{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T00:46:33Z","timestamp":1768005993084,"version":"3.49.0"},"publisher-location":"New York, NY, USA","reference-count":105,"publisher":"ACM","license":[{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"vor","delay-in-days":84,"URL":"http:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01MH119099 and 2P50MH109429"],"award-info":[{"award-number":["R01MH119099 and 2P50MH109429"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2238711"],"award-info":[{"award-number":["2238711"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2025,7,29]]},"DOI":"10.1145\/3736731.3746147","type":"proceedings-article","created":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T11:58:19Z","timestamp":1761047899000},"page":"62-75","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Executable Science: Research Software Engineering Practices for Replicating Neuroscience Findings"],"prefix":"10.1145","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-8482-3356","authenticated-orcid":false,"given":"Gabriel","family":"Kressin Palacios","sequence":"first","affiliation":[{"name":"Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2248-2982","authenticated-orcid":false,"given":"Zhuoyang","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Neuroscience, Johns Hopkins University, Baltimore, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8391-8965","authenticated-orcid":false,"given":"Kristijan","family":"Armeni","sequence":"additional","affiliation":[{"name":"Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, USA"}]}],"member":"320","published-online":{"date-parts":[[2025,10,21]]},"reference":[{"key":"e_1_3_3_3_2_2","doi-asserted-by":"publisher","unstructured":"A.F. Ackerman L.S. Buchwald and F.H. Lewski. 1989. Software inspections: an effective verification process. IEEE Software 6 3 (May 1989) 31\u201336. 10.1109\/52.28121","DOI":"10.1109\/52.28121"},{"key":"e_1_3_3_3_3_2","doi-asserted-by":"publisher","unstructured":"Mohammed Alser Brendan Lawlor Richard\u00a0J. Abdill Sharon Waymost Ram Ayyala Neha Rajkumar Nathan LaPierre Jaqueline Brito Andr\u00e9\u00a0M. Ribeiro-dos Santos Nour Almadhoun Varuni Sarwal Can Firtina Tomasz Osinski Eleazar Eskin Qiyang Hu Derek Strong Byoung-Do Kim Malak\u00a0S. Abedalthagafi Onur Mutlu and Serghei Mangul. 2024. Packaging and containerization of computational methods. Nature Protocols 19 9 (Sept. 2024) 2529\u20132539. 10.1038\/s41596-024-00986-0","DOI":"10.1038\/s41596-024-00986-0"},{"key":"e_1_3_3_3_4_2","doi-asserted-by":"publisher","unstructured":"Kristijan Armeni Loek Brinkman Rickard Carlsson Anita Eerland Rianne Fijten Robin Fondberg Vera\u00a0E Heininga Stephan Heunis Wei\u00a0Qi Koh Maurits Masselink Niall Moran Andrew\u00a0\u00d3 Baoill Alexandra Sarafoglou Antonio Schettino Hardy Schwamm Zsuzsika Sjoerds Marta Teperek Olmo\u00a0R van\u00a0den Akker Anna van\u2019t Veer and Raul Zurita-Milla. 2021. Towards wide-scale adoption of open science practices: The role of open science communities. Science and Public Policy 48 5 (Oct. 2021) 605\u2013611. 10.1093\/scipol\/scab039","DOI":"10.1093\/scipol\/scab039"},{"key":"e_1_3_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.5555\/2486788.2486882"},{"key":"e_1_3_3_3_6_2","doi-asserted-by":"publisher","unstructured":"Gabriel Balaban Ivar Grytten Knut\u00a0Dagestad Rand Lonneke Scheffer and Geir\u00a0Kjetil Sandve. 