske, Carina Haupt, Stephan Janosch, Frank Löffler, Bernhard Rumpe, Robert Speck
Softwaretechnik-Trends, 43(3), 2023
https://dl.gi.de/items/e91d1e43-6168-4686-a81d-b29f27090752 -
ENCORE. A practical implementation to improve reproducibility and transparency of computational research.
Antoine van Kampen, Utkarsh Mahamune, Aldo Jongejan, Barbera van Schaik, Daria Balashova, Danial Lashgari, Mia Pras-Raves, Eric Wever, Rodrigo Garcia Valiente, Adrie Dane, others
2023 -
Research software engineering and the importance of scientific models
Benoit Combemale, Jeff Gray, Bernhard Rumpe
Software and Systems Modeling, 22(4), pp. 1081--1083, 2023
DOI: 10.1007/s10270-023-01119-z -
Research Software - from ugly ducklings to beautiful swans
Bernadette Fritzsch
2023
DOI: 10.5281/ZENODO.8341375 -
Ten simple rules for working with other people's code
Charlie Pilgrim, Paul Kent, Kasra Hosseini, Ed Chalstrey
PLOS Computational Biology, 19(4), pp. e1011031, 2023
DOI: 10.1371/journal.pcbi.1011031 -
From Research to Regulated Software
Christoph Kämpf, Alexander Scholz, Markus Kreuz, Kristin Reiche
2023
DOI: 10.5281/ZENODO.7751723 -
Sustainable software engineering: Reflections on advances in research and practice
Colin C. Venters, Rafael Capilla, Elisa Yumi Nakagawa, Stefanie Betz, Birgit Penzenstadler, Tom Crick, Ian Brooks
Information and Software Technology, 164, pp. 107316, 2023
DOI: 10.1016/j.infsof.2023.107316 -
Better incentives are needed to reward academic software development
Cory Merow, Brad Boyle, Brian J. Enquist, Xiao Feng, Jamie M. Kass, Brian S. Maitner, Brian McGill, Hannah Owens, Daniel S. Park, Andrea Paz, Gonzalo E. Pinilla-Buitrago, Mark C. Urban, Sara Varela, Adam M. Wilson
Nature Ecology & Evolution, 2023
DOI: 10.1038/s41559-023-02008-w -
Advancing Software Citation Implementation (Software Citation Workshop 2022)
Daina Bouquin, Ana Trisovic, Oliver Bertuch, Elena Colón-Marrero
2023
DOI: 10.48550/ARXIV.2302.07500 -
The Changing Role of RSEs over the Lifetime of Parsl
Daniel S. Katz, Ben Clifford, Yadu Babuji, Kevin Hunter Kesling, Anna Woodard, Kyle Chard
2023
DOI: 10.48550/ARXIV.2307.11060 -
Research Software Engineering in 2030
Daniel S. Katz, Simon Hettrick
2023 IEEE 19th International Conference on e-Science (e-Science), 2023
DOI: 10.1109/e-science58273.2023.10254813 -
Understanding practices and challenges of developing sustainable research software: a pilot interview.
Daniela Feitosa, Christina von Flach, Joenio Costa
WORKSHOP DE PRÁTICAS DE CIÊNCIA ABERTA PARA ENGENHARIA DE SOFTWARE (OPENSCIENSE), 2023 -
Research software engineering accelerates the translation of biomedical research for health
David Horsfall, Jonah Cool, Simon Hettrick, Angela Oliveira Pisco, Neil Chue Hong, Muzlifah Haniffa
Nature Medicine, 29(6), pp. 1313--1316, 2023
DOI: 10.1038/s41591-023-02353-0 -
Containers for computational reproducibility
David Moreau, Kristina Wiebels, Carl Boettiger
Nature Reviews Methods Primers, 3(1), 2023
DOI: 10.1038/s43586-023-00236-9 -
A multi-level analysis of data quality for formal software citation
David Schindler, Tazin Hossain, Sascha Spors, Frank Krüger
2023
DOI: 10.48550/ARXIV.2306.17535 -
Computational Reproducibility in Computational Social Science
David Schoch, Chung-hong Chan, Claudia Wagner, Arnim Bleier
2023
DOI: 10.48550/ARXIV.2307.01918 -
Ten simple rules for providing bioinformatics support within a hospital
Davide Chicco, Giuseppe Jurman
BioData Mining, 16(1), 2023
DOI: 10.1186/s13040-023-00326-0 -
FAIRSECO: An Extensible Framework for Impact Measurement of Research Software
Deekshitha, Siamak Farshidi, Jason Maassen, Rena Bakhshi, Rob Van Nieuwpoort, Slinger Jansen
2023 IEEE 19th International Conference on e-Science (e-Science), 2023
DOI: 10.1109/e-science58273.2023.10254664 -
Sicherstellung der Reproduzierbarkeit von Forschungsergebnissen durch Bewahrung des Zugriffs auf Forschungssoftware
Dirk von Suchdoletz, Peter Brettschneider, Alexandra Axtmann, Maximilian Heber, Lars Oberländer, Jan Leendertse, Irene Schumm, Olaf Brandt, Karsten Schmidt, Livia Gertis, Michael Selzer, Robert Ulrich, Dorothea Iglezakis, Valerie Boda
2023
DOI: 10.17192/BFDM.2023.5.8555 -
Where is all the research software? An analysis of software in UK academic repositories
Domhnall Carlin, Austen Rainer, David Wilson
PeerJ Computer Science, 9, pp. e1546, 2023
DOI: 10.7717/peerj-cs.1546 -
SoftWhere? Searching for research software in the UK
Domhnall Carlin
2023
https://se4science.org/workshops/se4rse23/index.htm -
Continuously Accelerating Research
Earl Barr, Jonathan Bell, Michael Hilton, Sergey Mechtaev, Christopher Timperley
2023 -
Management of mathematical research software and data
Emil Løvbak, Mustafa Dikmen, Naeem Muhammad, Giovanni Samaey
proceedings 2023, 2023
DOI: 10.21428/1192f2f8.e175b077 -
Cited But Not Archived: Analyzing the Status of Code References in Scholarly Articles
Emily Escamilla, Martin Klein, Talya Cooper, Vicky Rampin, Michele C. Weigle, Michael L. Nelson
Lecture Notes in Computer Science, pp. 194--207, 2023
DOI: 10.1007/978-981-99-8088-8_17 -
From Code to Tenure: Valuing Research Software in Academia
Eric A. Jensen, Daniel S. Katz
Commonplace, 2023 -
Investigating Developers' Perception on Success Factors for Research Software Development
Erica Mourão, Daniela Trevisan, José Viterbo, Carlos Eduardo Pantoja
New Sustainable Horizons in Artificial Intelligence and Digital Solutions, pp. 14--26, 2023
DOI: 10.1007/978-3-031-50040-4_2 -
Policy recommendations to ensure that research software is openly accessible and reusable
Erin C. McKiernan, Lorena Barba, Philip E. Bourne, Caitlin Carter, Zach Chandler, Sayeed Choudhury, Stephen Jacobs, Daniel S. Katz, Stefanie Lieggi, Beth Plale, Greg Tananbaum
PLOS Biology, 21(7), pp. e3002204, 2023
DOI: 10.1371/journal.pbio.3002204 -
Grand challenges in bioinformatics education and training
Esra Büşra Işık, Michelle D. Brazas, Russell Schwartz, Bruno Gaeta, Patricia M. Palagi, Celia W. G. van Gelder, Prashanth Suravajhala, Harpreet Singh, Sarah L. Morgan, Hilyatuz Zahroh, Maurice Ling, Venkata P. Satagopam, Annette McGrath, Kenta Nakai, Tin Wee Tan, Ge Gao, Nicola Mulder, Christian Schönbach, Yun Zheng, Javier De Las Rivas, Asif M. Khan
Nature Biotechnology, 41(8), pp. 1171--1174, 2023
DOI: 10.1038/s41587-023-01891-9 -
Softalias-KG: Reconciling Software Mentions in Scientific Literature.
Esteban González-Guardia, Hector Lopez, Daniel Garijo
ISWC (Posters/Demos/Industry), 2023 -
Soft-Search: Two Datasets to Study the Identification and Production of Research Software
Eva Maxfield Brown, Lindsey Schwartz, Richard Lewei Huang, Nicholas Weber
2023
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Making Bioinformatics Training Events and Material More Discoverable Using TeSS, the ELIXIR Training Portal
Finn Bacall, Aitor Apaolaza, Munazah Andrabi, Chris Child, Carole Goble, Olivier Sand, Alexander Botzki
Current Protocols, 3(2), 2023
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An Open Community-Driven Model For Sustainable Research Software: Sustainable Research Software Institute
Gregory R. Watson, Addi Malviya-Thakur, Daniel S. Katz, Elaine M. Raybourn, Bill Hoffman, Dana Robinson, John Kellerman, Clark Roundy
2023
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Lessons in FAIR software from the Community Surface Dynamics Modeling System
Gregory Tucker, Albert Kettner, Eric Hutton, Mark Piper, Tian Gan, Benjamin Campforts, Irina Overeem, Matthew Rossi
2023
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3. Helmholtz Open Science Forum Forschungssoftware. Helmholtz Open Science Briefing
Heinz Pampel, Lea Maria Ferguson, Stephan Druskat, Uwe Konrad, Martin Hammitzsch, Christian Meeßen, David Schäfer, Robert Speck, Markus Diesmann, Achim Streit, Rene Caspart
2023
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Establishing a national research software award
Isabelle Blanc Catala, Roberto Di Cosmo, Mathieu Giraud, Daniel Le Berre, Violaine Louvet, Sophie Renaudin
Open Research Europe, 3, pp. 185, 2023
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The in silico lab: Improving academic code using lessons from biology
Jason Y. Cain, Jessica S. Yu, Neda Bagheri
Cell Systems, 14(1), pp. 1--6, 2023
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Revisiting the reproducibility of empirical software engineering studies based on data retrieved from development repositories
Jesus M. Gonzalez-Barahona, Gregorio Robles
Information and Software Technology, 164, pp. 107318, 2023
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Professionalization of Research Computing and Data: An Expanded Agenda
Joel Cutcher-Gershenfeld, Torey Battelle, Dana Brunson, Thomas Cheatham, Jacob Fosso Tande, Douglas Jennewein, Julie Ma, Lauren A. Michael, Timothy Middelkoop, Henry Neeman, Patrick Schmitz
Practice and Experience in Advanced Research Computing, 2023
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Better Research Software Tools to Elevate the Rate of Scientific Discovery – or why we need to invest in research software engineering
Joran Deschamps, Damian Dalle Nogare, Florian Jug
2023
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Implementation of micro-credentials in higher education: A systematic literature review
Kamrul Ahsan, Suraiyah Akbar, Booi Kam, Muhammad Dan-Asabe Abdulrahman
Education and Information Technologies, 2023
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Human factors in industrial research software engineering
Katharina Dworatzyk, Tobias Schlauch
The PASC23 Conference - Minisymposium Code complete and more: Emerging efforts to improve software quality, 2023
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Earth beyond six of nine planetary boundaries
Katherine Richardson, Will Steffen, Wolfgang Lucht, Jørgen Bendtsen, Sarah E. Cornell, Jonathan F. Donges, Markus Drüke, Ingo Fetzer, Govindasamy Bala, Werner von Bloh, Georg Feulner, Stephanie Fiedler, Dieter Gerten, Tom Gleeson, Matthias Hofmann, Willem Huiskamp, Matti Kummu, Chinchu Mohan, David Nogués-Bravo, Stefan Petri, Miina Porkka, Stefan Rahmstorf, Sibyll Schaphoff, Kirsten Thonicke, Arne Tobian, Vili Virkki, Lan Wang-Erlandsson, Lisa Weber, Johan Rockström
Science Advances, 9(37), pp. eadh2458, 2023
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Bioschemas training profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources
Leyla Jael Castro, Patricia M. Palagi, Niall Beard, Teresa K. Attwood, Michelle D. Brazas
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A cast of thousands: How the IDEAS Productivity project has advanced software productivity and sustainability
Lois Curfman McInnes, Michael Heroux, David E. Bernholdt, Anshu Dubey, Elsa Gonsiorowski, Rinku Gupta, Osni Marques, J. David Moulton, Hai Ah Nam, Boyana Norris, Elaine M. Raybourn, Jim Willenbring, Ann Almgren, Ross Bartlett, Kita Cranfill, Stephen Fickas, Don Frederick, William Godoy, Patricia Grubel, Rebecca Hartman-Baker, Axel Huebl, Rose Lynch, Addi Malviya Thakur, Reed Milewicz, Mark C. Miller, Miranda Mundt, Erik Palmer, Suzanne Parete-Koon, Megan Phinney, Katherine Riley, David M. Rogers, Ben Sims, Deborah Stevens, Gregory R. Watson
2023
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GREENER principles for environmentally sustainable computational science
Loïc Lannelongue, Hans-Erik G. Aronson, Alex Bateman, Ewan Birney, Talia Caplan, Martin Juckes, Johanna McEntyre, Andrew D. Morris, Gerry Reilly, Michael Inouye
Nature Computational Science, 3(6), pp. 514--521, 2023
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Shared metadata for data-centric materials science
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Teaching open and reproducible scholarship: a critical review of the evidence base for current pedagogical methods and their outcomes
Madeleine Pownall, Flávio Azevedo, Laura M. König, Hannah R. Slack, Thomas Rhys Evans, Zoe Flack, Sandra Grinschgl, Mahmoud M. Elsherif, Katie A. Gilligan-Lee, Catia M. F. de Oliveira, Biljana Gjoneska, Tamara Kalandadze, Katherine Button, Sarah Ashcroft-Jones, Jenny Terry, Nihan Albayrak-Aydemir, Filip Děchtěrenko, Shilaan Alzahawi, Bradley J. Baker, Merle-Marie Pittelkow, Lydia Riedl, Kathleen Schmidt, Charlotte R. Pennington, John J. Shaw, Timo Lüke, Matthew C. Makel, Helena Hartmann, Mirela Zaneva, Daniel Walker, Steven Verheyen, Daniel Cox, Jennifer Mattschey, Tom Gallagher-Mitchell, Peter Branney, Yanna Weisberg, Kamil Izydorczak, Ali H. Al-Hoorie, Ann-Marie Creaven, Suzanne L. K. Stewart, Kai Krautter, Karen Matvienko-Sikar, Samuel J. Westwood, Patrícia Arriaga, Meng Liu, Myriam A. Baum, Tobias Wingen, Robert M. Ross, Aoife O'Mahony, Agata Bochynska, Michelle Jamieson, Myrthe Vel Tromp, Siu Kit Yeung, Martin R. Vasilev, Amélie Gourdon-Kanhukamwe, Leticia Micheli, Markus Konkol, David Moreau, James E. Bartlett, Kait Clark, Gwen Brekelmans, Theofilos Gkinopoulos, Samantha L. Tyler, Jan Philipp Röer, Zlatomira G. Ilchovska, Christopher R. Madan, Olly Robertson, Bethan J. Iley, Samuel Guay, Martina Sladekova, Shanu Sadhwani, FORTT
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Automated Software Metadata Conversion and Publication Based on CodeMeta
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Supporting Software Development Processes for Academia with GitLab
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Toward Research Software Engineering Research
Michael Felderer, Michael Goedicke, Lars Grunske, Wilhelm Hasselbring, Bernhard Rumpe
2023
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Developing a Metadata Profile for Higher Education OER Repositories
Michael Menzel
Distributed Learning Ecosystems, pp. 263--278, 2023
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Morane Gruenpeter
2023
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Can software metrics improve (research) software quality?
