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Sustainable computational science: the ReScience initiative

Nicolas P. Rougier, Konrad Hinsen, Frédéric Alexandre, Thomas Arildsen, Lorena A. Barba, Fabien C.Y. Benureau, C. Titus Brown, Pierre de Buyl, Ozan Caglayan, Andrew P. Davison, Marc-André Delsuc, Georgios Detorakis (+33 others)
2017 PeerJ Computer Science  
Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results; however, computational science lags behind.  ...  ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to  ...  Surprisingly, the computational sciences (in the broad sense) and computer sciences (in the strict sense) are no exception (Donoho, Maleki, Rahman, Shahram, & Stodden, 2009; Manninen, Havela, & Linne,  ... 
doi:10.7717/peerj-cs.142 pmid:34722870 pmcid:PMC8530091 fatcat:yiqk77gs2vaorf46o64eh7awyu

Neural Science

Thomas D Albright, Thomas M Jessell, Eric R Kandel, Michael I Posner
2000 Cell  
delinalmost invariably gave rise to two types of extensions: eate the problems that still confront neural science.  ...  Thus, one consequence of this top-down analy-New York, New York 10032 sis has been initial demystification of aspects of mental ‡ Sackler Institute function: of language perception, action, learning, and  ...  . pathways that could sustain reverberatory information.  ... 
doi:10.1016/s0092-8674(00)00251-8 pmid:10698132 fatcat:rjtvbny2fncm3e4akjgnythii4

CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility

Daniel Nüst, Stephen J. Eglen
2021 F1000Research  
The traditional scientific paper falls short of effectively communicating computational research.  ...  While CODECHECK has clear limitations, it may represent a building block in Open Science and publishing ecosystems for improving the reproducibility, appreciation, and, potentially, the quality of non-textual  ...  Kirk (PLOS Computational Biology), Scott Edmunds (GigaScience), and Andrew Hufton (Scientific Data).  ... 
doi:10.12688/f1000research.51738.1 pmid:34367614 pmcid:PMC8311796 fatcat:rxh2hekl3ffk3owa75fose4th4

CODECHECK: An Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility

Daniel Nüst, Stephen J Eglen
2021 Zenodo  
Kirk (PLOS Computational Biology), Scott Edmunds (GigaScience), and Andrew Hufton (Scientific Data).  ...  Acknowledgements We are grateful to the following individuals for discussions regarding the work presented here: Andy Collings, Melissa Harrison, Giuliano Maciocci, Naomi Penfold, Emmy Tsang (eLife), Rebecca  ...  Early proponents of this initiative were Buckheit and Donoho [2, 3] , who noted: "An article about computational science in a scientific publication is not the scholarship itself, it is merely advertising  ... 
doi:10.5281/zenodo.4593367 fatcat:escmjonjjfft7jnr2waivj422u

Neural Science: A Century of Progress and the Mysteries that Remain

Thomas D. Albright, Thomas M. Jessell, Eric R. Kandel, Michael I. Posner
2000 Neuron  
delinalmost invariably gave rise to two types of extensions: eate the problems that still confront neural science.  ...  Thus, one consequence of this top-down analy-New York, New York 10032 sis has been initial demystification of aspects of mental ‡ Sackler Institute function: of language perception, action, learning, and  ...  . pathways that could sustain reverberatory information.  ... 
doi:10.1016/s0896-6273(00)80912-5 pmid:10718192 fatcat:56a3cn3im5hpritw6uwdh5hvo4

[¬Rp] Reproducibility of 'Poincaré dodecahedral space parameter estimates'

Boudewijn F. Roukema
2020 Zenodo  
It was found that the effort in upgrading the Fortran 77 code at the heart of the software, interfaced with a C front end, and originally compiled with g77, in the content of the contemporary gfortran  ...  The software and a script to reproduce the steps of this incomplete reproduction are combined in a new git repository named 0807.4260, following the ArXiv identity code (arXiv:0807.4260) of RBG08.  ...  Part of this research has been supported by the "A next-generation worldwide quantum sensor network with optical atomic clocks" project of the TEAM IV programme of the Foundation for Polish Science co-financed  ... 
doi:10.5281/zenodo.3956058 fatcat:chq3tdse6fe6rmpeqy7hwpgudy

[¬Rp] Reproducibility of 'Poincaré dodecahedral space parameter estimates'

Boudewijn F. Roukema
2020 Zenodo  
It was found that the effort in upgrading the Fortran 77 code at the heart of the software, interfaced with a C front end, and originally compiled with g77, in the content of the contemporary gfortran  ...  The software and a script to reproduce the steps of this incomplete reproduction are combined in a new git repository named 0807.4260, following the ArXiv identity code of RBG08. 1  ...  Part of this research has been supported by the "A next-generation worldwide quantum sensor network with optical atomic clocks" project of the TEAM IV programme of the Foundation for Polish Science co-financed  ... 
doi:10.5281/zenodo.3943749 fatcat:lh7ujz6daneilpgxpa3hl4dtyy

