Reproducible Research in Computational Science

Cited by (1,003)

Items 301–400 of 1,003

1. Gene name errors: Lessons not learned
   Abeysooriya, Mandhri, Soria, Megan, Kasu, Mary Sravya, Ziemann, Mark · 2021 · PLOS Computational Biology
2. From fossils to mind
   Alexandra Allison de Sousa, Amélie Beaudet, Tanya Calvey, Ameline Bardo, Julien Benoît, Christine J. Charvet, Colette Dehay, Aida Gómez‐Robles, Philipp Gunz, Katja Heuer et al. · 2023 · Communications Biology
3. G-Cimp Status Prediction Of Glioblastoma Samples Using mRNA Expression Data
   Mehmet Selman Baysan, Serdar Bozdag, Margaret C. Cam, Svetlana E. Kotliarova, Susie J. Ahn, Jennifer Walling, Jonathan Keith Killian, Holly S. Stevenson, Paul S. Meltzer, Howard Alan Fine · 2012 · PLoS ONE
4. A call for virtual experiments: Accelerating the scientific process
   Jonathan Cooper, Jon Olav Vik, Dagmar Waltemath · 2014 · Progress in Biophysics and Molecular Biology
5. A Practical Taxonomy of Reproducibility for Machine Learning Research
   Rachael Tatman, Jake Vanderplas, Sohier Dane · 2018
6. A visual tool for defining reproducibility and replicability
   Prasad Patil, Roger D. Peng, Jeffrey T. Leek · 2019 · Nature Human Behaviour
7. Conducting reproducible ecosystem modeling using the open source mass balance model Rpath
   Sean M. Lucey, Sarah Gaichas, Kerim Aydin · 2020 · Ecological Modelling
8. Orienting, Framing, Bridging, Magic, and Counseling: How Data Scientists Navigate the Outer Loop of Client Collaborations in Industry and Academia
   Sean Kross, Philip J. Guo · 2021 · Proceedings of the ACM on Human-Computer Interaction
9. Research project tasks, data, and perceptions of data quality in a condensed matter physics community
   Besiki Stvilia, Charles C. Hinnant, Shuheng Wu, Adam Worrall, Dong Joon Lee, Kathleen Burnett, Gary Burnett, Michelle M. Kazmer, Paul F. Marty · 2014 · Journal of the Association for Information Science and Technology
10. On the path of time: temporal motion in typological perspective
    Michele I. Feist, Sarah E. Duffy · 2020 · Language and Cognition
11. Perceived benefits of open data are improving but scientists still lack resources, skills, and rewards
    Joshua Borycz, Robert Olendorf, Alison Specht, Bruce W. Grant, Kevin Crowston, Carol Tenopir, Suzie L. Allard, Natalie M. Rice, Rachael Hu, Robert J. Sandusky · 2023 · Humanities and Social Sciences Communications
12. A physiological and biophysical model of coppice willow ( S alix spp.) production yields for the contiguous USA in current and future climate scenarios
    Dan Wang, Deepak Jaiswal, David Shaner LeBauer, Timothy M. Wertin, Germán A. Bollero, Andrew D. B. Leakey, Stephen P. Long · 2015 · Plant Cell & Environment
13. Handling Metadata in a Neurophysiology Laboratory
    Lyuba Zehl, Florent Jaillet, Stoewer Adrian, Jan Grewe, Andrey Sobolev, Thomas Wächtler, Thomas G. Brochier, Alexa Riehle C, Michael Denker, Sonja Grün · 2016 · Frontiers in Neuroinformatics
14. A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD
    Andrius Merkys, Nicolas Mounet, Andrea Cepellotti, Nicola Marzari, Saulius Gražulis, Giovanni Pizzi · 2017 · Journal of Cheminformatics
15. Reproducible big data science: A case study in continuous FAIRness
    Ravi Madduri, Kyle Chard, Mike D’Arcy, Segun C. Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric W. Deutsch, Cory C. Funk, Ben Heavner, Matthew A. Richards et al. · 2019 · PLoS ONE
16. EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology
    Sébastien Picault, Yu-Lin Huang, Vianney Sicard, Sandie Arnoux, Gaël Beaunée, Pauline Ezanno · 2019 · PLoS Computational Biology
17. How to Conduct Rigorous Supervised Machine Learning in Information Systems Research: The Supervised Machine Learning Report Card
    Niklas Kühl, Robin Hirt, Lucas Baier, Björn Schmitz, Gerhard Satzger · 2021 · Communications of the Association for Information Systems
18. A Critical Review on Lignocellulosic Biomass Yield Modeling and the Bioenergy Potential from Marginal Land
    Jan Haberzettl, Pia Hilgert, Moritz von Cossel · 2021 · Agronomy
19. GNOM v1.0: an optimized steady-state model of the modern marine neodymium cycle
    Benoît Pasquier, S.K.V. Hines, Hengdi Liang, Yingzhe Wu, S. L. Goldstein, Seth G. John · 2022 · Geoscientific model development
20. Polymers and Nanomedicine: Considerations on Variability and Reproducibility When Combining Complex Systems
    Robert Luxenhofer · 2015 · Nanomedicine
21. A Minimum Standard for Publishing Computational Results in the Weather and Climate Sciences
    Damien Irving · 2015 · Bulletin of the American Meteorological Society
22. A long journey into reproducible computational neuroscience
    Meropi Topalidou, Arthur Leblois, Thomas Boraud, Nicolas P. Rougier · 2015 · Frontiers in Computational Neuroscience
23. Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry
    Étienne Caron, Romain Roncagalli, Takeshi Hase, Witold Wolski, Meena Choi, Marisa Goncalves Menoita, Stéphane Durand, Antonio García‐Blesa, Ivo Fierro-Monti, Tatjana Sajic et al. · 2017 · Cell Reports
24. Towards Predicting Trend of Scientific Research Topics using Topic Modeling
    Tesfamariam M. Abuhay, Yemisrach G. Nigatie, Sergey Valerevich Kovalchuk · 2018 · Procedia Computer Science
25. A method for the updating of stochastic kriging metamodels
    Bogumił Kamiński · 2015 · European Journal of Operational Research
26. Snakes on a Spaceship - An Overview of Python in Heliophysics
    Burrell, A.G., David Stansby, Karl Magnus Laundal, Ma, J., R. Stoneback, Jeffrey H. Klenzing, Andrew M. Annex, Steven Karl Morley, Adam C. Kellerman, Alexa Jean Halford · NASA STI Repository (National Aeronautics and Space Administration)
27. The zoon r package for reproducible and shareable species distribution modelling
    Nick Golding, Tom August, Tim C. D. Lucas, David J. Gavaghan, E. Emiel van Loon, Greg McInerny · 2017 · Methods in Ecology and Evolution
28. XCorpus – An executable Corpus of Java Programs.
    Jens B. Dietrich, Henrik Schole, Li Sui, Ewan D. Tempero · 2017 · The Journal of Object Technology
29. How measurement science can improve confidence in research results
    Anne L. Plant, Chandler A. Becker, R. J. Hanisch, Ronald F. Boisvert, Antonio M. Possolo, John T. Elliott · 2018 · PLoS Biology
30. Radiogenomics of lung cancer
    Chi Wah Wong, Ammar Ahmed Chaudhry · 2020 · Journal of Thoracic Disease
31. TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation
    Fédérico Marini, Denise Scherzinger, Sven Danckwardt · 2020 · Nucleic Acids Research
32. Febio finite element models of the human cervical spine
    Michael R. Herron, Jeeone Park, Andrew T. Dailey, Douglas L. Brockmeyer, Benjamin J. Ellis · 2020 · Journal of Biomechanics
33. A review of open software resources in python for electrical resistivity modelling
    Yonatan Garkebo Doyoro, Ping‐Yu Chang, Jordi Mahardika Puntu, Ding-Jiun Lin, Tran Van Huu, Diah Ayu Rahmalia, Meng-Shiun Shie · 2022 · Geoscience Letters
34. Transparent, Open, and Reproducible Prevention Science