2021. Ten simple rules for quick and dirty scientific programming. PLOS Computational Biology 17 3 (March 2021) e1008549. 10.1371\/journal.pcbi.1008549Publisher: Public Library of Science.","DOI":"10.1371\/journal.pcbi.1008549"},{"key":"e_1_3_3_3_7_2","doi-asserted-by":"publisher","unstructured":"Lorena Barba. 2024. The path to frictionless reproducibility is still under construction. Harvard Data Science Review 6 1 (Jan. 2024). 10.1162\/99608f92.d73c0559Publisher: The MIT Press.","DOI":"10.1162\/99608f92.d73c0559"},{"key":"e_1_3_3_3_8_2","doi-asserted-by":"publisher","unstructured":"Lorena\u00a0A. Barba. 2012. Reproducibility PI Manifesto. 10.6084\/M9.FIGSHARE.104539.V1Artwork Size: 0 Bytes Pages: 0 Bytes.","DOI":"10.6084\/M9.FIGSHARE.104539.V1"},{"key":"e_1_3_3_3_9_2","volume-title":"Test-driven development: by example (20. printing ed.)","author":"Beck Kent","year":"2015","unstructured":"Kent Beck. 2015. Test-driven development: by example (20. printing ed.). Addison-Wesley, Boston."},{"key":"e_1_3_3_3_10_2","unstructured":"Kent Beck Mike Beedle Arie van Bennekum Alistair Cockburn Ward Cunningham Martin Fowler James Grenning Jim Highsmith Andrew Hunt Ron Jeffries Jon Kern Brian Marick Robert\u00a0C. Martin Steve Mellor Ken Schwaber Jeff Sutherland and Dave Thomas. 2001. Manifesto for agile software development. http:\/\/www.agilemanifesto.org\/"},{"key":"e_1_3_3_3_11_2","doi-asserted-by":"publisher","unstructured":"G.\u00a0Bruce Berriman Ewa Deelman Gideon Juve Mats Rynge and Jens-S. V\u00f6ckler. 2013. The application of cloud computing to scientific workflows: a study of cost and performance. Philosophical Transactions of the Royal Society A: Mathematical Physical and Engineering Sciences 371 1983 (Jan. 2013) 20120066. 10.1098\/rsta.2012.0066Publisher: Royal Society.","DOI":"10.1098\/rsta.2012.0066"},{"key":"e_1_3_3_3_12_2","doi-asserted-by":"publisher","unstructured":"Jeffrey\u00a0R. Binder Rutvik\u00a0H. Desai William\u00a0W. Graves and Lisa\u00a0L. Conant. 2009. Where Is the semantic system? A critical review and meta-analysis of 120 functional neuroimaging studies. Cerebral Cortex 19 12 (Dec. 2009) 2767\u20132796. 10.1093\/cercor\/bhp055","DOI":"10.1093\/cercor\/bhp055"},{"key":"e_1_3_3_3_13_2","doi-asserted-by":"publisher","unstructured":"Marcel Binz Stephan Alaniz Adina Roskies Balazs Aczel Carl\u00a0T. Bergstrom Colin Allen Daniel Schad Dirk Wulff Jevin\u00a0D. West Qiong Zhang Richard\u00a0M. Shiffrin Samuel\u00a0J. Gershman Vencislav Popov Emily\u00a0M. Bender Marco Marelli Matthew\u00a0M. Botvinick Zeynep Akata and Eric Schulz. 2025. How should the advancement of large language models affect the practice of science? Proceedings of the National Academy of Sciences 122 5 (Feb. 2025) e2401227121. 10.1073\/pnas.2401227121Publisher: Proceedings of the National Academy of Sciences.","DOI":"10.1073\/pnas.2401227121"},{"key":"e_1_3_3_3_14_2","doi-asserted-by":"publisher","unstructured":"Abeba Birhane Atoosa Kasirzadeh David Leslie and Sandra Wachter. 2023. Science in the age of large language models. Nature Reviews Physics 5 5 (May 2023) 277\u2013280. 