Neil Chue Hong
2023
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D5.2 - Metrics for automated FAIR software assessment in a disciplinary context
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Afterlife: the post-research affect and effect of software
Nicolas E Gold, Ian Lawson, Neil P Oxtoby
Research Ethics, 19(4), pp. 433--448, 2023
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Machine-Actionable Metadata for Software and Software Management Plans for NFDI
Olga Giraldo, Danilo Dessi, Stefan Dietze, Dietrich Rebholz-Schuhmann, Leyla Jael Castro
Proceedings of the Conference on Research Data Infrastructure, 1, 2023
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Olga L Giraldo, Renato Alves, Dimitrios Bampalikis, José M Fernández, Eva Martin Del Pico, Fotis E Psomopoulos, Nelson Quiñones, Dhwani Solanki, Allegra Via, Leyla Jael Castro
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Seeking Enlightenment: Incorporating Evidence-Based Practice Techniques in a Research Software Engineering Team
Reed Milewicz, Jon Bisila, Miranda Mundt, Joshua Teves
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Towards Evidence-Based Software Quality Practices for Reproducibility: Preliminary Results and Research Directions
Reed Milewicz, Miranda Mundt
Proceedings of the 2023 ACM Conference on Reproducibility and Replicability, 2023
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Rinku Gupta, David E Bernholdt, Roscoe A Bartlett, Patricia A Grubel, Michael A Heroux, LC McInnes, MC Miller, K Salim, J Shuler, D Stevens, others
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Defining the roles of research software
Rob van Nieuwpoort, Daniel S. Katz
2023
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Development of an Austrian OER Certification for Higher Education Institutions and Their Employees
Sandra Schön, Martin Ebner, Elfriede Berger, Gerhard Brandhofer, Sarah Edelsbrunner, Ortrun Gröblinger, Claudia Hackl, Tanja Jadin, Michael Kopp, Kristina Neuböck, Judith Proinger, Alexander Schmölz, Hans-Peter Steinbacher
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Galaxy Training: A powerful framework for teaching!
Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D. Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J. Griffin, Coline Royaux, Yvan Le Bras, Subina Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi Bacon, Fotis Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A. Doyle, Beatriz Serrano-Solano, Anne Claire Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, Galaxy Training Network, Björn Grüning, Bérénice Batut
PLOS Computational Biology, 19(1), pp. e1010752, 2023
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Sustainability is Stratified: Toward a Better Theory of Sustainable Software Engineering
Sean McGuire, Erin Shultz, Bimpe Ayoola, Paul Ralph
2023
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Journal Production Guidance for Software and Data Citations
Shelley Stall, Geoffrey Bilder, Matthew Cannon, Neil Chue Hong, Scott Edmunds, Christopher C. Erdmann, Michael Evans, Rosemary Farmer, Patricia Feeney, Michael Friedman, Matthew Giampoala, R. Brooks Hanson, Melissa Harrison, Dimitris Karaiskos, Daniel S. Katz, Viviana Letizia, Vincent Lizzi, Catriona MacCallum, August Muench, Kate Perry, Howard Ratner, Uwe Schindler, Brian Sedora, Martina Stockhause, Randy Townsend, Jake Yeston, Timothy Clark
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Towards Research Software-ready Libraries: Forschungssoftware in Bibliotheken
Stephan Druskat, Oliver Bertuch, Alexander Struck
ABI Technik, 43(3), pp. 168--178, 2023
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The four elements of achieving research software sustainability for long tail projects
Stephan Druskat, Thomas Krause
2023
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The Citation File Format: Providing citation metadata for research software
Stephan Druskat
2023
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HERMES: Easing the path to FAIR software publications
Stephan Druskat, Oliver Bertuch, Oliver Knodel, Michael Meinel, Guido Juckeland, Tobias Schlauch, Jeffrey Kelling, David Pape
2023
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HERMES: Automating software publication with rich metadata
Stephan Druskat
2023
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And then there were users: Designing and implementing governance for open research software projects
Stephan Druskat, Jurriaan H. Spaaks
2023
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Towards Improved Findability of Energy Research Software by Introducing a Metadata-based Registry
Stephan Ferenz, Astrid Nieße
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The ESCAPE Open-source Software and Service Repository
Thomas Vuillaume, Mohammad Al-Turany, Matthias Füßling, Tamas Gal, Enrique Garcia, Kay Graf, Gareth Hughes, Mark Kettenis, Dmytro Kresan, Jutta Schnabel, Christian Tacke, Marjolein Verkouter
Open Research Europe, 3, pp. 46, 2023
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A sustainable infrastructure concept for improved accessibility, reusability, and archival of research software
Timo Koch, Dennis Gläser, Anett Seeland, Sarbani Roy, Katharina Schulze, Kilian Weishaupt, David Boehringer, Sibylle Hermann, Bernd Flemisch
2023
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Towards a Critical Open-Source Software Database
Tobias Dam, Lukas Daniel Klausner, Sebastian Neumaier
Companion Proceedings of the ACM Web Conference 2023, pp. 156--159, 2023
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Software ist kein Beiprodukt! Nachhaltige Forschungssoftware durch Software-Management-Pläne
Yves Vincent Grossmann, Michael Franke
b.i.t.online, 26(5), pp. 457--463, 2023
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2022
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Towards a Software Development Framework for Interconnected Science Ecosystems
Addi Malviya Thakur, Seth Hitefield, Marshall McDonnell, Matthew Wolf, Richard Archibald, Lance Drane, Kevin Roccapriore, Maxim Ziatdinov, Jesse McGaha, Robert Smith, others
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Research Software Engineering at Oak Ridge National Laboratory
Addi Malviya-Thakur, David E. Bernholdt, William F. Godoy, Gregory R. Watson, Mathieu Doucet, Mark A. Coletti, David M. Rogers, Marshall McDonnell, Jay Jay Billings, Barney Maccabe
Computing in Science & Engineering, 24(5), pp. 14--23, 2022
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Improving bioinformatics software quality through incorporation of software engineering practices
Adeeb Noor
PeerJ Computer Science, 8, pp. e839, 2022
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GitQ- towards using badges as visual cues for GitHub projects
Akhila Sri Manasa Venigalla, Kowndinya Boyalakuntla, Sridhar Chimalakonda
Proceedings of the 30th IEEE/ACM International Conference on Program Comprehension (ICPC 2022), pp. 157--161, 2022
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Creation of a core competency framework for clinical informatics: From genesis to maintaining relevance
Alan Davies, Alan Hassey, John Williams, Georgina Moulton
International Journal of Medical Informatics, 168, pp. 104905, 2022
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How to be a Good Member of a Scientific Software Community [Article v1.0]
Alan Grossfield
Living Journal of Computational Molecular Science, 3(1), pp. 1473, 2022
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It's your software! Get it cited the way you want!
Alice Allen
2022
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Socioeconomic roots of academic faculty
Allison C. Morgan, Nicholas LaBerge, Daniel B. Larremore, Mirta Galesic, Jennie E. Brand, Aaron Clauset
Nature Human Behaviour, 6(12), pp. 1625--1633, 2022
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SusTrainable: Promoting Sustainability as a Fundamental Driver in Software Development Training and Education
Ana Oprescu, Lukas Koedijk, Sander van Oostveen, Stephan Kok
Teacher Training, pp. 27--35, 2022
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A FAIR Digital Object Lab Software Stack
Andreas Pfeil, Thomas Jejkal, Sabrine Chelbi, Nicolas Blumenröhr
Research Ideas and Outcomes, 8, 2022
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Architecting the future of software engineering
Anita Carleton, Forrest Shull, Erin Harper
Computer, 55(9), pp. 89--93, 2022
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What Do We (Not) Know About Research Software Engineering?
Anna-Lena Lamprecht, Carlos Martinez-Ortiz, Michelle Barker, Sadie L. Bartholomew, Justin Barton, Neil Chue Hong, Jeremy Cohen, Stephan Druskat, Jeremy Forest, Jean-Noël Grad, Daniel S. Katz, Robin Richardson, Robert Rosca, Douwe Schulte, Alexander Struck, Marion Weinzierl
Journal of Open Research Software, 10, 2022
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Teaching computational genomics and bioinformatics on a high performance computing cluster--a primer
Arun Sethuraman
Biology Methods and Protocols, 7(1), 2022
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From dual digitalization to digital learning space: Exploring the digital transformation of higher education
Bendik Bygstad, Egil Øvrelid, Sten Ludvigsen, Morten Dæhlen
Computers & Education, 182, pp. 104463, 2022
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Ten simple rules for reporting a bug
Benjamin C. Haller
PLOS Computational Biology, 18(10), pp. e1010540, 2022
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Hidden Figures - wo sind sie? Frauen in der Entwicklung von Forschungssoftware
Bernadette Fritzsch
CampusSource Tagung 2022, 2022 -
Research Software and the people behind it
Bernadette Fritzsch
2022
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Pots of Gold at the End of the Rainbow: What is Success for Open Source Contributors?
Bianca Trinkenreich, Mariam Guizani, Igor Wiese, Tayana Conte, Marco Gerosa, Anita Sarma, Igor Steinmacher
IEEE Transactions on Software Engineering, 48(10), pp. 3940--3953, 2022
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Best Practice Guide: How to Find New Attendees for Training Courses
CASTIEL, EuroCC Network
Training Best Practice Seminar (CASTIEL), 2022
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(Research-)Software-Entwicklung für Non-IT'ler
Carina Haupt
OOP Digital 2022, 2022
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FAIR4RS: Adoption support
Carlos Martinez-Ortiz, Daniel S. Katz, Anna-Lena Lamprecht, Michelle Barker, Axel Loewe, Anne Fouilloux, Jane Wyngaard, Daniel Garijo, Javier Moldon, Leyla Jael Castro, Daniel Wheeler, Joost Rutger Demian Albers, Allen Lee
2022
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How does software fit into the FDO landscape?