[Re] Modeling habits as self-sustained patterns of sensorimotor behavior

Tristan Gillard, Jérémy Fix, Alain Dutech
2022 Zenodo  
Althought we were unable to reproduce all the results, we thank the author for the efforts of sharing his code base with us.  ...  Acknowledgment We would like to thank Matthew Egbert for the fruitfull exchanges which helped to clarify the content of the reproduced paper and to correct typos in our original submission.  ...  ReScience C 8.1 (#2) -Gillard, Fix and Dutech 2022 [Re] Modeling habits as self-sustained patterns of sensorimotor behavior Section 3.1,below figure 5 of the original paper: "The motor component  ... 
doi:10.5281/zenodo.6478461 fatcat:xy76k65ptveqrbtubtfgyar27a

[Re] Modeling habits as self-sustained patterns of sensorimotor behavior

Tristan Gillard, Jérémy Fix, Alain Dutech
2022 Zenodo  
Althought we were unable to reproduce all the results, we thank the author for the efforts of sharing his code base with us.  ...  Acknowledgment We would like to thank Matthew Egbert for the fruitfull exchanges which helped to clarify the content of the reproduced paper and to correct typos in our original submission.  ...  ReScience C 7.1 (#13) -Gillard, Fix and Dutech 2022 [Re] Modeling habits as self-sustained patterns of sensorimotor behavior Section 3.1,below figure 5 of the original paper: "The motor component  ... 
doi:10.5281/zenodo.6478462 fatcat:yid5dmjkoneprgxye2b6xkjxpa

Microsoft Academic Graph: When experts are not enough

Kuansan Wang, Zhihong Shen, Chi-Yuan Huang, Chieh-Han Wu, Yuxiao Dong, Anshul Kanakia
2020 Quantitative Science Studies  
of science by deploying software agents equipped with natural language understanding capabilities to read scholarly publications on the web.  ...  The knowledge extracted by these AI agents is organized into a heterogeneous graph, called Microsoft Academic Graph (MAG), where the nodes and the edges represent the entities engaging in scholarly communications  ...  The work would not be possible without the strong support from Microsoft Bing engineering teams and colleagues in Microsoft Research labs around the globe.  ... 
doi:10.1162/qss_a_00021 fatcat:h5zlrnuhvrehfltjm3ipns6o4e

Code Replicability in Computer Graphics [article]

Nicolas Bonneel and David Coeurjolly and Julie Digne and Nicolas Mellado
2020 arXiv   pre-print
In this work, we assess replicability in Computer Graphics, by evaluating whether the code is available and whether it works properly.  ...  This analysis shows a clear increase in the number of papers with available and operational research codes with a dependency on the subfields, and indicates a correlation between code replicability and  ...  ACKNOWLEDGMENTS We thank Roberto Di Cosmo for insightful discussions and the reviewers for their constructive feedback.  ... 
arXiv:2005.00554v1 fatcat:zsw4liyqana33nabdomw3zgt3i

Referee report. For: CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility [version 2; peer review: 2 approved]

Nicolas P. Rougier
2021
Barba LA: Praxis of Reproducible Computational Science. Authorea. 2018. Publisher Full Text 24.  ...  The traditional scientific paper falls short of effectively communicating computational research.  ...  all authors of auditable computational workflows for their participation.  ... 
doi:10.5256/f1000research.57857.r89926 fatcat:bz7uyjqrwrfnnmyjafxvtj55za

American Pediatric Society Presidential Address at the 100th Annual Meeting: Let the Walls Come Tumbling Down

Melvin M Grumbach
1990 Pediatric Research  
National Institutes of Health (NIH) rescience.  ...  They will basic sciences, especially when the commitment to this career need to have a firm foundation in experimental design, computer pathway is not made until the housestaff years.  ... 
doi:10.1203/00006450-199012000-00002 pmid:2284150 fatcat:m3l53saofjhknecmkppp6baetm

How to Read a Research Compendium [article]

Daniel Nüst, Carl Boettiger, Ben Marwick
2018 arXiv   pre-print
Unlike the original, this article is not build upon a long history but intends to provide guidance at the outset of an emerging practice.  ...  We introduce the existing conventions for research compendia and suggest how to utilise their shared properties in a structured reading process.  ...  At this point you should be able to judge whether the software works and if it is sustainable.  ... 
arXiv:1806.09525v1 fatcat:2joy4suud5h6do7tp3bqxxbbiu

A multi-disciplinary perspective on emergent and future innovations in peer review

Jonathan P. Tennant, Jonathan M. Dugan, Daniel Graziotin, Damien C. Jacques, François Waldner, Daniel Mietchen, Yehia Elkhatib, Lauren B. Collister, Christina K. Pikas, Tom Crick, Paola Masuzzo, Anthony Caravaggi (+21 others)
2017 F1000Research  
(e.g., Library & Information Science Abstracts (LISA) and PubMed).  ...  We conclude that there is considerable scope for new peer review initiatives to be developed, each with their own potential issues and advantages.  ...  DG has been supported by the Alexander von Humboldt (AvH) Foundation.  ... 
doi:10.12688/f1000research.12037.1 pmid:29188015 pmcid:PMC5686505 fatcat:smf7myegjzbj7mkxadfeuza5g4
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