10.1038\/s42254-023-00581-4Publisher: Nature Publishing Group.","DOI":"10.1038\/s42254-023-00581-4"},{"key":"e_1_3_3_3_15_2","doi-asserted-by":"publisher","unstructured":"Rishi Bommasani Drew\u00a0A. Hudson Ehsan Adeli Russ Altman Simran Arora Sydney\u00a0von Arx Michael\u00a0S. Bernstein Jeannette Bohg Antoine Bosselut Emma Brunskill Erik Brynjolfsson Shyamal Buch Dallas Card Rodrigo Castellon Niladri Chatterji Annie Chen Kathleen Creel Jared\u00a0Quincy Davis Dora Demszky Chris Donahue Moussa Doumbouya Esin Durmus Stefano Ermon John Etchemendy Kawin Ethayarajh Li Fei-Fei Chelsea Finn Trevor Gale Lauren Gillespie Karan Goel Noah Goodman Shelby Grossman Neel Guha Tatsunori Hashimoto Peter Henderson John Hewitt Daniel\u00a0E. Ho Jenny Hong Kyle Hsu Jing Huang Thomas Icard Saahil Jain Dan Jurafsky Pratyusha Kalluri Siddharth Karamcheti Geoff Keeling Fereshte Khani Omar Khattab Pang\u00a0Wei Koh Mark Krass Ranjay Krishna Rohith Kuditipudi Ananya Kumar Faisal Ladhak Mina Lee Tony Lee Jure Leskovec Isabelle Levent Xiang\u00a0Lisa Li Xuechen Li Tengyu Ma Ali Malik Christopher\u00a0D. Manning Suvir Mirchandani Eric Mitchell Zanele Munyikwa Suraj Nair Avanika Narayan Deepak Narayanan Ben Newman Allen Nie Juan\u00a0Carlos Niebles Hamed Nilforoshan Julian Nyarko Giray Ogut Laurel Orr Isabel Papadimitriou Joon\u00a0Sung Park Chris Piech Eva Portelance Christopher Potts Aditi Raghunathan Rob Reich Hongyu Ren Frieda Rong Yusuf Roohani Camilo Ruiz Jack Ryan Christopher R\u00e9 Dorsa Sadigh Shiori Sagawa Keshav Santhanam Andy Shih Krishnan Srinivasan Alex Tamkin Rohan Taori Armin\u00a0W. Thomas Florian Tram\u00e8r Rose\u00a0E. Wang William Wang Bohan Wu Jiajun Wu Yuhuai Wu Sang\u00a0Michael Xie Michihiro Yasunaga Jiaxuan You Matei Zaharia Michael Zhang Tianyi Zhang Xikun Zhang Yuhui Zhang Lucia Zheng Kaitlyn Zhou and Percy Liang. 2022. On the opportunities and risks of foundation models. 10.48550\/arXiv.2108.07258arXiv:https:\/\/arXiv.org\/abs\/2108.07258 [cs].","DOI":"10.48550\/arXiv.2108.07258"},{"key":"e_1_3_3_3_16_2","doi-asserted-by":"publisher","unstructured":"Rotem Botvinik-Nezer Felix Holzmeister Colin\u00a0F. Camerer Anna Dreber Juergen Huber Magnus Johannesson Michael Kirchler Roni Iwanir Jeanette\u00a0A. Mumford R.\u00a0Alison Adcock Paolo Avesani Blazej\u00a0M. Baczkowski Aahana Bajracharya Leah Bakst Sheryl Ball Marco Barilari Nad\u00e8ge Bault Derek Beaton Julia Beitner Roland\u00a0G. Benoit Ruud M. W.\u00a0J. Berkers Jamil\u00a0P. Bhanji Bharat\u00a0B. Biswal Sebastian Bobadilla-Suarez Tiago Bortolini Katherine\u00a0L. Bottenhorn Alexander Bowring Senne Braem Hayley\u00a0R. Brooks Emily\u00a0G. Brudner Cristian\u00a0B. Calderon Julia\u00a0A. Camilleri Jaime\u00a0J. Castrellon Luca Cecchetti Edna\u00a0C. Cieslik Zachary\u00a0J. Cole Olivier Collignon Robert\u00a0W. Cox William\u00a0A. Cunningham Stefan Czoschke Kamalaker Dadi Charles\u00a0P. Davis Alberto\u00a0De Luca Mauricio\u00a0R. Delgado Lysia Demetriou Jeffrey\u00a0B. Dennison Xin Di Erin\u00a0W. Dickie Ekaterina Dobryakova Claire\u00a0L. Donnat Juergen Dukart Niall\u00a0W. Duncan Joke Durnez Amr Eed Simon\u00a0B. Eickhoff Andrew Erhart Laura Fontanesi G.\u00a0Matthew Fricke Shiguang Fu Adriana Galv\u00e1n Remi Gau Sarah Genon Tristan Glatard Enrico Glerean Jelle\u00a0J. Goeman Sergej A.