Carlos Martinez-Ortiz, Carole Goble, Daniel Katz, Tom Honeyman, Paula Martinez, Michelle Barker, Leyla Jael Castro, Neil Chue Hong, Morane Gruenpeter, Jennifer Harrow, Anna-Lena Lamprecht, Fotis Psomopoulos
Research Ideas and Outcomes, 8, 2022
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Ten simple rules for funding scientific open source software
Carly Strasser, Kate Hertweck, Josh Greenberg, Dario Taraborelli, Elizabeth Vu
PLOS Computational Biology, 18(11), pp. e1010627--e1010627, 2022
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Why science needs more research software engineers
Chris Woolston
Nature, pp. d41586--022--01516--2, 2022
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Characterizing the US Research Computing and Data (RCD) Workforce
Christina Maimone, Scott Yockel, Timothy Middelkoop, Ashley Stauffer, Chris Reidy
2022
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Testing Software Systems
Christof Ebert, Divith Bajaj, Michael Weyrich
IEEE Software, 39(4), pp. 8--17, 2022
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SURESOFT: Towards Sustainable Research Software
Christopher Blech, Nils Dreyer, Matthias Friebel, Christoph Jacob, Mostafa Shamil Jassim, Leander Jehl, Rüdiger Kapitza, Manfred Krafczyk, Thomas Kürner, Sabine Christine Langer, Jan Linxweiler, Mohammad Mahhouk, Sven Marcus, Ines Messadi, Sören Peters, Jan-Marc Pilawa, Harikrishnan K. Sreekumar, Robert Strötgen, Katrin Stump, Arne Vogel, Mario Wolter
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ROSA22 - Citing and Improving the Discoverability of Your Research Software
Christopher Erdmann
2022
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Nine best practices for research software registries and repositories
Daniel Garijo, Hervé Ménager, Lorraine Hwang, Ana Trisovic, Michael Hucka, Thomas Morrell, Alice Allen
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The role of software in science: a knowledge graph-based analysis of software mentions in PubMed Central
David Schindler, Felix Bensmann, Stefan Dietze, Frank Krüger
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Bus factor in practice
Elgun Jabrayilzade, Mikhail Evtikhiev, Eray Tüzün, Vladimir Kovalenko
Proceedings of the 44th International Conference on Software Engineering: Software Engineering in Practice (ICSE-SEIP '22), pp. 97--106, 2022
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Transforming Trajectories for Women of Color in Tech
Engineering, National Academies of Sciences, Medicine
2022
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Taking the TU Delft Carpentries Workshops Online
Esther Plomp, Emmy Tsang, Paula M. Martinez Lavanchy
Journal of eScience Librarianship, 11(1), 2022
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FAIRsoft-A practical implementation of FAIR principles for research software
Eva Martı\ʼn del Pico, ́ Josep Lluı\ ́and Capella-Gutiérrez, Salvador Gelpı
bioRxiv, pp. 2022--05--2022--05, 2022 -
Cognition in software engineering: a taxonomy and survey of a half-century of research
Fabian Fagerholm, Michael Felderer, Davide Fucci, Michael Unterkalmsteiner, Bogdan Marculescu, Markus Martini, Lars Göran Wallgren Tengberg, Robert Feldt, Bettina Lehtelä, Balázs Nagyváradi, Jehan Khattak
ACM Computing Surveys, 54(11s), 2022
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ProvBench: A performance provenance capturing framework for heterogeneous research computing environments
Fang (Cherry) Liu, Mehmet Belgin, Nuyun Zhang, Kevin Manalo, Ruben Lara, Christopher P. Stone, Paul Manno
Concurrency and Computation: Practice and Experience, 2022
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Curriculum Development for FAIR Data Stewardship
Francisca Oladipo, Sakinat Folorunso, Ezekiel Ogundepo, Obinna Osigwe, Akinyinka Akindele
Data Intelligence, 4(4), pp. 991--1012, 2022
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The European Bioinformatics Institute (EMBL-EBI) in 2021
Gaia Cantelli, Alex Bateman, Cath Brooksbank, Anton I. Petrov, Rahuman S. Malik-Sheriff, Michele Ide-Smith, Henning Hermjakob, Paul Flicek, Rolf Apweiler, Ewan Birney, Johanna McEntyre
Nucleic Acids Research, 50(D1), pp. D11--D19, 2022
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AI4SD Video: Reproducibility, Jupyter notebooks and associated research software engineering
Hans Fangohr
2022
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The Princeton University Research Software Engineering Group Model: Operational and Organizational Approaches
Ian A. Cosden
Computing in Science & Engineering, 24(5), pp. 24--31, 2022
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Research Software Engineers: Career Entry Points and Training Gaps
Ian A. Cosden, Kenton McHenry, Daniel S. Katz
2022 -
An RSE Group Model: Operational and Organizational Approaches From Princeton University's Central Research Software Engineering Group
Ian A. Cosden
2022
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Connecting the astronomical testbed community - the CAOTIC project: optimized teaching methods for software version control concepts
Iva Laginja, Pablo Robles, Kevin Barjot, Lucie Leboulleux, Rebecca Jensen-Clem, Keira J. Brooks, Christopher Moriarty
Adaptive Optics Systems VIII, 12185, pp. 121853A, 2022
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Evaluating the Sustainability of Computational Science and Engineering Software: Empirical Observations
James Willenbring, Gursimran Walia
2022 -
A survey of the state of the practice for research software in the United States
Jeffrey C. Carver, Nic Weber, Karthik Ram, Sandra Gesing, Daniel S. Katz
PeerJ Computer Science, 8, pp. e963, 2022
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Software Development Metrics With a Purpose
Jesus M. Gonzalez-Barahona, Daniel Izquierdo-Cortazar, Gregorio Robles
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SciCodes: Astronomy Research Software and Beyond
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Daniel S. Katz, Neil P. Chue Hong, Tim Clark, August Muench, Shelley Stall, Daina Bouquin, Matthew Cannon, Scott Edmunds, Telli Faez, Patricia Feeney, Martin Fenner, Michael Friedman, Gerry Grenier, Melissa Harrison, Joerg Heber, Adam Leary, Catriona MacCallum, Hollydawn Murray, Erika Pastrana, Katherine Perry, Douglas Schuster, Martina Stockhause, Jake Yeston
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Science-Software Linkage: The Challenges of Traceability between Scientific Knowledge and Software Artifacts
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A Practical Guide to Metabolomics Software Development
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The US-RSE Association: Bringing Together Research Software Engineers
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Learning to Fly: Development and Design of a Micro-Credentialing System for an Educator Preparation Program in the Absence of a Required Educational Technology Course
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Bringing Green Software to Computer Science Curriculum: Perspectives from Researchers and Educators
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Aquarium: open-source laboratory software for design, execution and data management
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Empirical Software Engineering, 27(1), 2022, 2021
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Sean Goggins, Kevin Lumbard, Matt Germonprez
Proceedings of the 2021 IEEE/ACM 4th International Workshop on Software Health in Projects, Ecosystems and Communities (SoHeal), pp. 25--33, 2021
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Sean P. Goggins, Matt Germonprez, Kevin Lumbard
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Shoaib Sufi
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An Appraisal of Skill Gaps in Bioinformatics Education
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Research Data Management and Data Stewardship Competences in University Curriculum
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Proceedings of the 2001 IEEE Global Engineering Education Conference (EDUCON), 2021
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Nine Best Practices for Research Software Registries and Repositories: A Concise Guide
Alain Monteil, Alejandra Gonzalez-Beltran, Alexandros Ioannidis, Alice Allen, Allen Lee, Anita Bandrowski, Bruce E. Wilson, Bryce Mecum, Cai Fan Du, Carly Robinson, Daniel Garijo, Daniel S. Katz, David Long, Genevieve Milliken, Hervé Ménager, Jessica Hausman, Jurriaan H. Spaaks, Katrina Fenlon, Kristin Vanderbilt, Lorraine Hwang, Lynn Davis, Martin Fenner, Michael R. Crusoe, Michael Hucka, Mingfang Wu, Neil Chue Hong, Peter Teuben, Shelley Stall, Stephan Druskat, Ted Carnevale, Thomas Morrell
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Journal of the Association for Information Science and Technology, 71(3), pp. 325--337, 2020
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Emulation Encounters: Software Preservation in Libraries, Archives, and Museums
Amelia Acker
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International Journal of Managing Projects in Business, 13(6), pp. 1339--1361--1339--1361, 2020
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Bioinformatics-Based Activities in High School: Fostering Students' Literacy, Interest, and Attitudes on Gene Regulation, Genomics, and Evolution
Ana Martins, Maria João Fonseca, Marina Lemos, Leonor Lencastre, Fernando Tavares
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Andreas Wernitznig, Jesse J. Lipp, Thomas Zichner, Daniel Gerlach, Markus J. Bauer, Tilman Voss, Andreas Schlattl, Christian Haslinger, Philip G. Montgomery, Mahdi Zamanighomi, William R. Sellers, Norbert Kraut
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Umgang mit Forschungssoftware an der Universität Stuttgart
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, Kilian Weishaupt
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Brandon C. LeBeau, Ariel M. Aloe
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Caroline Jay, Robert Haines, Daniel S. Katz
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FAIR, FLOSS and Sustainable: Complementary Paradigms for Research Software
Christian E. Busse
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On the Usage of Badges in Open Source Packages on GitHub
Damien Legay, Alexandre Decan, Tom Mens
Proceedings of the 18th Edition of the Belgian-Netherlands Software Evolution Symposium (BENEVOL 2019), 2020
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Daniel Mendez, Daniel Graziotin, Stefan Wagner, Heidi Seibold
Contemporary Empirical Methods in Software Engineering, pp. 477--501--477--501, 2020
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Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science
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Daniel S. Katz, Neil P. Chue Hong, Tim Clark, Martin Fenner, Maryann E. Martone
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Connecting Workplace Learning and Academic Credentials via Digital Badges
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New Directions for Community Colleges, 2020(189), pp. 39--51, 2020
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A Figure One Web Tool for Visualization of Experimental Designs
Foo Cheung
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ESiWACE2 Services: RSE collaborations in Weather and Climate
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Methods for training collaborative biostatisticians
Gina-Maria Pomann, L. Ebony Boulware, Shari Messinger Cayetano, Manisha Desai, Felicity T. Enders, John A. Gallis, Jonathan Gelfond, Steven C. Grambow, Alexandra L. Hanlon, Angelean Hendrix, Pandurang Kulkarni, Jodi Lapidus, Hui-Jie Lee, Jonathan D. Mahnken, Julie P. McKeel, Rebecca Moen, Robert A. Oster, Sarah Peskoe, Greg Samsa, Thomas G. Stewart, Tracy Truong, Lisa Wruck, Samantha M. Thomas
Journal of Clinical and Translational Science, 5(1), pp. e26, 2020
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An Environment for Sustainable Research Software in Germany and Beyond: Current State, Open Challenges, and Call for Action
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A Software Institute for Data-Intensive Sciences, Joining Computer Science Academia and Natural Science Research
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Ismael Canales-Negrón
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Data Without Software Are Just Numbers
James Harold Davenport, James Grant, Catherine Mary Jones
Data Science Journal, 19, 2020
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Jan-Patrick Lehra, Tomislav Maricb, Dieter Botheb, Christian Bischofa
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FAIR digital objects in environmental and life sciences should comprise workflow operation design data and method information for repeatability of study setups and reproducibility of results
Janno Harjes, Anton Link, Tanja Weibulat, Dagmar Triebel, Gerhard Rambold
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Domain-Based Ranking of Software Test--Effort Estimation Techniques for Academic Projects
Jatinderkumar R. Saini, Vikas S. Chomal
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RSEs in Research? RSEs in IT?: Finding a suitable home for RSEs
Jeremy Cohen, Mark Woodbridge
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The role of metadata in reproducible computational research
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Free and Low-Cost Twitter Research Software Tools for Social Science
Jingyuan Yu, Juan Muñoz-Justicia
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Ten simple rules for writing a paper about scientific software
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Better together: Elements of successful scientific software development in a distributed collaborative community
Julia Koehler Leman, Brian D. Weitzner, P. Douglas Renfrew, Steven M. Lewis, Rocco Moretti, Andrew M. Watkins, Vikram Khipple Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason W. Labonte, Justyna Krys, RosettaCommons Consortium, Christopher Bystroff, William Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland Dunbrack, Tanja Kortemme, Andrew Leaver-Fay, Charlie E. M. Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J. Gray, Richard Bonneau
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The Journal of Computational Science Education, 11(1), pp. 106--107, 2020
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The HPC Certification Forum: Toward a Globally Acknowledged HPC Certification
Julian Kunkel, Weronika Filinger, Christian Meesters, Anja Gerbes
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One Year HPC Certification Forum in Retrospective
Julian Martin Kunkel, Kai Himstedt, Weronika Filinger, Jean-Thomas Acquaviva, Anja Gerbes, Lev Lafayette
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Short communication: Landlab v2.0: A software package for Earth surface dynamics
Katherine R. Barnhart, Eric W. H. Hutton, Gregory E. Tucker, Nicole M. Gasparini, Erkan Istanbulluoglu, Daniel E. J. Hobley, Nathan J. Lyons, Margaux Mouchene, Sai Siddhartha Nudurupati, Jordan M. Adams, Christina Bandaragoda
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Doing Data Science on the Shoulders of Giants: The Value of Open Source Software for the Data Science Community
Katie Malone, Rich Wolski
Harvard Data Science Review, 2020
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(Deep) FAIR mathematics
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PLOS Computational Biology, 16(7), pp. e1007976, 2020
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The case for free and open source software in research and scholarship
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Barking up the same tree? Lessons from workplace-based assessment and digital badges
Leslie Martin, Matthew Sibbald
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Ten simple rules for making training materials FAIR
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Software as a first-class citizen in research
Leyla Jael Garcia Castro, Michelle Barker, Neil P. Chue Hong, Fotis Psomopoulos, Jennifer Harrow, Daniel S. Katz, Mateusz Kuzak, Paula Andrea Martinez, Allegra Via
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Louise Bezuidenhout, Johanna Havemann
F1000Research, 9, pp. 1292--1292, 2020
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Analysis and Categorisation of Research Software in the Digital Humanities
Lukas Harzenetter, Johanna Barzen Uwe Breitenbücher, Frank Leymann, Brigitte Mathiak, Philip Schildkamp, Claes Neuefeind
2020 -
The place of models and modelling in Digital Humanities: Intersections with a Research Software Engineering perspective
Maher Brian, Arianna Ciula, Noël Geoffroy, Ferraro Ginestra, Vieira Miguel, Caton Paul
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Does stress impact technical interview performance?