    Sean Grant, Kathleen Ellen Wendt, Bonnie J. Ross Leadbeater, Lauren H. Supplee, Evan Mayo‐Wilson, Frances E. M. Gardner, Catherine P. Bradshaw · 2022 · Prevention Science
35. Figurative Thought and Language
    2017 · Figurative thought and language
36. DataCite as a Novel Bibliometric Source: Coverage, Strengths and Limitations
    Robinson-Garcia, Nicolas, Mongeon, Philippe, Jeng, Wei, Costas, Rodrigo · 2017 · Journal of Informetrics
37. Three ‘Rs’ of Econometrics: Repetition, Reproduction and Replication
    Laura Camfield, Richard Palmer‐Jones · 2013 · The Journal of Development Studies
38. Detecting the corruption of online questionnaires by artificial intelligence
    Benjamin Lebrun, Sharon Temtsin, Andrew James Vonasch, Christoph Bartneck · 2024 · Frontiers in Robotics and AI
39. FAST: FAST Analysis of Sequences Toolbox
    Travis J. Lawrence, Kyle T Kauffman, Katherine C. H. Amrine, Dana L. Carper, Raymond S Lee, Peter J. Becich, Claudia J Canales, David H. Ardell · 2015 · Frontiers in Genetics
40. Looking before Leaping: Creating a Software Registry
    Alice Allen, Judy Schmidt · 2015 · Journal of Open Research Software
41. A Primer on Infectious Disease Bacterial Genomics
    Tarah Lynch, Aaron Petkau, Natalie Knox, Morag Graham, Gary Van Domselaar · 2016 · Clinical Microbiology Reviews
42. Ignoring the modeling approaches: Towards the shadowy paths in nanomedicine
    Parichehr Hassanzadeh, Fatemeh Atyabi, Rassoul Dinarvand · 2018 · Journal of Controlled Release
43. CG‐SENSE revisited: Results from the first ISMRM reproducibility challenge
    Oliver Maier, Steven H. Baete, Alexander Fyrdahl, Kerstin Hammernik, Seb Harrevelt, Lars Kasper, Agah Karakuzu, Michael Loecher, Franz Patzig, Ye Tian et al. · 2020 · Magnetic Resonance in Medicine
44. RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS
    Gaurav N. Kaushik, Sinisa Ivkovic, Janko Simonovic, Nebojša Tijanić, Brandi N. Davis‐Dusenbery, Deniz Kural · 2016 · Pacific Symposium on Biocomputing (PSB)
45. Snakes on a Spaceship—An Overview of Python in Heliophysics
    A. G. Burrell, A. Halford, J. Klenzing, R. A. Stoneback, S. K. Morley, A. M. Annex, K. M. Laundal, A. C. Kellerman, David Stansby, J. Ma · 2018 · Journal of Geophysical Research Space Physics
46. Provoking a Cultural Shift in Data Quality
    Sarah E. McCord, Nicholas P. Webb, Justin W. Van Zee, Sarah H. Burnett, Erica M. Christensen, Ericha M. Courtright, Christine Laney, Claire K. Lunch, Connie M. Maxwell, Jason W. Karl et al. · 2021 · BioScience
47. A practical guide to interpreting low energy ion scattering (LEIS) spectra
    Stanislav Průša, Matthew R. Linford, Elena Vaníčková, Pavel Bábík, Joshua W. Pinder, Tomáš Šikola, Hidde H. Brongersma · 2023 · Applied Surface Science
48. Exploring the Impact of Analysis Software on Task fMRI Results
    Alexander Bowring, Camille Maumet, Thomas E. Nichols · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
49. Text as big data: Develop codes of practice for rigorous computational text analysis in energy social science
    Müller-Hansen, Finn, Callaghan, Max W., Minx, Jan C. · 2020 · Energy Research & Social Science
50. Replication of quantitative work in development studies: Experiences and suggestions
    Maren Duvendack, Richard Palmer‐Jones · 2013 · Progress in Development Studies
51. Exploring Research Trends of Metaverse: A Bibliometric Analysis
    Sanaa Hassan Zubon Al-Enzi, Sammar Abbas, Abdul Nasser Abdul Jabbar Abbood, Yousif Raad Muhsen, Ahmed Abbas Jasim Al-Hchaimi, Zainab Almosawi · 2023 · Lecture notes in networks and systems