\u00a0E. Golowin Carlos Gonz\u00e1lez-Garc\u00eda Krzysztof\u00a0J. Gorgolewski Cheryl\u00a0L. Grady Mikella\u00a0A. Green Jo\u00e3o\u00a0F. Guassi\u00a0Moreira Olivia Guest Shabnam Hakimi J.\u00a0Paul Hamilton Roeland Hancock Giacomo Handjaras Bronson\u00a0B. Harry Colin Hawco Peer Herholz Gabrielle Herman Stephan Heunis Felix Hoffstaedter Jeremy Hogeveen Susan Holmes Chuan-Peng Hu Scott\u00a0A. Huettel Matthew\u00a0E. Hughes Vittorio Iacovella Alexandru\u00a0D. Iordan Peder\u00a0M. Isager Ayse\u00a0I. Isik Andrew Jahn Matthew\u00a0R. Johnson Tom Johnstone Michael J.\u00a0E. Joseph Anthony\u00a0C. Juliano Joseph\u00a0W. Kable Michalis Kassinopoulos Cemal Koba Xiang-Zhen Kong Timothy\u00a0R. Koscik Nuri\u00a0Erkut Kucukboyaci Brice\u00a0A. Kuhl Sebastian Kupek Angela\u00a0R. Laird Claus Lamm Robert Langner Nina Lauharatanahirun Hongmi Lee Sangil Lee Alexander Leemans Andrea Leo Elise Lesage Flora Li Monica Y.\u00a0C. Li Phui\u00a0Cheng Lim Evan\u00a0N. Lintz Schuyler\u00a0W. Liphardt Annabel\u00a0B. Losecaat\u00a0Vermeer Bradley\u00a0C. Love Michael\u00a0L. Mack Norberto Malpica Theo Marins Camille Maumet Kelsey McDonald Joseph\u00a0T. McGuire Helena Melero Adriana\u00a0S. M\u00e9ndez\u00a0Leal Benjamin Meyer Kristin\u00a0N. Meyer Glad Mihai Georgios\u00a0D. Mitsis Jorge Moll Dylan\u00a0M. Nielson Gustav Nilsonne Michael\u00a0P. Notter Emanuele Olivetti Adrian\u00a0I. Onicas Paolo Papale Kaustubh\u00a0R. Patil Jonathan\u00a0E. Peelle Alexandre P\u00e9rez Doris Pischedda Jean-Baptiste Poline Yanina Prystauka Shruti Ray Patricia\u00a0A. Reuter-Lorenz Richard\u00a0C. Reynolds Emiliano Ricciardi Jenny\u00a0R. Rieck Anais\u00a0M. Rodriguez-Thompson Anthony Romyn Taylor Salo Gregory\u00a0R. Samanez-Larkin Emilio Sanz-Morales Margaret\u00a0L. Schlichting Douglas\u00a0H. Schultz Qiang Shen Margaret\u00a0A. Sheridan Jennifer\u00a0A. Silvers Kenny Skagerlund Alec Smith David\u00a0V. Smith Peter Sokol-Hessner Simon\u00a0R. Steinkamp Sarah\u00a0M. Tashjian Bertrand Thirion John\u00a0N. Thorp Gustav Tingh\u00f6g Loreen Tisdall Steven\u00a0H. Tompson Claudio Toro-Serey Juan\u00a0Jesus Torre\u00a0Tresols Leonardo Tozzi Vuong Truong Luca Turella Anna\u00a0E. van\u00a0\u2018t Veer Tom Verguts Jean\u00a0M. Vettel Sagana Vijayarajah Khoi Vo Matthew\u00a0B. Wall Wouter\u00a0D. Weeda Susanne Weis David\u00a0J. White David Wisniewski Alba Xifra-Porxas Emily\u00a0A. Yearling Sangsuk Yoon Rui Yuan Kenneth S.\u00a0L. Yuen Lei Zhang Xu Zhang Joshua\u00a0E. Zosky Thomas\u00a0E. Nichols Russell\u00a0A. Poldrack and Tom Schonberg. 2020. Variability in the analysis of a single neuroimaging dataset by many teams. Nature 582 7810 (June 2020) 84\u201388. 10.1038\/s41586-020-2314-9Publisher: Nature Publishing Group.","DOI":"10.1038\/s41586-020-2314-9"},{"key":"e_1_3_3_3_17_2","doi-asserted-by":"publisher","unstructured":"Rotem Botvinik-Nezer and Tor\u00a0D. Wager. 2023. Reproducibility in neuroimaging analysis: Challenges and solutions. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging 8 8 (Aug. 2023) 780\u2013788. 10.1016\/j.bpsc.2022.12.006","DOI":"10.1016\/j.bpsc.2022.12.006"},{"key":"e_1_3_3_3_18_2","doi-asserted-by":"publisher","unstructured":"Geoffrey\u00a0M. Boynton Stephen\u00a0A. Engel Gary\u00a0H. Glover and David\u00a0J. Heeger. 1996. Linear systems analysis of functional magnetic resonance imaging in human V1. The Journal of Neuroscience 16 13 (July 1996) 4207\u20134221. 