Mahnaz Behroozi, Shivani Shirolkar, Titus Barik, Chris Parnin
Proceedings of the 28th ACM joint meeting on European Software Engineering Conference and symposium on the Foundations of Software Engineering (ESEC/FSE 2020), pp. 481--492, 2020
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Leipzig-Berlin-Erklärung zu NFDI-Querschnittsthemen der Infrastrukturentwicklung
Maik Bierwirth, Frank Oliver Glöckner, Christian Grimm, Sonja Schimmler, Franziska Boehm, Christian Busse, Andreas Degkwitz, Oliver Koepler, Heike Neuroth
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On Energy Debt: Managing Consumption on Evolving Software
Marco Couto, Daniel Maia, João Saraiva, Rui Pereira
Proceedings of the 3rd International Conference on Technical Debt, pp. 62--66, 2020
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Publishing computational research. A review of infrastructures for reproducible and transparent scholarly communication
Markus Konkol, Daniel Nüst, Laura Goulier
2020 -
Enabling Synergy: Improving the Information Infrastructure for Planetary Science
Michael J. Kurtz, Alberto Accomazzi, Edwin A. Henneken
2020 -
How Research Software Engineers Can Support Scientific Software
Miranda Mundt, Evan Harvey
2020 -
EVER-EST: The Platform Allowing Scientists to Cross-Fertilize and Cross-Validate Data
Mirko Albani, Rosemarie Leone, Federica Foglini, Francesco De Leo, Fulvio Marelli, Iolanda Maggio
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A Survey of Computational Tools in Solar Physics
Monica G. Bobra, Stuart J. Mumford, Russell J. Hewett, Steven D. Christe, Kevin Reardon, Sabrina Savage, Jack Ireland, Tiago M. D. Pereira, Bin Chen, David Pérez-Suárez
Solar Physics, 295(4), pp. 57--57, 2020
DOI: 10.1007/s11207-020-01622-2 -
M2.15 Assessment report on 'FAIRness of software'
Morane Gruenpeter, Roberto Di Cosmo, Hylke Koers, Patricia Herterich, Rob Hooft, Jessica Parland-von Essen, Jonas Tana, Tero Aalto, Sarah Jones
2020
DOI: 10.5281/zenodo.4095092 -
Testing Research Software: A Case Study
Nasir U. Eisty, Danny Perez, Jeffrey C. Carver, J. David Moulton, Hai Ah Nam
Lecture Notes in Computer Science, pp. 457--463--457--463, 2020
DOI: 10.1007/978-3-030-50436-6_33 -
Implementing FAIR Data Infrastructures (Dagstuhl Perspectives Workshop 18472)
Natalia Manola, Peter Mutschke, Guido Scherp, Klaus Tochtermann, Peter Wittenburg, Kathleen Gregory, Wilhelm Hasselbring, Kees den Heijer, Paolo Manghi, Dieter Van Uytvanck
2020
DOI: 10.4230/DAGMAN.8.1.1 -
TeSS: a platform for discovering life-science training opportunities
Niall Beard, Finn Bacall, Aleksandra Nenadic, Milo Thurston, Carole A. Goble, Susanna-Assunta Sansone, Teresa K. Attwood
Bioinformatics, 36(10), pp. 3290--3291, 2020
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Finite and infinite games: An ethnography of institutional logics in research software sustainability
Nicholas Weber
Proceedings of the Association for Information Science and Technology, 57(1), 2020
DOI: 10.1002/pra2.281 -
A graduate student perspective on overcoming barriers to interacting with open-source software
Oihane Cereceda, Danielle E. A. Quinn
FACETS, 5(1), pp. 289--303, 2020
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State of FAIRness in ESFRI Projects
Peter Wittenburg, Franciska de Jong, Dieter van Uytvanck, Massimo Cocco, Keith Jeffery, Michael Lautenschlager, Hannes Thiemann, Margareta Hellström, Ari Asmi, Petr Holub
Data Intelligence, 2(1-2), pp. 230--237, 2020
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Attributing and Referencing (Research) Software: Best Practices and Outlook From Inria
Pierre Alliez, Roberto Di Cosmo, Benjamin Guedj, Alain Girault, Mohand-Saïd Hacid, Arnaud Legrand, Nicolas Rougier
Computing in Science Engineering, 22(1), pp. 39--52, 2020
DOI: 10.1109/MCSE.2019.2949413 -
Building a Scalable Infrastructure
Ravi Tripathi, William Stonewall Monroe, Mike Hanby, John-Paul Robinson
2020
DOI: 10.1145/3311790.3399620 -
Developing an Open Source Digital Scholarship Ecosystem
Ray Uzwyshyn
2020 -
Open Source Digital Ecosystems for Accelerating Global Research, Innovation and Collaboration
Raymond Uzwyshyn
2020 -
Towards Evidence-Based Practice in Scientific Software Develop-ment
Reed Milewicz
2020 -
Research, Develop, Deploy: Building a Full Spectrum Software Engineering and Research Department
Reed Milewicz, James Willenbring, Dena Vigil
2020 -
NFDI4Ing - the National Research Data Infrastructure for Engineering Sciences
Robert H. Schmitt, Verena Anthofer, Sören Auer, Sait Başkaya, Christian Bischof, Torsten Bronger, Florian Claus, Florian Cordes, Évariste Demandt, Thomas Eifert, Bernd Flemisch, Matthias Fuchs, Marc Fuhrmans, Regine Gerike, Eva-Maria Gerstner, Vanessa Hanke, Ina Heine, Louis Huebser, Dorothea Iglezakis, Gerald Jagusch, Axel Klinger, Manfred Krafczyk, Angelina Kraft, Patrick Kuckertz, Ulrike Küsters, Roland Lachmayer, Christian Langenbach, Iryna Mozgova, Matthias S. Müller, Britta Nestler, Peter Pelz, Marius Politze, Nils Preuß, Marie-Dominique Przybylski-Freund, Nanette Rißler-Pipka, Martin Robinius, Joachim Schachtner, Hartmut Schlenz, Annett Schwarz, Jürgen Schwibs, Michael Selzer, Irina Sens, Thomas Stäcker, Christian Stemmer, Wolfgang Stille, Detlef Stolten, Rainer Stotzka, Achim Streit, Robert Strötgen, Wei Min Wang
2020
DOI: 10.5281/ZENODO.4015201 -
Referencing Source Code Artifacts: A Separate Concern in Software Citation
Roberto Di Cosmo, Morane Gruenpeter, Stefano Zacchiroli
Computing in Science & Engineering, 22(2), pp. 33--43--33--43, 2020
DOI: 10/ggzwsg -
Announcing biblatex-software
Roberto Di Cosmo
ACM SIGSOFT Software Engineering Notes, 45(4), pp. 22--23--22--23, 2020
DOI: 10.1145/3417564.3417570 -
BibL A TEX style extension for Software
Roberto Di Cosmo
2020 -
Archiving and Referencing Source Code with Software Heritage
Roberto Di Cosmo
Mathematical Software – ICMS 2020, pp. 362--373--362--373, 2020
DOI: 10.1007/978-3-030-52200-1_36 -
Social Data: CESSDA Best Practices
Ron Dekker
Data Intelligence, 2(1-2), pp. 220--229, 2020
DOI: 10.1162/dint_a_00044 -
Perceived relevance of digital badges predicts longitudinal change in program engagement
Ross Higashi, Christian D. Schunn
Journal of Educational Psychology, 112(5), pp. 1020--1041, 2020
DOI: 10.1037/edu0000401 -
Discussion Towards a Library of Software Sustainability Requirements
Rui Carvalho, A. Silva
2020 -
Software Engineering as Research Method: Aligning Roles in Econ-ARK
Sebastian Benthall, Mridul Seth
2020 -
Design, delivery and evaluation of a bioinformatics education workshop for 13-16-year-olds
Stevie A. Bain, Thomas R. Meagher, Daniel Barker
Journal of Biological Education, 56(5), pp. 570--580, 2020
DOI: 10.1080/00219266.2020.1858932 -
Nine quick tips for efficient bioinformatics curriculum development and training
Susan McClatchy, Kristin M. Bass, Daniel M. Gatti, Adam Moylan, Gary Churchill
PLOS Computational Biology, 16(7), pp. e1008007, 2020
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Software Analysis Method for Assessing Software Sustainability
Theresia Ratih Dewi Saputri, Seok-Won Lee
International Journal of Software Engineering and Knowledge Engineering, 30(01), pp. 67--95, 2020
DOI: 10/ggnd4h -
Reproducibility and replication of experimental particle physics results
Thomas Junk, Louis Lyons
Harvard Data Science Review, 2(4), 2020
DOI: 10.1162/99608f92.250f995b -
Digitale Dienste für die Wissenschaft - wohin geht die Reise?
Uwe Konrad, Konrad Förstner, Johannes Reetz, Klaus Wannemacher, Jürgen Kett, Florian Mannseicher
2020
DOI: 10.5281/ZENODO.4301924 -
Experience in engineering of scientific software: The case of an optimization software for oil pipelines
Vahid Garousi, Ehsan Abbasi, Bedir Tekinerdogan
2020 -
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko
Nucleic Acids Research, 48(14), pp. 8205--8207, 2020
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko
Nucleic Acids Research, 48(W1), pp. W395--W402, 2020
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Kieker: A monitoring framework for software engineering research
Wilhelm Hasselbring, André van Hoorn
Software Impacts, 5, pp. 100019--100019, 2020
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Open Source Research Software
Wilhelm Hasselbring, Leslie Carr, Simon Hettrick, Heather Packer, Thanassis Tiropanis
Computer, 53(8), pp. 84--88--84--88, 2020
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From FAIR research data toward FAIR and open research software
Wilhelm Hasselbring, Leslie Carr, Simon Hettrick, Heather Packer, Thanassis Tiropanis
it - Information Technology, 62(1), pp. 39--47, 2020
DOI: 10.1515/itit-2019-0040 -
The Use of Metadata in Open Educational Resources Repositories: An Exploratory Study
William Simão de Deus, Ellen Francine Barbosa
Proceedings of the 2020 IEEE 44th Annual Computers, Software, and Applications Conference (COMPSAC), 2020
DOI: 10.1109/compsac48688.2020.00025 -
Vorlesung Digitale Nachhaltigkeit:Open Source Lizenzen
Wolfgang Straub, Matthias Stürmer
2020 -
Reproducibility Starts from You Today
Yasemin Turkyilmaz-van der Velden, Nicolas Dintzner, Marta Teperek
Patterns, 1(6), pp. 100099--100099, 2020
DOI: 10.1016/j.patter.2020.100099
2019
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Giving software its due
Nature Methods, 16(3), pp. 207--207, 2019
DOI: 10/gfv4pq -
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks
Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
PLOS Computational Biology, 15(7), pp. e1007007, 2019
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Accredit scientific software for sustainability
Alexander L. R. Lubbock
Nature, 572(7771), pp. 586--586, 2019
DOI: 10/ggcmcp -
Curation as Interoperability With the Future: Preserving Scholarly Research Software in Academic Libraries
Alexandra Chassanoff, Micah Altman
Journal of the Association for Information Science and Technology, 2019
DOI: 10/gf5m4r -
Receiving Credit for Research Software
Alice Allen
, 523, pp. 593--593, 2019
https://ui.adsabs.harvard.edu/abs/2019ASPC..523..593A -
Enabling FAIR research in Earth Science through research objects
Andres Garcia-Silva, Jose Manuel Gomez-Perez, Raul Palma, Marcin Krystek, Simone Mantovani, Federica Foglini, Valentina Grande, Francesco De Leo, Stefano Salvi, Elisa Trasatti, Vito Romaniello, Mirko Albani, Cristiano Silvagni, Rosemarie Leone, Fulvio Marelli, Sergio Albani, Michele Lazzarini, Hazel J. Napier, Helen M. Glaves, Timothy Aldridge, Charles Meertens, Fran Boler, Henry W. Loescher, Christine Laney, Melissa A. Genazzio, Daniel Crawl, Ilkay Altintas
Future Generation Computer Systems, 98, pp. 550--564, 2019
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D3.2 FAIR Data Practice Analysis
Angus Whyte, Claudia Engelhart, Daniel Bangert, Gabin Kayumbi-Kabeya, Simon Lambert, Mark Thorley, Ryan O'Connor, Patricia Herterich, Joy Davidson
2019
DOI: 10.5281/zenodo.3581353 -
How to support open-source software and stay sane
Anna Nowogrodzki
Nature, 571(7763), pp. 133--134, 2019
DOI: 10.1038/d41586-019-02046-0 -
Towards FAIR principles for research software
Anna-Lena Lamprecht, Leyla Garcia, Mateusz Kuzak, Carlos Martinez, Ricardo Arcila, Eva Martin Del Pico, Victoria Dominguez Del Angel, Stephanie van de Sandt, Jon Ison, Paula Andrea Martinez, Peter McQuilton, Alfonso Valencia, Jennifer Harrow, Fotis Psomopoulos, Josep Ll Gelpi, Neil Chue Hong, Carole Goble, Salvador Capella-Gutierrez
Data Science, Preprint(Preprint), pp. 1--23, 2019
DOI: 10.3233/DS-190026 -
Diversity and inclusion in digital scholarship and pedagogy: the case of The Programming Historian
Anna-Maria Sichani, James Baker, Maria José Afanador-Llach, Brandon Walsh
Insights: the UKSG journal, 32(1), pp. 16, 2019
DOI: 10.1629/uksg.465 -
From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training
Annette McGrath, Katherine Champ, Catherine A. Shang, Ellen van Dam, Cath Brooksbank, Sarah L. Morgan
PLOS Computational Biology, 15(6), pp. e1006923, 2019
DOI: 10.1371/journal.pcbi.1006923 -
Software Sustainability: A Systematic Literature Review and Comprehensive Analysis
Asif Imran, Tevfik Kosar
2019
http://arxiv.org/abs/1910.06109v1 -
SuLMaSS - Sustainable Lifecycle Management for Scientific Software
Axel Loewe, Gunnar Seemann, Eike Moritz Wülfers, Yung-Lin Huang, Jorge Sánchez, Felix Bach, Robert Ulrich, Michael Selzer
2019
DOI: 10/gf5tgs -
The FAIR Principles: First Generation Implementation Choices and Challenges
Barend Mons, Erik Schultes, Fenghong Liu, Annika Jacobsen
Data Intelligence, 2(1-2), pp. 1--9, 2019
DOI: 10.1162/dint_e_00023 -
Scholarly Makerspaces – Ein Zwischenbericht zum DFG-Projekt FuReSH
Ben Kaden, Michael Kleineberg
LIBREAS. Library Ideas, 2019
DOI: 10/gf69ts -
Enabling coordinated, distributed development of scientific software: A research agenda for adapting a team of teams approach
Benjamin Hayden Sims
2019 -
Software engineering for scientific big data analysis
Björn A Grüning, Samuel Lampa, Marc Vaudel, Daniel Blankenberg
GigaScience, 8(5), 2019
DOI: 10.1093/gigascience/giz054 -
Integrating Molecular Biology and Bioinformatics Education
Boas Pucker, Hanna Marie Schilbert, Sina Franziska Schumacher
Journal of Integrative Bioinformatics, 16(3), 2019
DOI: 10.1515/jib-2019-0005 -
Comparing badges and learning goals in low- and high-stakes learning contexts
Bradley J. Morris, Colleen Dragovich, Rachael Todaro, Sebiha Balci, Eve Dalton
Journal of Computing in Higher Education, 31(3), pp. 573--603, 2019
DOI: 10.1007/s12528-019-09228-9 -
FAIR Computational Workflows
Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober
Data Intelligence, 2(1-2), pp. 108--121, 2019
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Theory-Software Translation: Research Challenges and Future Directions
Caroline Jay, Robert Haines, Daniel S. Katz, Jeffrey Carver, James C. Phillips, Anshu Dubey, Sandra Gesing, Matthew Turk, Hui Wan, Hubertus van Dam, James Howison, Vitali Morozov, Steven R. Brandt
2019
http://arxiv.org/abs/1910.09902v1 -
Open Source Tools and Methods
Christophe Bernard
eNeuro, 6(5), pp. ENEURO.0342--19.2019, 2019
DOI: 10/ggcmcn -
Top 10 FAIR Data & Software Things
Christopher Erdmann, Natasha Simons, Reid Otsuji, Stephanie Labou, Ryan Johnson, Guilherme Castelao, Bia Villas Boas, Anna-Lena Lamprecht, Carlos Martinez Ortiz, Leyla Garcia, Mateusz Kuzak, Paula Andrea Martinez, Liz Stokes, Tom Honeyman, Sharyn Wise, Josh Quan, Scott Peterson, Amy Neeser, Lena Karvovskaya, Otto Lange, Iza Witkowska, Jacques Flores, Fiona Bradley, Kristina Hettne, Peter Verhaar, Ben Companjen, Laurents Sesink, Fieke Schoots, Erik Schulte, Rajaram Kaliyaperumal, Erzsebet Toth-Czifra, Ricardo De Miranda Azevedo, Sanne Muurling, John Brown, Janice Chan, Niamh Quigley, Lisa Federer, Douglas Joubert, Allissa Dillman, Kenneth Wilkins, Ishwar Chandramouliswaran, Vivek Navale, Susan Wright, Silvia Di Giorgio, Akinyemi Mandela Fasemore, Konrad Förstner, Till Sauerwein, Eva Seidlmayer, Ilja Zeitlin, Susannah Bacon, Katie Hannan, Richard Ferrers, Keith Russell, Deidre Whitmore, Tim Dennis
2019
DOI: 10.5281/zenodo.2555498 -
Towards Sustainable Software Engineering and Citable Software Publications at GEOMAR
Claas Faber, Markus Scheinert, Barbara Schmidt
2019
DOI: 10/gf5m4s -
SSHOC D3.1 Report on SSHOC (meta)data interoperability problems
Daan Broeder, Thorsten Trippel, Emiliano Degl'Innocenti, Roberta Giacomi, Maurizio Sanesi, Mari Kleemola, Katja Moilanen, Henri Ala-Lahti, Caspar Jordan, Iris Alfredsson, Hervé L'Hours, Matej Ďurčo
2019
DOI: 10.5281/ZENODO.3569867 -
Ten simple rules for helping newcomers become contributors to open projects
Dan Sholler, Igor Steinmacher, Denae Ford, Mara Averick, Mike Hoye, Greg Wilson
PLOS Computational Biology, 15(9), pp. e1007296, 2019
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Open Science in Software Engineering
Daniel Méndez Fernández, Daniel Graziotin, Stefan Wagner, Heidi Seibold
2019 -
The State of Sustainable Research Software: Learning from the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1)
Daniel S. Katz, Stephan Druskat, Robert Haines, Caroline Jay, Alexander Struck
Journal of Open Research Software, 7, 2019
DOI: 10/gf5tgr -
Recognizing competencies vs. completion vs. participation: Ideal roles for web-enabled digital badges
Daniel T. Hickey, Grant T. Chartrand
Education and Information Technologies, 25(2), pp. 943--956, 2019
DOI: 10.1007/s10639-019-10000-w -
SortingHat: Wizardry on Software Project Members
David Moreno, Santiago Dueñas, Valerio Cosentino, Miguel Angel Fernandez, Ahmed Zerouali, Gregorio Robles, Jesus M. Gonzalez-Barahona
Proceedings of the 2019 IEEE/ACM 41st International Conference on Software Engineering: Companion Proceedings (ICSE-Companion), pp. 51--54, 2019
DOI: 10.1109/icse-companion.2019.00036 -
The changing role of the software engineer
Edward Meade, Emma O'Keeffe, Niall Lyons, Dean Lynch, Murat Yilmaz, Ulas Gulec, Rory V. O'Connor, Paul M. Clarke
Systems, software and services process improvement, pp. 682--694, 2019
DOI: 10.1007/978-3-030-28005-5_53 -
Getting Research Software to Work: A Case Study on Artifact Evaluation for OOPSLA 2019
Erin Dahlgren
2019 -
How successfully is open-source research software adopted? Results and implications of surveying the users of a sensitivity analysis toolbox
Francesca Pianosi, Fanny Sarrazin, Thorsten Wagener
Environmental Modelling & Software, pp. 104579--104579, 2019
DOI: 10/ggc6j8 -
RSE4NFDI - Safeguarding software sustainability in the NFDI
Frank Löffler, Martin Hammitzsch, Ina Schieferdecker, Daniel Nüst, Stephan Druskat
2019
DOI: 10/gf2hxr -
Generic tools and individual research needs in the Digital Humanities – Can agile development help?