52. Enable cloud DevOps approach for industry and higher education
    Mohammed Airaj · 2016 · Concurrency and Computation Practice and Experience
53. Reproducible and Replicable Computational Fluid Dynamics: It’s Harder Than You Think
    Olivier Mesnard, Lorena A. Barba · 2017 · Computing in Science & Engineering
54. Software Engineering for Computational Science: Past, Present, Future
    Arne Johanson, Wilhelm Hasselbring · 2018 · Computing in Science & Engineering
55. Integrating scientific cyberinfrastructures to improve reproducibility in computational hydrology: Example for HydroShare and GeoTrust
    Bakinam Tarik Essawy, Jonathan L. Goodall, Wesley O. Zell, Daniel Voce, Mohamed M. Morsy, Jeffrey M. Sadler, Zhihao Yuan, Tanu Malik · 2018 · Environmental Modelling & Software
56. MoveApps: a serverless no-code analysis platform for animal tracking data
    Andrea Kölzsch, Sarah C. Davidson, Dominik Gauggel, Clemens Hahn, Julian Hirt, Roland Kays, Ilona Lang, Ashley Lohr, Benedict Russell, Anne K. Scharf et al. · 2022 · Movement Ecology
57. Writing Empirical Articles: Transparency, Reproducibility, Clarity, and Memorability
    Morton Ann Gernsbacher · 2018 · Advances in Methods and Practices in Psychological Science
58. The State of Empirical Evaluation in Static Feature Location
    Abdul Razzaq, Asanka Wasala, Chris Exton, Jim Buckley · 2018 · ACM Transactions on Software Engineering and Methodology
59. Image acquisition and quality assurance in the Boston Adolescent Neuroimaging of Depression and Anxiety study
    Viviana Siless, Nicholas A. Hubbard, Robert J. Jones, Jonathan Wang, Nicole Lo, Clemens C. C. Bauer, Mathias Goncalves, Isabelle R. Frosch, Daniel J. Norton, Genesis A. Vergara et al. · 2020 · NeuroImage Clinical
60. Evaluating the declarations of open defecation free status under the Swachh Bharat (‘Clean India’) Mission: repeated cross-sectional surveys in Rajasthan, India
    Natalie G. Exum, Emma May Gorin, Goutam Sadhu, Anoop Khanna, Kellogg J. Schwab · 2020 · BMJ Global Health
61. Kinfitr — an open-source tool for reproducible PET modelling: validation and evaluation of test-retest reliability
    Jonathan Tjerkaski, Simon Červenka, Lars Farde, Granville James Matheson · 2020 · EJNMMI Research
62. Elevation models for reproducible evaluation of terrain representation
    Patrick J. Kennelly, Tom Patterson, Bernhard Jenny, Daniel P. Huffman, Brooke E. Marston, Sarah Bell, Alexander M. Tait · 2020 · Cartography and Geographic Information Science
63. Software vs. data in the context of citation
    Daniel S. Katz, Kyle Evan Niemeyer, Arfon M. Smith, William L Anderson, Carl Boettiger, Konrad Hinsen, Rob W W Hooft, Michael Hucka, Allen Lee, Frank Löffler et al. · 2016
64. Reproducible research: a minority opinion
    Chris Drummond · 2017 · Journal of Experimental & Theoretical Artificial Intelligence
65. Leveraging heterogeneity for neural computation with fading memory in layer 2/3 cortical microcircuits
    Renato Duarte, Abigail Morrison · 2019 · PLoS Computational Biology
66. The critical need to foster computational reproducibility
    Robert Reinecke, Tim Trautmann, Thorsten Wagener, Katja Schüler · 2022 · Environmental Research Letters
67. Semantic Array Programming for Environmental Modelling: Application of the Mastrave Library
    Daniele de Rigo · 2012 · ScholarsArchive (Brigham Young University)
68. Model-independent comparison of simulation output
    Nuno Fachada, Vítor V. Lopes, Rui C. Martins, Agostinho C. Rosa · 2017 · Simulation Modelling Practice and Theory