10.1523\/JNEUROSCI.16-13-04207.1996","DOI":"10.1523\/JNEUROSCI.16-13-04207.1996"},{"key":"e_1_3_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.495360"},{"key":"e_1_3_3_3_20_2","doi-asserted-by":"publisher","unstructured":"Joshua Carp. 2012. The secret lives of experiments: methods reporting in the fMRI literature. NeuroImage 63 1 (Oct. 2012) 289\u2013300. 10.1016\/j.neuroimage.2012.07.004","DOI":"10.1016\/j.neuroimage.2012.07.004"},{"key":"e_1_3_3_3_21_2","doi-asserted-by":"publisher","unstructured":"Gary Charness Brian Jabarian and John\u00a0A. List. 2025. The next generation of experimental research with LLMs. Nature Human Behaviour (March 2025) 1\u20133. 10.1038\/s41562-025-02137-1Publisher: Nature Publishing Group.","DOI":"10.1038\/s41562-025-02137-1"},{"key":"e_1_3_3_3_22_2","doi-asserted-by":"publisher","unstructured":"Monojit Choudhury Zohar Elyoseph Nathanael\u00a0J. Fast Desmond\u00a0C. Ong Elaine\u00a0O. Nsoesie and Ellie Pavlick. 2025. The promise and pitfalls of generative AI. Nature Reviews Psychology 4 2 (Jan. 2025) 75\u201380. 10.1038\/s44159-024-00402-0","DOI":"10.1038\/s44159-024-00402-0"},{"key":"e_1_3_3_3_23_2","doi-asserted-by":"publisher","unstructured":"Neil\u00a0P. Chue\u00a0Hong Daniel\u00a0S. Katz Michelle Barker Anna-Lena Lamprecht Carlos Martinez Fotis\u00a0E. Psomopoulos Jen Harrow Leyla\u00a0Jael Castro Morane Gruenpeter Paula\u00a0Andrea Martinez Tom Honeyman Alexander Struck Allen Lee Axel Loewe Ben van Werkhoven Catherine Jones Daniel Garijo Esther Plomp Francoise Genova Hugh Shanahan Joanna Leng Maggie Hellstr\u00f6m Malin Sandstr\u00f6m Manodeep Sinha Mateusz Kuzak Patricia Herterich Qian Zhang Sharif Islam Susanna-Assunta Sansone Tom Pollard Udayanto\u00a0Dwi Atmojo Alan Williams Andreas Czerniak Anna Niehues Anne\u00a0Claire Fouilloux Bala Desinghu Carole Goble C\u00e9line Richard Charles Gray Chris Erdmann Daniel N\u00fcst Daniele Tartarini Elena Ranguelova Hartwig Anzt Ilian Todorov James McNally Javier Moldon Jessica Burnett Juli\u00e1n Garrido-S\u00e1nchez Khalid Belhajjame Laurents Sesink Lorraine Hwang Marcos\u00a0Roberto Tovani-Palone Mark\u00a0D. Wilkinson Mathieu Servillat Matthias Liffers Merc Fox Nadica Miljkovi\u0107 Nick Lynch Paula Martinez\u00a0Lavanchy Sandra Gesing Sarah Stevens Sergio Martinez\u00a0Cuesta Silvio Peroni Stian Soiland-Reyes Tom Bakker Tovo Rabemanantsoa Vanessa Sochat Yo Yehudi and RDA\u00a0FAIR4RS WG. 2022. FAIR Principles for Research Software (FAIR4RS Principles). (May 2022). 10.15497\/RDA00068Publisher: Zenodo.","DOI":"10.15497\/RDA00068"},{"key":"e_1_3_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1190\/1.1822162"},{"key":"e_1_3_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1002\/9781118882139.ch16"},{"key":"e_1_3_3_3_26_2","doi-asserted-by":"publisher","unstructured":"Rowan Cockett Franklin Koch Steve Purves Angus Hollands Yuxi Wang Dylan Grandmont Chris Holdgraf Andrea Jan-Hendrik M\u00fcller Spencer Lyon Cristian Le Jim Madge wwx Sugan Reden Yuanhao Geng Ryan Lovett Mikkel Roald-Arb\u00f8l Matt McKay Matthew Brett M Bussonnier Mridul Seth Nicolas\u00a0M. Thi\u00e9ry Raniere Silva Sarah Brown Sinan Bekar Tavin Cole Thad Guidry and Toby Driscoll. 2025. jupyter-book\/mystmd: v1.3.24. 