Gerhard Heyer, Christian Kahmann, Cathleen Kantner
, pp. 175--180, 2019
DOI: 10/ggnd4c -
Towards a New Peer Review Concept for Scientific Computing ensuring Technical Quality, Software Sustainability, and Result Reproducibility
Hartwig Anzt, Terry Cojean, Eileen Kühn
PAMM, 19(1), 2019
DOI: 10/ggnd39 -
D2.1 Report on FAIR requirements for persistence and interoperability 2019
Heikki Lehväslaiho, Jessica Parland-von Essen, Claudia Behnke, Heidi Laine, Leah Riungu-Kalliosaari, Yann Le Franc, Christine Staiger
2019
DOI: 10.5281/zenodo.3557381 -
Naming the Pain in Developing Scientific Software
Igor Scaliante Wiese, Ivanilton Polato, Gustavo Pinto
IEEE Software, 2019
DOI: 10.1109/ms.2019.2899838 -
Which Are the Tools Available for Scholars? A Review of Assisting Software for Authors during Peer Reviewing Process
J. Israel Martı\ʼnez-López, Samantha Barrón-González, Alejandro Martı\ʼnez López
Publications, 7(3), pp. 59--59, 2019
DOI: 10/ggcmcq -
Professional Development of Digital Competences: Standardised Frameworks Supporting Evolving Digital Badging Practices
Jaana Kullaslahti, Sanna Ruhalahti, Sanna Brauer
Journal of Siberian Federal University. Humanities & Social Sciences, 12(2), pp. 175--186, 2019
DOI: 10.17516/1997-1370-0387 -
Assessing data availability and research reproducibility in hydrology and water resources
James H. Stagge, David E. Rosenberg, Adel M. Abdallah, Hadia Akbar, Nour A. Attallah, Ryan James
Scientific Data, 6(1), pp. 190030, 2019
DOI: 10.1038/sdata.2019.30 -
Concerns of young protesters are justified
Jennifer Sills, Gregor Hagedorn, Peter Kalmus, Michael Mann, Sara Vicca, Joke Van den Berge, Jean-Pascal van Ypersele, Dominique Bourg, Jan Rotmans, Roope Kaaronen, Stefan Rahmstorf, Helga Kromp-Kolb, Gottfried Kirchengast, Reto Knutti, Sonia I. Seneviratne, Philippe Thalmann, Raven Cretney, Alison Green, Kevin Anderson, Martin Hedberg, Douglas Nilsson, Amita Kuttner, Katharine Hayhoe
Science, 364(6436), pp. 139--140, 2019
DOI: 10.1126/science.aax3807 -
Implementation and relevance of FAIR data principles in biopharmaceutical R&D
John Wise, Alexandra Grebe de Barron, Andrea Splendiani, Beeta Balali-Mood, Drashtti Vasant, Eric Little, Gaspare Mellino, Ian Harrow, Ian Smith, Jan Taubert, Kees van Bochove, Martin Romacker, Peter Walgemoed, Rafael C. Jimenez, Rainer Winnenburg, Tom Plasterer, Vibhor Gupta, Victoria Hedley
Drug Discovery Today, 24(4), pp. 933--938, 2019
DOI: 10.1016/j.drudis.2019.01.008 -
D3.1 FAIR Policy Landscape Analysis
Joy Davidson, Claudia Engelhardt, Vanessa Proudman, Lennart Stoy, Angus Whyte
2019
DOI: 10.5281/zenodo.3558173 -
Towards an HPC Certification Program
Julian Kunkel, Kai Himstedt, Nathanael Hübbe, Hinnerk Stüben, Sandra Schröer, Michael Kuhn, Matthias Riebisch, Stephan Olbrich, Thomas Ludwig, Weronika Filinger, Jean-Thomas Acquaviva, Anja Gerbes, Lev Lafayette
The Journal of Computational Science Education, 10(1), pp. 88--89, 2019
DOI: 10.22369/issn.2153-4136/10/1/14 -
Sustainable Research Software Hand-Over
Jörg Fehr, Christian Himpe, Stephan Rave, Jens Saak
2019
http://arxiv.org/abs/1909.09469v1 -
„Möchten Sie das Programm wirklich löschen?
Jörg Hörnschemeyer
Quellen und Forschungen aus italienischen Archiven und Bibliotheken, 99(1), pp. 491--501, 2019
DOI: 10/ggnd4d -
Challenges of measuring software impact through citations: An examination of the lme4 R package
Kai Li, Pei-Ying Chen, Erjia Yan
Journal of Informetrics, 13(1), pp. 449--461, 2019
DOI: 10/gf8qz5 -
Tracking citations to research software via PIDs
Lars H. Nielsen, Stephanie Van De Sandt
2019
DOI: 10/ggcmcr -
What Makes Research Software Sustainable? An Interview Study With Research Software Engineers
Mario Rosado de Souza, Robert Haines, Markel Vigo, Caroline Jay
CoRR, abs/1903.06039, 2019
http://arxiv.org/abs/1903.06039 -
Addendum: The FAIR Guiding Principles for scientific data management and stewardship
Mark D. Wilkinson, Michel Dumontier, Ijsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, Mercè Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J. G. Gray, Paul Groth, Carole Goble, Jeffrey S. Grethe, Jaap Heringa, Peter A. C. 't Hoen, Rob Hooft, Tobias Kuhn, Ruben Kok, Joost Kok, Scott J. Lusher, Maryann E. Martone, Albert Mons, Abel L. Packer, Bengt Persson, Philippe Rocca-Serra, Marco Roos, Rene van Schaik, Susanna-Assunta Sansone, Erik Schultes, Thierry Sengstag, Ted Slater, George Strawn, Morris A. Swertz, Mark Thompson, Johan van der Lei, Erik van Mulligen, Jan Velterop, Andra Waagmeester, Peter Wittenburg, Katherine Wolstencroft, Jun Zhao, Barend Mons
Scientific Data, 6(1), 2019
DOI: 10.1038/s41597-019-0009-6 -
Happy Belly Bioinformatics: an open-source resource dedicated to helping biologists utilize bioinformatics
Michael Lee
Journal of Open Source Education, 2(19), pp. 53, 2019
DOI: 10.21105/jose.00053 -
Making Open Source Research Software Visible: A Path to Better Sustainability?
Neil Chue Hong
2019
https://www.software.ac.uk/blog/2019-09-12-making-open-source-research-software-visible-path-better-sustainability -
Science needs to rethink how it interacts with big data: Five principles for effective scientific big data systems
Niall H. Robinson, Joe Hamman, Ryan Abernathey
2019
http://arxiv.org/pdf/1908.03356v1 -
Susereum: Towards a Reward Structure for Sustainable Scientific Research Software
Omar Badreddin, Wahab Hamou-Lhadj, Swapnil Chauhan
, pp. 51--54, 2019
DOI: 10.1109/SE4Science.2019.00015 -
D6.1 Overview of needs for competence centres
Patricia Herterich, Joy Davidson, Angus Whyte, Laura Molloy, Brian Matthews, Gabin Kayumbi Kabeya
2019
DOI: 10.5281/zenodo.3549791 -
Building Transparency and Trustworthiness in Inductive Research Through Computer-Aided Qualitative Data Analysis Software
Paula O'Kane, Anne Smith, Michael P. Lerman
Organizational Research Methods, pp. 109442811986501--109442811986501, 2019
DOI: 10/gf63wz -
Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software
Peter Georgeson, Anna Syme, Clare Sloggett, Jessica Chung, Harriet Dashnow, Michael Milton, Andrew Lonsdale, David Powell, Torsten Seemann, Bernard Pope
GigaScience, 8(9), 2019
DOI: 10.1093/gigascience/giz109 -
Establishing a computational biology flipped classroom
Phillip Compeau
PLOS Computational Biology, 15(5), pp. e1006764, 2019
DOI: 10.1371/journal.pcbi.1006764 -
A FAIRer future
Radovan Bast
Nature Physics, 15(8), pp. 728--730, 2019
DOI: 10/gf69tq -
Position Paper: Towards Usability as a First-Class Quality of HPC Scientific Software
Reed Milewicz, Paige Rodeghero
Proceedings of the 2019 IEEE/ACM 14th International Workshop on Software Engineering for Science (SE4Science), 2019
DOI: 10.1109/se4science.2019.00012 -
Towards FAIR protocols and workflows: The OpenPREDICT case study
Remzi Celebi, Joao Rebelo Moreira, Ahmed A. Hassan, Sandeep Ayyar, Lars Ridder, Tobias Kuhn, Michel Dumontier
arXiv:1911.09531 [cs], 2019
http://arxiv.org/abs/1911.09531 -
Software Heritage. A revolutionary infrastructure for Open Science
Roberto Di Cosmo
2019
https://annex.softwareheritage.org/public/talks/2019/2019-02-05-MaxPlankDL.pdf -
Curated Archiving of Research Software Artifacts: lessons learned from the French open archive (HAL)
Roberto Di Cosmo, Morane Gruenpeter, Bruno Marmol, Alain Monteil, Laurent Romary, Jozefina Sadowska
2019
https://hal.inria.fr/hal-02475835 -
The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training
Rochelle E. Tractenberg, Jessica M. Lindvall, Teresa K. Attwood, Allegra Via
PLOS ONE, 14(11), pp. e0225256, 2019
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Workshop deRSE19: Libraries for Research Software & Engineers
Ronny Gey, Katrin Leinweber, Alexander Struck, Robert Strøtgen, Christian Pietsch
LIBREAS. Library Ideas, 36, 2019
DOI: 10.18452/21407 -
The Future Is Open: Open-Source Tools for Behavioral Neuroscience Research
Samantha R. White, Linda M. Amarante, Alexxai V. Kravitz, Mark Laubach
eNeuro, 6(4), pp. ENEURO.0223--19.2019, 2019
DOI: 10/ggcmcv -
Online scaffolding in digital open badge-driven learning
Sanna Brauer, Anne-Maria Korhonen, Pirkko Siklander
Educational Research, 61(1), pp. 53--69, 2019
DOI: 10.1080/00131881.2018.1562953 -
Improving the usability and archival stability of bioinformatics software
Serghei Mangul, Lana S. Martin, Eleazar Eskin, Ran Blekhman
Genome Biology, 20(1), 2019
DOI: 10/ggc6j6 -
Challenges and recommendations to improve the installability and archival stability of omics computational tools
Serghei Mangul, Thiago Mosqueiro, Richard J. Abdill, Dat Duong, Keith Mitchell, Varuni Sarwal, Brian Hill, Jaqueline Brito, Russell Jared Littman, Benjamin Statz, Angela Ka-Mei Lam, Gargi Dayama, Laura Grieneisen, Lana S. Martin, Jonathan Flint, Eleazar Eskin, Ran Blekhman
PLOS Biology, 17(6), pp. e3000333, 2019
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Software and their Dependencies in Research Citation Graphs
Stephan Druskat
2019
http://arxiv.org/abs/1906.06141v1 -
Dare to be mair than just FAIR! - FAIR PLAY to research software, courtesy of RSEs
Stephan Druskat
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DOI: 10.6084/M9.FIGSHARE.10565717 -
Practice meets Principle: Tracking Software and Data Citations to Zenodo DOIs
Stephanie van de Sandt, Lars Holm Nielsen, Alexandros Ioannidis, August Muench, Edwin Henneken, Alberto Accomazzi, Chiara Bigarella, Jose Benito Gonzalez Lopez, Sünje Dallmeier-Tiessen
2019
https://arxiv.org/pdf/1911.00295.pdf -
A Badge Design Framework for a Gamified Learning Environment: Cases Analysis and Literature Review for Badge Design
Sungjin Park, Sangkyun Kim
JMIR Serious Games, 7(2), pp. e14342, 2019
DOI: 10.2196/14342 -
Empfehlungen zur Implementierung von Leit- und Richtlinien zum Umgang mit Forschungssoftware an den Helmholtz-Zentren. Positionspapier
Task Group Forschungssoftware Des Arbeitskreises Open Science Der Helmholtz-Gemeinschaft
2019
DOI: 10/ggzwsc -
Muster-Richtlinie Nachhaltige Forschungssoftware an den Helmholtz-Zentren
Task Group Forschungssoftware Des Arbeitskreises Open Science Der Helmholtz-Gemeinschaft
2019
DOI: 10/ggzwsd -
On the evaluation of research software: the CDUR procedure
Teresa Gomez-Diaz, Tomas Recio
F1000Research, 8, pp. 1353--1353, 2019
DOI: 10/gf69tr -
A global perspective on evolving bioinformatics and data science training needs
Teresa K. Attwood, Sarah Blackford, Michelle D. Brazas, Angela Davies, Maria Victoria Schneider
Briefings in Bioinformatics, 20(2), pp. 398--404, 2019
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Challenges for Verifying and Validating Scientific Software in Computational Materials Science
Thomas Vogel, Stephan Druskat, Markus Scheidgen, Claudia Draxl, Lars Grunske