69. gcamdata: An R Package for Preparation, Synthesis, and Tracking of Input Data for the GCAM Integrated Human-Earth Systems Model
    Ben Bond‐Lamberty, Kalyn Dorheim, Ryna Yiyun Cui, Russell Horowitz, Abigail Snyder, Katherine Calvin, Leyang Feng, Rachel Hoesly, Jill Horing, Page G. Kyle et al. · 2019 · Journal of Open Research Software
70. Emergent Challenges for Science sUAS Data Management: Fairness through Community Engagement and Best Practices Development
    Jane Wyngaard, Lindsay K. Barbieri, Andrea K. Thomer, Josip Adams, Don Sullivan, Cynthia Sims Parr, Sudhir Raj Shrestha, Christopher Crosby, Jens Klump, Tom W. Bell · 2019 · Remote Sensing
71. Data‐driven glass/ceramic science research: Insights from the glass and ceramic and data science/informatics communities
    Eileen De Guire, Laura M. Bartolo, Ross Brindle, Ram Devanathan, Elizabeth C. Dickey, Justin Fessler, Roger H. French, Ulrich Fotheringham, Martin P. Harmer, Edgar Lara‐Curzio et al. · 2019 · Journal of the American Ceramic Society
72. Epistemic issues in computational reproducibility: software as the elephant in the room
    Alexandre Hocquet, Frédéric Wieber · 2021 · European Journal for Philosophy of Science
73. Risk‐Based Wellhead Protection Decision Support: A Repeatable Workflow Approach
    Michael N. Fienen, Nicholas Corson‐Dosch, Jeremy T. White, Andrew T. Leaf, Randall J. Hunt · 2021 · Ground Water
74. Estimating the reproducibility of social learning research published between 1955 and 2018
    Riana Minocher, Silke Atmaca, Claudia Bavero, Richard L. McElreath, Bret Beheim · 2021 · Royal Society Open Science
75. Predicting decadal trends and transient responses of radiocarbon storage and fluxes in a temperate forest soil
    Carlos A. Sierra, Susan Elizabeth Trumbore, Eric A. Davidson, Serita D. Frey, KATHLEEN E. SAVAGE, Francesca M. Hopkins · 2012 · Biogeosciences
76. Science in the cloud (SIC): A use case in MRI connectomics
    Gregory Kiar, Krzysztof J. Gorgolewski, Dean M. Kleissas, William Gray Roncal, Brian Litt, Brian A. Wandell, Russell Alan Poldrack, Martin Wiener, R. Jacob Vogelstein, Randal C. Burns et al. · 2017 · GigaScience
77. How to Share Data for Collaboration
    Shannon Ellis, Jeffrey T. Leek · 2017 · The American Statistician
78. A Review of Scalable Bioinformatics Pipelines
    Bjørn Fjukstad, Lars Ailo Bongo · 2017 · Data Science and Engineering
79. Verifying and Validating Simulations
    Nuno David, Nuno Fachada, Agostinho C. Rosa · 2017 · Understanding complex systems
80. Exploring customers’ likeliness to use e-service touchpoints in brick and mortar retail
    Benjamin Barann, Jan Hendrik Betzing, Marco Niemann, Benedikt Hoffmeister, Jörg Becker · 2020 · Electronic Markets
81. Versioning Data Is About More than Revisions: A Conceptual Framework and Proposed Principles
    Jens Klump, Lesley Wyborn, Mingfang Wu, J.A. Ramírez San Martín, Robert R. Downs, Ari Asmi · 2021 · Data Science Journal
82. Reproducible Cartography
    Timothée Giraud, Nicolas Lambert · 2017 · Lecture notes in geoinformation and cartography
83. A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in Metabolomics
    Elizabeth C. Considine, Reza M. Salek · 2019 · Metabolites
84. Democratizing cheminformatics: interpretable chemical grouping using an automated KNIME workflow
    José Teófilo Moreira‐Filho, Dhruv Ranganath, Mike Conway, Charles Schmitt, Nicole Kleinstreuer, Kamel Mansouri · 2024 · Journal of Cheminformatics
85. A tutorial on Bayesian models of perception