2019 IEEE/ACM 14ᵗʰ International Workshop on Software Engineering for Science (SE4Science), 2019
DOI: 10.1109/SE4Science.2019.00010 -
Analytics and insights about cultivating a software engineering community at DLR
Tobias Schlauch, Carina Haupt, Michael Meinel, Andreas Schreiber
2019 IEEE aerospace conference, 2019
DOI: 10.1109/AERO.2019.8741902 -
Making Data and Workflows Findable for Machines
Tobias Weigel, Ulrich Schwardmann, Jens Klump, Sofiane Bendoukha, Robert Quick
Data Intelligence, 2(1-2), pp. 40--46, 2019
DOI: 10.1162/dint_a_00026 -
A Thousand and One Software for Proteomics: Tales of the Toolmakers of Science
Vasileios Tsiamis, Hans-Ioan Ienasescu, Dovydas Gabrielaitis, Magnus Palmblad, Veit Schwämmle, Jon Ison
Journal of Proteome Research, 2019
DOI: 10/gf69tt -
Microservices as Architectural Style for Research Software
Wilhelm Hasselbring
2019
http://oceanrep.geomar.de/47554/ -
FAIR and Open Computer Science Research Software
Wilhelm Hasselbring, Leslie Carr, Simon Hettrick, Heather Packer, Thanassis Tiropanis
2019 -
(the struggle) Towards an open source policy
Y. G. Grange, T. Jürges, T. J. Dijkema, R. Halfwerk, G. W. Schoonderbeek
2019
http://arxiv.org/abs/1911.00534v1 -
Open Source Software Sustainability Models: Initial White Paper from the Informatics Technology for Cancer Research Sustainability and Industry Partnership Work Group
Y. Ye, R. D. Boyce, M. K. Davis, K. Elliston, C. Davatzikos, A. Fedorov, J. C. Fillion-Robin, I. Foster, J. Gilbertson, M. Heiskanen, J. Klemm, A. Lasso, J. V. Miller, M. Morgan, S. Pieper, B. Raumann, B. Sarachan, G. Savova, J. C. Silverstein, D. Taylor, J. Zelnis, G. Q. Zhang, M. J. Becich
2019 -
Using digital badges as goal-setting facilitators: a multiple case study
Zui Cheng, Jennifer C. Richardson, Timothy J. Newby
Journal of Computing in Higher Education, 32(2), pp. 406--428, 2019
DOI: 10.1007/s12528-019-09240-z
2018
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Research Software Discovery: Challenges, Risks And Opportunities
Alexander Struck
IEEE eScience 2018, 2018
DOI: 10/gfvpq5 -
Research Software Discovery: An Overview
Alexander Struck
2018 IEEE 14th International Conference on e-Science (e-Science), pp. 33--37, 2018
DOI: 10.1109/eScience.2018.00016 -
Software Engineering for Computational Science: Past, Present, Future
Arne Johanson, Wilhelm Hasselbring
Computing in Science & Engineering, 20(2), pp. 90--109, 2018
DOI: 10.1109/mcse.2018.021651343 -
Adding sparkle to social coding: an empirical study of repository badges in the npm ecosystem
Asher Trockman, Shurui Zhou, Christian Kästner, Bogdan Vasilescu
Proceedings of the 40th International Conference on Software Engineering (ICSE 2018), pp. 511--522, 2018
DOI: 10.1145/3180155.3180209 -
Packaging data analytical work reproducibly using R (and friends)
Ben Marwick, Carl Boettiger, Lincoln Mullen
2018
DOI: 10.7287/peerj.preprints.3192v2 -
Ten simple rules for documenting scientific software
Benjamin D. Lee
PLOS Computational Biology, 14(12), pp. e1006561--e1006561, 2018
DOI: 10/gfrk2t -
Practical Computational Reproducibility in the Life Sciences
Björn Grüning, John Chilton, Johannes Köster, Ryan Dale, Nicola Soranzo, Marius van den Beek, Jeremy Goecks, Rolf Backofen, Anton Nekrutenko, James Taylor
Cell Systems, 6(6), pp. 631--635--631--635, 2018
DOI: 10.1016/j.cels.2018.03.014 -
Community-Driven Data Analysis Training for Biology
Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon Ryan, Florian Christoph Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, James Taylor, Rolf Backofen, Anton Nekrutenko, Björn Grüning
Cell Systems, 6(6), pp. 752--758.e1, 2018
DOI: 10.1016/j.cels.2018.05.012 -
The software engineering initiative of DLR
Carina Haupt, Tobias Schlauch, Michael Meinel
Proceedings of the SE4Science '18: 2018 IEEE/ACM 13th International Workshop on Software Engineering for Science, pp. 16--19, 2018
DOI: 10.1145/3194747.3194749 -
The software engineering initiative of DLR: overcome the obstacles and develop sustainable software
Carina Haupt, Michael Meinel, Tobias Schlauch
, pp. 16--19, 2018
DOI: 10/gf3twn -
Presentations for EGU GA Townhall meeting: Research Software Engineers in the Geosciences
Daniel Nüst, Martin Hammitzsch, David Topping, Niels Drost, Bernadette Fritzsch, Anusuriya Devaraju
2018
DOI: 10/gfzgkh -
Langzeitverfügbarkeit von wissenschaftlicher Software im Bereich historisch-kritischer Musikedition
Daniel Röwenstrunk
Bibliothek Forschung und Praxis, 42(2), pp. 302--308, 2018
DOI: 10/ggcmcs -
Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained
Daniel S. Katz, Lois Curfman McInnes, David E. Bernholdt, Abigail Cabunoc Mayes, Neil P. Chue Hong, Jonah Duckles, Sandra Gesing, Michael A. Heroux, Simon Hettrick, Rafael C. Jimenez, Marlon Pierce, Belinda Weaver, Nancy Wilkins-Diehr
Computing in Science & Engineering, pp. 1--1, 2018
DOI: 10/gfvpq3 -
Commission Recommendation (EU) 2018/790 of 25 April 2018 on access to and preservation of scientific information
European Commission
Official Journal of the European Union, 61(134), pp. 12--18, 2018
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An Introduction to Applied Bioinformatics: a free, open, and interactive text.
Evan Bolyen, Jai Ram Rideout, John Chase, T. Anders Pitman, Arron Shiffer, Willow Mercurio, Matthew R. Dillon, J. Gregory Caporaso
Journal of Open Source Education, 1(5), pp. 27, 2018
DOI: 10.21105/jose.00027 -
The future of scientific workflows
Ewa Deelman, Tom Peterka, Ilkay Altintas, Christopher D Carothers, Kerstin Kleese van Dam, Kenneth Moreland, Manish Parashar, Lavanya Ramakrishnan, Michela Taufer, Jeffrey Vetter
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SARA-Dienst: Software langfristig verfügbar machen
Franziska Rapp, Stefan Kombrink, Volodymyr Kushnarenko, Matthias Fratz, Daniel Scharon
o-bib. Das offene Bibliotheksjournal / herausgegeben vom VDB, Bd. 5, pp. Nr. 2 (2018)--, 2018
DOI: 10/gfvpqt -
Enabling precision medicine via standard communication of HTS provenance, analysis, and results
Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder
PLOS Biology, 16(12), pp. e3000099, 2018
DOI: 10.1371/journal.pbio.3000099 -
Building the Universal Archive of Source Code
Jean-François Abramatic, Roberto Di Cosmo, Stefano Zacchiroli
Communications of the ACM, 61(10), pp. 29--31, 2018
DOI: 10/gfvpqx -
A toolkit for data transparency takes shape
Jeffrey M. Perkel
Nature, 560(7719), pp. 513--515, 2018
DOI: 10/gd2xs9 -
Perspectives on Reproducibility and Sustainability of Open-Source Scientific Software from Seven Years of the Dedalus Project
Jeffrey S. Oishi, Benjamin P. Brown, Keaton J. Burns, Daniel Lecoanet, Geoffrey M. Vasil
2018
DOI: 10/gf2hxs -
Excuse Me, Do You Have a Moment to Talk About Version Control?
Jennifer Bryan
The American Statistician, 72(1), pp. 20--27, 2018
DOI: 10.1080/00031305.2017.1399928 -
Building a Sustainable Structure for Research Software Engineering Activities
Jeremy Cohen, Daniel S. Katz, Michelle Barker, Robert Haines, Neil Chue Hong
2018 IEEE 14th International Conference on e-Science (e-Science), 2018
DOI: 10/gfvpq4 -
Library Carpentry: Software Skills Training for Library Professionals
Jez Cope, James Baker
International Journal of Digital Curation, 12(2), pp. 266--273, 2018
DOI: 10.2218/ijdc.v12i2.576 -
Research data management in the French National Research Center (CNRS)
Joachim Schöpfel, Coline Ferrant, Francis André, Renaud Fabre
Data Technologies and Applications, 52(2), pp. 248--265, 2018
DOI: 10.1108/DTA-01-2017-0005 -
Digital Badges for Motivating Introductory Programmers: Qualitative Findings from Focus Groups
Lisa Facey-Shaw, Marcus Specht, Jeanette Bartley-Bryan
2018 IEEE Frontiers in Education Conference (FIE), 2018
DOI: 10.1109/fie.2018.8659227 -
Semantic Software Metadata for Workflow Exploration and Evolution
Lucas Augusto M. C. Carvalho, Daniel Garijo, Claudia Bauzer Medeiros, Yolanda Gil
2018 IEEE 14th International Conference on e-Science (e-Science), pp. 431--441, 2018
DOI: 10.1109/eScience.2018.00132 -
The FAIR guiding principles for data stewardship: fair enough?
Martin Boeckhout, Gerhard A. Zielhuis, Annelien L. Bredenoord
European Journal of Human Genetics, 26(7), pp. 931--936, 2018
DOI: 10.1038/s41431-018-0160-0 -
Ten simple rules for biologists learning to program
Maureen A. Carey, Jason A. Papin
PLOS Computational Biology, 14(1), pp. e1005871, 2018
DOI: 10.1371/journal.pcbi.1005871 -
Infrastructure and Tools for Teaching Computing Throughout the Statistical Curriculum
Mine Çetinkaya-Rundel, Colin Rundel
The American Statistician, 72(1), pp. 58--65, 2018
DOI: 10.1080/00031305.2017.1397549 -
The development and application of bioinformatics core competencies to improve bioinformatics training and education
Nicola Mulder, Russell Schwartz, Michelle D. Brazas, Cath Brooksbank, Bruno Gaeta, Sarah L. Morgan, Mark A. Pauley, Anne Rosenwald, Gabriella Rustici, Michael Sierk, Tandy Warnow, Lonnie Welch
PLOS Computational Biology, 14(2), pp. e1005772, 2018
DOI: 10.1371/journal.pcbi.1005772 -
Use of digital badges for training in digital skills within higher education
Oriol Borrás-Gené
2018 International Symposium on Computers in Education (SIIE), 2018
DOI: 10.1109/siie.2018.8586734 -
PARTHENOS Guidelines to FAIRify data management and make data reusable
PARTHENOS, Hella Hollander, Francesca Morselli, Frank Uiterwaal, Femmy Admiraal, Thorsten Trippel, Sara Di Giorgio
2018
DOI: 10.5281/zenodo.2668479 -
A large-scale analysis of bioinformatics code on GitHub
Pamela H. Russell, Rachel L. Johnson, Shreyas Ananthan, Benjamin Harnke, Nichole E. Carlson
PLOS ONE, 13(10), pp. e0205898, 2018
DOI: 10.1371/journal.pone.0205898 -
Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health
Petr Holub, Florian Kohlmayer, Fabian Prasser, Michaela Th. Mayrhofer, Irene Schlünder, Gillian M. Martin, Sara Casati, Lefteris Koumakis, Andrea Wutte, Łukasz Kozera, Dominik Strapagiel, Gabriele Anton, Gianluigi Zanetti, Osman Ugur Sezerman, Maimuna Mendy, Dalibor Valík, Marialuisa Lavitrano, Georges Dagher, Kurt Zatloukal, GertJan B. van Ommen, Jan-Eric Litton
Biopreservation and Biobanking, 16(2), pp. 97--105, 2018
DOI: 10.1089/bio.2017.0110 -
Before reproducibility must come preproducibility
Philip B. Stark
Nature, 557(7707), pp. 613--613, 2018
DOI: 10/gdh9xc -
Identifiers for Digital Objects: the Case of Software Source Code Preservation
Roberto Di Cosmo, Morane Gruenpeter, Stefano Zacchiroli
iPRES 2018 - 15th International Conference on Digital Preservation, 2018
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Ireland's Higher Education Teachers Have a National Professional Development Framework, Now What?
Roisin Donnelly, Terry Maguire
Transforming our World Through Design, Diversity and Education, 256, pp. 655--666, 2018
DOI: 10.3233/978-1-61499-923-2-655 -
Building a local community of practice in scientific programming for life scientists
Sarah L. R. Stevens, Mateusz Kuzak, Carlos Martinez, Aurelia Moser, Petra Bleeker, Marc Galland
PLOS Biology, 16(11), pp. e2005561, 2018
DOI: 10.1371/journal.pbio.2005561 -
Challenges and recommendations to improve installability and archival stability of omics computational tools
Serghei Mangul, Thiago Mosqueiro, Richard J. Abdill, Dat Duong, Keith Mitchell, Varuni Sarwal, Brian Hill, Jaqueline Brito, Russell Jared Littman, Benjamin Statz, Angela Ka-Mei Lam, Gargi Dayama, Laura Grieneisen, Lana S. Martin, Jonathan Flint, Eleazar Eskin, Ran Blekhman
2018
DOI: 10/gfgntm -
An Empirical Study on Security Knowledge Sharing and Learning in Open Source Software Communities
Shao-Fang Wen
Computers, 7(4), pp. 49--49, 2018
DOI: 10/ggcmct -
ProvBook: Provenance-based Semantic Enrichment of Interactive Notebooks for Reproducibility
Sheeba Samuel, Birgitta König-Ries
2018 -
Digital badges, do they live up to the hype?
Sherre Roy, Damien Clark
British Journal of Educational Technology, 50(5), pp. 2619--2636, 2018
DOI: 10.1111/bjet.12709 -
Computational astrophysics for the future
Simon Portegies Zwart
Science, 361(6406), pp. 979--980, 2018
DOI: 10/gd546p -
Checklist for a Software Management Plan
The Software Sustainability Institute
2018
DOI: 10/gf2hxq -
The use of digital badges by undergraduate nursing students: A three-year study
Timna Garnett, Didy Button
Nurse Education in Practice, 32, pp. 1--8, 2018
DOI: 10.1016/j.nepr.2018.06.013 -
Software-Engineering-Empfehlungen des DLR
Tobias Schlauch, Michael Meinel, Carina Haupt
2018
DOI: 10/gf3twm -
Interoperable and accessible census and survey data from IPUMS
Tracy A. Kugler, Catherine A. Fitch
Scientific Data, 5(1), pp. 180007, 2018
DOI: 10.1038/sdata.2018.7 -
Testing Scientific Software: A Systematic Literature Review
Upulee Kanewala, James M. Bieman
2018
http://arxiv.org/abs/1804.01954v1 -
An empirical analysis of journal policy effectiveness for computational reproducibility
Victoria Stodden, Jennifer Seiler, Zhaokun Ma
Proceedings of the National Academy of Sciences, 115(11), pp. 2584--2589, 2018
DOI: 10/gc8gkw -
Software Articles and Open Source Research Software: The Why, the What, and the How
Vincent Cicirello
EAI Endorsed Transactions on Cognitive Communications, pp. 168507--168507, 2018
DOI: 10.4108/eai.28-1-2021.168507
2017
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Engineering Academic Software (Dagstuhl Perspectives Workshop 16252)
Alice Allen, Cecilia Aragon, Christoph Becker, Jeffrey Carver, Andrei Chis, Benoit Combemale, Mike Croucher, Kevin Crowston, Daniel Garijo, Ashish Gehani, Carole Goble, Robert Haines, Robert Hirschfeld, James Howison, Kathryn Huff, Caroline Jay, Daniel S. Katz, Claude Kirchner, Katie Kuksenok, Ralf Lämmel, Oscar Nierstrasz, Matt Turk, Rob van Nieuwpoort, Matthew Vaughn, Jurgen J. Vinju
Dagstuhl Manifestos, 6(1), pp. 1--20, 2017
DOI: 10/b7xv -
Research Software Engineers: State Of The Nation Report 2017
Alys Brett, Michael Croucher, Robert Haines, Simon Hettrick, James Hetherington, Mark Stillwell, Claire Wyatt
2017
DOI: 10/gfvpqz -
Zugang zu und Nachnutzung von wissenschaftlicher Software.
Arbeitskreis Open Science
2017
https://os.helmholtz.de/index.php?id=2766 -
Evaluation of the OntoSoft Ontology for describing metadata for legacy hydrologic modeling software
Bakinam T. Essawy, Jonathan L. Goodall, Hao Xu, Yolanda Gil
Environmental Modelling & Software, 92, pp. 317--329, 2017
DOI: 10.1016/j.envsoft.2017.01.024 -
Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud
Barend Mons, Cameron Neylon, Jan Velterop, Michel Dumontier, Luiz Olavo Bonino da Silva Santos, Mark D. Wilkinson
Information Services & Use, 37(1), pp. 49--56, 2017
DOI: 10.3233/ISU-170824 -
Determinants of Mobile Learning in Indigenous/Cultural Contexts: The Phenomenon in Canadian First Nations
Ben Akoh
Tomorrow's Learning: Involving Everyone, 515, pp. 24--34, 2017
DOI: 10.1007/978-3-319-74310-3_4 -
Track 1 Paper: The Software Engineering Community at DLR -- How we got where we are
Carina Haupt, Tobias Schlauch
Proceedings of the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1), 2017
DOI: 10.6084/m9.figshare.5331703 -
Software Systems Engineering programmes a capability approach
Carl Landwehr, Jochen Ludewig, Robert Meersman, David Lorge Parnas, Peretz Shoval, Yair Wand, David Weiss, Elaine Weyuker
Journal of Systems and Software, 125, pp. 354--364, 2017
DOI: 10.1016/j.jss.2016.12.016 -
The Research Software Engineer- An Emerging New Role in Academia in the UK.pdf
Chris Richardson
2017
DOI: 10/gf5tgv -
How Can We Make Computing Lessons More Inclusive?
Chris Shelton
Tomorrow's Learning: Involving Everyone, 515, pp. 506--514, 2017
DOI: 10.1007/978-3-319-74310-3_51 -
Computing Camps for Girls – A First-Time Experience at the University of Limerick
Clare McInerney, Anna-Lena Lamprecht, Tiziana Margaria
Tomorrow's Learning: Involving Everyone, 515, pp. 494--505, 2017
DOI: 10.1007/978-3-319-74310-3_50 -
Abstract, link, publish, exploit: An end to end framework for workflow sharing
Daniel Garijo, Yolanda Gil, Oscar Corcho
Future Generation Computer Systems, 75, pp. 271--283, 2017
DOI: 10.1016/j.future.2017.01.008 -
On the Unhappiness of Software Developers
Daniel Graziotin, Fabian Fagerholm, Xiaofeng Wang, Pekka Abrahamsson
Proceedings of the 21st International Conference on Evaluation and Assessment in Software Engineering - EASE'17, 2017
DOI: 10/gfvpqv -
Software in Research: Underappreciated and Underrewarded
Daniel S. Katz
2017
DOI: 10.6084/m9.figshare.5518933.v1 -
Developing data interoperability using standards: A wheat community use case
Esther Dzale Yeumo, Michael Alaux, Elizabeth Arnaud, Sophie Aubin, Ute Baumann, Patrice Buche, Laurel Cooper, Hanna Ćwiek-Kupczyńska, Robert P. Davey, Richard Allan Fulss, Clement Jonquet, Marie-Angélique Laporte, Pierre Larmande, Cyril Pommier, Vassilis Protonotarios, Carmen Reverte, Rosemary Shrestha, Imma Subirats, Aravind Venkatesan, Alex Whan, Hadi Quesneville
F1000Research, 6, pp. 1843, 2017
DOI: 10.12688/f1000research.12234.1 -
BioContainers: an open-source and community-driven framework for software standardization
Felipe da Veiga Leprevost, Björn A Grüning, Saulo Alves Aflitos, Hannes L. Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C. Jimenez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I. Nesvizhskii, Yasset Perez-Riverol
Bioinformatics, 33(16), pp. 2580--2582, 2017
DOI: 10.1093/bioinformatics/btx192 -
All biology is computational biology
Florian Markowetz
PLOS Biology, 15(3), pp. e2002050--e2002050, 2017
DOI: 10/gf3krm -
Track 1 Paper: Good Usability Practices in Scientific Software Development
Francisco Queiroz, Raniere Silva, Jonah Miller, Sandor Brockhauser, Hans Fangohr
Proceedings of the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1), 2017
DOI: 10.6084/m9.figshare.5331814 -
SARA-Service: Langzeitverfügbarkeit und Publikation von Softwareartefakten
Franziska Ackermann, Petra Enderle, Matthias Fratz, Vladimir Kushnarenko, Daniel Scharon, Pia Schmücker, Marcel Waldvogel, Stefan Wesner
E-Science-Tage 2017: Forschungsdaten managen, 2017
DOI: 10/gfvpq8 -
Good enough practices in scientific computing
Greg Wilson, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, Tracy K. Teal
PLOS Computational Biology, 13(6), pp. e1005510, 2017
DOI: 10/gbkbwp -
Energy Efficiency: A New Concern for Application Software Developers
Gustavo Pinto, Fernando Castor
Communications of the ACM, 60(12), pp. 68--75, 2017
DOI: 10.1145/3154384 -
Track 2 Lightning Talk: Software Development Best Practices at the Netherlands eScience Center
Jason Maassen, Niels Drost, Willem van Hage, Rob van Nieuwpoort
Proceedings of the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1), 2017
DOI: 10.6084/m9.figshare.5327587 -
Game-Play: Effects of Online Gamified and Game-Based Learning on Dispositions, Abilities and Behaviours of Primary Learners
Jawaher Alghamdi, Charlotte Holland
Tomorrow's Learning: Involving Everyone, 515, pp. 55--63, 2017
DOI: 10.1007/978-3-319-74310-3_7 -
Badges for Visualization Micro-Certification
Jeff Sale
Blue Waters Webinars, 2017
https://bluewaters.ncsa.illinois.edu/liferay-content/document-library/BW%20Webinars/Slides/Badges%20for%20Visualization%20Micro-Certification%20by%20Jeff%20Sale.pdf -
Democratizing data science through data science training
John Darrell Van Horn, Lily Fierro, Jeana Kamdar, Jonathan Gordon, Crystal Stewart, Avnish Bhattrai, Sumiko Abe, Xiaoxiao Lei, Caroline O'Driscoll, Aakanchha Sinha, Priyambada Jain, Gully Burns, Kristina Lerman, José Luis Ambite
Proceedings of the Pacific Symposium on Biocomputing 2018, pp. 292--303, 2017
DOI: 10.1142/9789813235533_0027 -
Comment on ``Most computational hydrology is not reproducible, so is it really science?'' by Christopher Hutton et al.
Juan A. Añel
Water Resources Research, 53(3), pp. 2572--2574, 2017
DOI: 10.1002/2016WR020190 -
Do badges increase user activity? A field experiment on the effects of gamification
Juho Hamari
Computers in Human Behavior, 71, pp. 469--478, 2017
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Our path to better science in less time using open data science tools
Julia S. Stewart Lowndes, Benjamin D. Best, Courtney Scarborough, Jamie C. Afflerbach, Melanie R. Frazier, Casey C. O'Hara, Ning Jiang, Benjamin S. Halpern
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Helmholtz Open Science Workshop „Zugang zu und Nachnutzung von wissenschaftlicher Software``
Katharina Sara Scheliga, Heinz Pampel, Erik Bernstein, Christoph Bruch, Wolfgang Zu Castell, Markus Diesmann, Bernadette Fritzsch, Jürgen Fuhrmann, Holger Haas, M. Hammitzsch, David Laehnemann, Alice McHardy, Uwe Konrad, Gianna Scharnberg, Andreas Schreiber, Dirk Steglich
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Citations for Software: Providing Identification, Access and Recognition for Research Software
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Ten Principles for Creating Usable Software for Science
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Ten Simple Rules for Developing Usable Software in Computational Biology
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Upon the Shoulders of Giants: Open-Source Hardware and Software in Analytical Chemistry
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Ten simple rules for making research software more robust
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Software Heritage: Why and How to Preserve Software Source Code
Roberto Di Cosmo, Stefano Zacchiroli
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Taxonomy and metadata for wind energy Research &Development
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Quality Assessment for the Sustainable Provision of Software Components and Digital Research Infrastructures for the Arts and Humanities
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Bibliothek Forschung und Praxis, 41(2), 2017
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Computational Chemistry: The Fate of Current Methods and Future Challenges
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Building Tools to Facilitate Data Reuse
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Correction: Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators
The PLOS Computational Biology Staff
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Reproducibility in Research: Systems, Infrastructure, Culture
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Journal of Open Research Software, 5(1), pp. 32, 2017
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Exploring software development at the very large-scale: a revelatory case study and research agenda for agile method adaptation
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British Journal of Educational Technology, 49(3), pp. 427--438, 2017
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2016
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Foundation of Digital Badges and Micro-Credentials: Demonstrating and Recognizing Knowledge and Competencies
2016
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Identifying and Removing Gender Barriers in Open Learning Communities: The Programming Historian
Adam Crymble
Blended Learning in Practice(Autumn), pp. 49--60, 2016
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Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates
Anders Eklund, Thomas E. Nichols, Hans Knutsson
Proceedings of the National Academy of Sciences, 113(28), pp. 7900--7905, 2016
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2016
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Software citation principles
Arfon M. Smith, Daniel S. Katz, Kyle E. Niemeyer
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Caroline Jay, Rawan Sanyour, Robert Haines
Journal of open research software, pp. null--null, 2016
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Repeatability in computer systems research
Christian Collberg, Todd A. Proebsting
Communications of the ACM, 59(3), pp. 62--69, 2016
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Most computational hydrology is not reproducible, so is it really science?