    Benjamin Thomas Vincent · 2015 · Journal of Mathematical Psychology
86. Examining the impact of larval source management and insecticide-treated nets using a spatial agent-based model of Anopheles gambiae and a landscape generator tool
    SM Niaz Arifin, Gregory R. Madey, Frank H. Collins · 2013 · Malaria Journal
87. CG‐SENSE revisited: Results from the first ISMRM reproducibility challenge
    Oliver Maier, Steven H. Baete, Alexander Fyrdahl, Kerstin Hammernik, Seb D. Harrevelt, Lars Kasper, Agâh Karakuzu, Michael Loecher, Franz Patzig, Ye Tian et al. · 2021 · Zurich Open Repository and Archive (University of Zurich)
88. Reproducibility in Science: A Metrology Perspective
    Anne L. Plant, R. J. Hanisch · 2020 · Harvard Data Science Review
89. Introducing Point-of-Interest as an alternative to Area-of-Interest for fixation duration analysis
    Nakwon Rim, Kyoung Whan Choe, Coltan Scrivner, Marc G. Berman · 2021 · PLoS ONE
90. Detecting Disease Variants in Case-Parent Trio Studies Using the Bioconductor Software Packagetrio
    Holger R. Schwender, Qing Li, Christoph Neumann, Margaret A. Taub, Samuel G. Younkin, Philipp K. Berger, Robert B. Scharpf, Terri H. Beaty, Ingo Ruczinski · 2014 · Genetic Epidemiology
91. HESS Opinions: Repeatable research: what hydrologists can learn from the Duke cancer research scandal
    Michael N. Fienen, Mark Bakker · 2016 · Hydrology and earth system sciences
92. Research Note: Scraping Financial Data from the Web Using the R Language
    Vlad Krotov, Matthew F. Tennyson · 2018 · Journal of Emerging Technologies in Accounting
93. YAMP: a containerized workflow enabling reproducibility in metagenomics research
    Alessia Visconti, Tiphaine C. Martin, Mario Falchi · 2018 · GigaScience
94. Effect assessment of engineered nanoparticles in solid media – Current insight and the way forward
    Mónica J.B. Amorim, Carlos P. Roca, Janeck James Scott-Fordsmand · 2015 · Environmental Pollution
95. Using Make for Reproducible and Parallel Neuroimaging Workflow and Quality-Assurance
    Mary K. Askren, Trevor K. M. Day, Natalie Koh, Zoé Mestre, Jennifer N. Dines, Benjamin A. Korman, Susan J. Melhorn, Daniel J. Peterson, Matthew Peverill, Xiaoyan Angela Qin et al. · 2016 · Frontiers in Neuroinformatics
96. Badges for sharing data and code at Biostatistics: an observational study
    Anisa Rowhani-Farid, Adrian Gerard Barnett · 2018 · F1000Research
97. Massivizing Computer Systems: A Vision to Understand, Design, and Engineer Computer Ecosystems Through and Beyond Modern Distributed Systems
    Alexandru Iosup, Alexandru Uta, Laurens Versluis, Georgios Andreadis, Erwin van Eyk, Tim Hegeman, Sacheendra Talluri, Vincent van Beek, Lucian Toader · 2018 · IEEE International Conference on Distributed Computing Systems (ICDCS)
98. Jupyter Notebooks as Discovery Mechanisms for Open Science: Citation Practices in the Astronomy Community
    Morgan F. Wofford, Bernie Boscoe, Christine L. Borgman, Irene V. Pasquetto, Milena S. Golshan · 2019 · Computing in Science & Engineering
99. Kollaps
    Paulo Gouveia, João Neves, Carlos Segarra, Luca Liechti, Shady Issa, Valerio Schiavoni, Miguel Matos · 2020 · European Conference on Computer Systems
100. A community-led initiative for training in reproducible research
     Susann Auer, Nele A.T Haelterman, Tracey Lynn Weissgerber, Jeffrey C. Erlich, Damar Susilaradeya, Magdalena Julkowska, Małgorzata Anna Gazda, Benjamin Schwessinger, Nafisa M. Jadavji, Reproducibility for Everyone Team et al. · 2021 · eLife