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How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine
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Software vs. data in the context of citation
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Archiving Software Surrogates on the Web for Future Reference
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Beyond authorship: attribution, contribution, collaboration, and credit
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Caroline Jay, Robert Haines
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Dustin Heaton, Jeffrey C. Carver
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The Oracle Problem in Software Testing: A Survey
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Digital Badges: Beyond Learning Incentives
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Rule rewrite aims to clean up scientific software
Erika Check Hayden
Nature, 520(7547), pp. 276--277, 2015
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James Howison, Julia Bullard
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Understanding digital badges through feedback, reward, and narrative
Joseph Fanfarelli, Stephanie Vie, Rudy McDaniel
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Micro-Credentials, Nano Degrees, and Digital Badges
Pamela A. Lemoine, Michael D. Richardson
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Correction: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
Teresa K. Attwood, Erik Bongcam-Rudloff, Michelle E. Brazas, Manuel Corpas, Pascale Gaudet, Fran Lewitter, Nicola Mulder, Patricia M. Palagi, Maria Victoria Schneider, Celia W. G. van Gelder, GOBLET Consortium
PLOS Computational Biology, 11(5), pp. e1004281, 2015
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GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
Teresa K. Atwood, Erik Bongcam-Rudloff, Michelle E. Brazas, Manuel Corpas, Pascale Gaudet, Fran Lewitter, Nicola Mulder, Patricia M. Palagi, Maria Victoria Schneider, Celia W. G. van Gelder, GOBLET Consortium
PLOS Computational Biology, 11(4), pp. e1004143, 2015
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Reproducibility in Research: Systems, Infrastructure, Culture
Tom Crick, Benjamin A. Hall, Samin Ishtiaq
2015 -
Data Carpentry: Workshops to Increase Data Literacy for Researchers
Tracy K. Teal, Karen A. Cranston, Hilmar Lapp, Ethan White, Greg Wilson, Karthik Ram, Aleksandra Pawlik
International Journal of Digital Curation, 10(1), pp. 135--143, 2015
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2014
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Nature, 514(7524), pp. 536--536, 2014
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A Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research
Alejandra J. Magana, Manaz Taleyarkhan, Daniela Rivera Alvarado, Michael Kane, John Springer, Kari Clase
CBE--Life Sciences Education, 13(4), pp. 607--623, 2014
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Better Software, Better Research
Carole Goble
IEEE Internet Computing, 18(5), pp. 4--8, 2014
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On best practices in the development of bioinformatics software
Felipe da Veiga Leprevost, Valmir C. Barbosa, Eduardo L. Francisco, Yasset Perez-Riverol, Paulo C. Carvalho
Frontiers in Genetics, 5, 2014
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Best Practices for Scientific Computing
Greg Wilson, D. A. Aruliah, C. Titus Brown, Neil P. Chue Hong, Matt Davis, Richard T. Guy, Steven H. D. Haddock, Kathryn D. Huff, Ian M. Mitchell, Mark D. Plumbley, Ben Waugh, Ethan P. White, Paul Wilson
PLoS Biology, 12(1), pp. e1001745, 2014
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Open badges for education: what are the implications at the intersection of open systems and badging?
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Research in Learning Technology, 22, 2014
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Managing the Computational Chemistry Big Data Problem: The ioChem-BD Platform
M. Álvarez-Moreno, C. de Graaf, N. López, F. Maseras, J. M. Poblet, C. Bo
Journal of Chemical Information and Modeling, 55(1), pp. 95--103--95--103, 2014
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Design Principles for Digital Badge Systems
Nate Otto, Daniel T. Hickey
New Horizons in Web Based Learning, 8699, pp. 179--184, 2014
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Minimal information for reusable scientific software
Neil Chue Hong
2nd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2), 2014
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ROHub -- A Digital Library of Research Objects Supporting Scientists Towards Reproducible Science
Raúl Palma, Piotr Hołubowicz, Oscar Corcho, José Manuel Gómez-Pérez, Cezary Mazurek
Semantic Web Evaluation Challenge, 475, pp. 77--82, 2014
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Reproducible research is still a challenge
Rich FitzJohn, Matt Pennell, Amy Zanne, Will Cornwell
2014
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Social influences on secure development tool adoption: why security tools spread
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Supporting Self-regulated Learning Through Digital Badges: A Case Study
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New Horizons in Web Based Learning, 8699, pp. 133--142, 2014
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Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research
Victoria Stodden, Sheila Miguez
Journal of Open Research Software, 2(1), pp. e21, 2014
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2013
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Collaboration gets the most out of software
Andrew Morin, Ben Eisenbraun, Jason Key, Paul C. Sanschagrin, Michael A. Timony, Michelle Ottaviano, Piotr Sliz
eLife, 2, 2013
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Ten simple rules for reproducible computational research
Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig
PLOS Computational Biology, 9(10), pp. 1--4, 2013
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Why do newcomers abandon open source software projects?
Igor Steinmacher, Igor Wiese, Ana Paula Chaves, Marco Aurelio Gerosa
Proceedings of the 6th International Workshop on Cooperative and Human Aspects of Software Engineering (CHASE), 2013
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Benefits of open source code
James A. J. Wilson
2013
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Comet: An open-source MS/MS sequence database search tool
Jimmy K. Eng, Tahmina A. Jahan, Michael R. Hoopmann
Proteomics, 13(1), pp. 22--24, 2013
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Git can facilitate greater reproducibility and increased transparency in science
Karthik Ram
Source Code for Biology and Medicine, 8(1), pp. 7, 2013
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Troubling Trends in Scientific Software Use
L. N. Joppa, G. McInerny, R. Harper, L. Salido, K. Takeda, K. OHara, D. Gavaghan, S. Emmott
Science, 340(6134), pp. 814--815, 2013
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Practices in source code sharing in astrophysics
Lior Shamir, John F. Wallin, Alice Allen, Bruce Berriman, Peter Teuben, Robert J. Nemiroff, Jessica Mink, Robert J. Hanisch, Kimberly DuPrie
Astronomy and Computing, 1, pp. 54--58, 2013
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A Competency Framework Implementation for International Public in the Information, Communication and Technology
Lut-Ochir Vanganjil, Buyandelger Banzragch, Zolzaya Adiyasuren, Nyamsuren Boloo
Embedded Selforganising Systems, 10(Special Issue – Proceedings of the International Symposium on Computer Science and Educational Technologies 2023), pp. 23--27, 2013
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Current issues and research trends on open-source software communities
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The Many Faces of a Software Engineer in a Research Community
Maria C. Marinovici, Harold Kirkham
2013
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Navigating the changing learning landscape: perspective from bioinformatics.ca
Michelle D. Brazas, B. F. Francis Ouellette
Briefings in Bioinformatics, 14(5), pp. 556--562, 2013
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Just Imagine: New Paradigms for Medical Education
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Academic Medicine, 88(10), pp. 1418--1423, 2013
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Software Papers: improving the reusability and sustainability of scientific software
Neil Chue Hong, Brian Hole, Samuel Moore
1st Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1), 2013
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Some Results of the Study on Determining Digital Competence Needs of Citizens
Sanjaabadam Sed, Munkhmagnai Altangerel
Embedded Selforganising Systems, 10(Special Issue – Proceedings of the International Symposium on Computer Science and Educational Technologies 2023), pp. 48--54, 2013
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The Software Sustainability Institute: Changing Research Software Attitudes and Practices
Stephen Crouch, Neil Chue Hong, Simon Hettrick, Mike Jackson, Aleksandra Pawlik, Shoaib Sufi, Les Carr, David De Roure, Carole Goble, Mark Parsons
Computing in Science & Engineering, 15(6), pp. 74--80, 2013
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What makes computational open source software libraries successful?
Wolfgang Bangerth, Timo Heister
Computational Science & Discovery, 6(1), pp. 015010--015010, 2013
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2012
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Shining Light into Black Boxes
A. Morin, J. Urban, P. D. Adams, I. Foster, A. Sali, D. Baker, P. Sliz
Science, 336(6078), pp. 159--160, 2012
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Information, Communication & Society, 15(3), pp. 354--373, 2012
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Ten Simple Rules for the Open Development of Scientific Software
Andreas Prlić, James B. Procter
PLoS Computational Biology, 8(12), pp. e1002802, 2012
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A Quick Guide to Software Licensing for the Scientist-Programmer
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AMIA Board white paper: definition of biomedical informatics and specification of core competencies for graduate education in the discipline
Casimir A. Kulikowski, Edward H. Shortliffe, Leanne M. Currie, Peter L. Elkin, Lawrence E. Hunter, Todd R. Johnson, Ira J. Kalet, Leslie A. Lenert, Mark A. Musen, Judy G. Ozbolt, Jack W. Smith, Peter Z. Tarczy-Hornoch, Jeffrey J. Williamson
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The case for open computer programs
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Nature, 482(7386), pp. 485--488, 2012
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The Research Software Engineer
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Digital Research 2012, 2012
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2011
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Some future software engineering opportunities and challenges
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Ten Simple Rules for Teaching Bioinformatics at the High School Level
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PLoS Computational Biology, 7(10), pp. e1002243, 2011
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Proceedings of the ACM 2011 Conference on Computer Supported Cooperative Work (CSCW '11), pp. 513--522, 2011
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2011
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Reproducible Research in Computational Science
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ACM SIGMOD Record, 40(2), pp. 6--16, 2011
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2010
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A Framework for Software Preservation
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International Journal of Digital Curation, 5(1), pp. 91--105, 2010
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2010
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Advances in Computer Science and Information Technology, pp. 421--430, 2010
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A Survey of Scientific Software Development
Luke Nguyen-Hoan, Shayne Flint, Ramesh Sankaranarayana
Proceedings of the 2010 ACM-IEEE International Symposium on Empirical Software Engineering and Measurement, pp. 12:1--12:10, 2010
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2010
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Research Objects: Towards Exchange and Reuse of Digital Knowledge
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Nature Precedings, 2010
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Zeeya Merali
Nature, 467(7317), pp. 775--777, 2010
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2009
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Astronomical Software Wants To Be Free: A Manifesto
Benjamin J. Weiner, Michael R. Blanton, Alison L. Coil, Michael C. Cooper, Romeel Davé, David W. Hogg, Bradford P. Holden, Patrik Jonsson, Susan A. Kassin, Jennifer M. Lotz, John Moustakas, Jeffrey A. Newman, J. X. Prochaska, Peter J. Teuben, Christy A. Tremonti, Christopher N. A. Willmer
2009
http://arxiv.org/abs/0903.3971v1 -
Program Requirements for Fellowship Education in the Subspecialty of Clinical Informatics
Charles Safran, M. Michael Shabot, Benson S. Munger, John H. Holmes, Elaine B. Steen, John R. Lumpkin, Don E. Detmer, AMIA Board of Directors
Journal of the American Medical Informatics Association, 16(2), pp. 158--166, 2009
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The design and realisation of the Virtual Research Environment for social sharing of workflows
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Future Generation Computer Systems, 25(5), pp. 561--567, 2009
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Defining the Medical Subspecialty of Clinical Informatics
Don E. Detmer, John R. Lumpkin, Jeffrey J. Williamson
Journal of the American Medical Informatics Association, 16(2), pp. 167--168, 2009
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How do scientists develop and use scientific software?
Jo Erskine Hannay, Carolyn MacLeod, Janice Singer, Hans Petter Langtangen, Dietmar Pfahl, Greg Wilson
Proceedings of the 2009 ICSE Workshop on Software Engineering for Computational Science and Engineering, 2009
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Software Development Cultures and Cooperation Problems: A Field Study of the Early Stages of Development of Software for a Scientific Community
Judith Segal
Computer Supported Cooperative Work (CSCW), 18(5), pp. 581--606, 2009
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Proceedings of the 2009 ICSE Workshop on Software Engineering for Computational Science and Engineering, 2009
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Talking Amongst Ourselves - Communication in the Astronomical Software Community
Keith Shortridge
2009
http://arxiv.org/abs/0902.0255v1 -
Astroinformatics: A 21ˢᵗ Century Approach to Astronomy
Kirk D. Borne
2009
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Computing Has Changed Biology--Biology Education Must Catch Up
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Science, 325(5940), pp. 541--542, 2009
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Reed M. Gardner, J. Marc Overhage, Elaine B. Steen, Benson S. Munger, John H. Holmes, Jeffrey J. Williamson, Don E. Detmer, AMIA Board of Directors
Journal of the American Medical Informatics Association, 16(2), pp. 153--157, 2009
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The philosophy of simulation: hot new issues or same old stew?
Roman Frigg, Julian Reiss
Synthese, 169(3), pp. 593--613, 2009
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A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the ``-omics'' era
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Proceedings of the 2009 ICSE Workshop on Software Engineering for Computational Science and Engineering, 2009
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Cognitive and learning sciences in biomedical and health instructional design: A review with lessons for biomedical informatics education
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Journal of Biomedical Informatics, 42(1), pp. 176--197, 2009
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2008
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The intertwining of ethics and methodology in science and engineering: a virtue-ethical approach
Luca Consoli
Interdisciplinary Science Reviews, 33(3), pp. 234--243, 2008
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2007
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Recycling workflows and services through discovery and reuse
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Concurrency and Computation: Practice and Experience, 19(2), pp. 181--194, 2007
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Sharing Detailed Research Data Is Associated with Increased Citation Rate
Heather A. Piwowar, Roger S. Day, Douglas B. Fridsma
PLoS ONE, 2(3), pp. e308, 2007
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Israel Herraiz-Tabernero, Juan-Jose Amor-Iglesias, Alvaro del Castillo-San Felix
The European Journal for the Informatics Professional, 9(6), 2007
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Judith Segal
IEEE Symposium on Visual Languages and Human-Centric Computing (VL/HCC 2007), pp. 111--118, 2007
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Let's Go to the Whiteboard: How and Why Software Developers Use Drawings
Mauro Cherubini, Gina Venolia, Rob DeLine, Amy J. Ko
Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, 2007
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2006
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A scientist's nightmare: software problem leads to five retractions
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Science, 314(5807), pp. 1856--1857, 2006
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Where's the real bottleneck in scientific computing?
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American Scientist, 94(1), pp. 5--5, 2006
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Ontoolcole: An Ontology for the Semantic Search of CSCL Services
Guillermo Vega-Gorgojo, Miguel L. Bote-Lorenzo, Eduardo Gómez-Sánchez, Juan I. Asensio-Pérez, Yannis A. Dimitriadis, Iván M. Jorrı\ʼn-Abellán
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Computer Supported Cooperative Work, 15(4), pp. 385--411, 2006
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Scientific software development is not an oxymoron
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PLoS Computational Biology, 2(9), pp. e87, 2006
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2005
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Bioinformatics: Current practice and future challenges for life science education
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Empirical Software Engineering, 10(4), pp. 517--536, 2005
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Computer supported cooperative work (CSCW), 14(6), pp. 505--547, 2005
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2004
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Extending Ourselves: Computational Science, Empiricism, and Scientific Method
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2004
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Software engineering and the academy: uncomfortable bedfellows?
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ACM SIGCSE Bulletin, 36(2), pp. 14--14, 2004
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Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, 2004
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2002
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k-Anonymity: A Model For Protecting Privacy
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International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems, 10(05), pp. 557--570, 2002
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1999
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Software Engineering Code of Ethics is Approved
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1995
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1994
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1992
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1984
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1983
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1979
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1969
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