10.5281\/ZENODO.14805610","DOI":"10.5281\/ZENODO.14805610"},{"key":"e_1_3_3_3_27_2","doi-asserted-by":"publisher","unstructured":"The Turing\u00a0Way Community. 2022. The Turing Way: A handbook for reproducible ethical and collaborative research. 10.5281\/ZENODO.3233853","DOI":"10.5281\/ZENODO.3233853"},{"key":"e_1_3_3_3_28_2","doi-asserted-by":"publisher","unstructured":"Andrew Connolly Joseph Hellerstein Naomi Alterman David Beck Rob Fatland Ed Lazowska Vani Mandava and Sarah Stone. 2023. Software engineering practices in academia: Promoting the 3Rs\u2014Readability Resilience and Reuse. Harvard Data Science Review 5 2 (April 2023). 10.1162\/99608f92.018bf012Publisher: The MIT Press.","DOI":"10.1162\/99608f92.018bf012"},{"key":"e_1_3_3_3_29_2","doi-asserted-by":"publisher","unstructured":"Saskia\u00a0EJ de Vries Joshua\u00a0H Siegle and Christof Koch. 2023. Sharing neurophysiology data from the Allen Brain Observatory. eLife 12 (July 2023) e85550. 10.7554\/eLife.85550Publisher: eLife Sciences Publications Ltd.","DOI":"10.7554\/eLife.85550"},{"key":"e_1_3_3_3_30_2","doi-asserted-by":"publisher","unstructured":"Adrien Doerig Rowan\u00a0P. Sommers Katja Seeliger Blake Richards Jenann Ismael Grace\u00a0W. Lindsay Konrad\u00a0P. Kording Talia Konkle Marcel A.\u00a0J. Van\u00a0Gerven Nikolaus Kriegeskorte and Tim\u00a0C. Kietzmann. 2023. The neuroconnectionist research programme. Nature Reviews Neuroscience 24 7 (July 2023) 431\u2013450. 10.1038\/s41583-023-00705-w","DOI":"10.1038\/s41583-023-00705-w"},{"key":"e_1_3_3_3_31_2","doi-asserted-by":"publisher","unstructured":"David\u00a0L. Donoho. 2010. An invitation to reproducible computational research. Biostatistics 11 3 (July 2010) 385\u2013388. 10.1093\/biostatistics\/kxq028","DOI":"10.1093\/biostatistics\/kxq028"},{"key":"e_1_3_3_3_32_2","doi-asserted-by":"publisher","unstructured":"Elizabeth DuPre Chris Holdgraf Agah Karakuzu Lo\u00efc Tetrel Pierre Bellec Nikola Stikov and Jean-Baptiste Poline. 2022. Beyond advertising: New infrastructures for publishing integrated research objects. PLOS Computational Biology 18 1 (Jan. 2022) e1009651. 10.1371\/journal.pcbi.1009651Publisher: Public Library of Science.","DOI":"10.1371\/journal.pcbi.1009651"},{"key":"e_1_3_3_3_33_2","doi-asserted-by":"publisher","unstructured":"Elizabeth DuPre and Russell\u00a0Alan Poldrack. 2024. The future of data analysis is now: Integrating generative AI in neuroimaging methods development. Imaging Neuroscience 2 (July 2024) 1\u20138. 10.1162\/imaga00241","DOI":"10.1162\/imaga00241"},{"key":"e_1_3_3_3_34_2","doi-asserted-by":"publisher","unstructured":"Nasir\u00a0U. Eisty Upulee Kanewala and Jeffrey\u00a0C. Carver. 2025. Testing research software: An in-depth survey of practices methods and tools. 10.48550\/arXiv.2501.17739arXiv:https:\/\/arXiv.org\/abs\/2501.17739 [cs].","DOI":"10.48550\/arXiv.2501.17739"},{"key":"e_1_3_3_3_35_2","doi-asserted-by":"publisher","unstructured":"Timothy\u00a0M Errington Alexandria Denis Nicole Perfito Elizabeth Iorns and Brian\u00a0A Nosek. 2021. Challenges for assessing replicability in preclinical cancer biology. eLife 10 (Dec. 2021) e67995. 10.7554\/eLife.67995Publisher: eLife Sciences Publications Ltd.","DOI":"10.7554\/eLife.67995"},{"key":"e_1_3_3_3_36_2","doi-asserted-by":"publisher","unstructured":"Evelina Fedorenko Anna\u00a0A. Ivanova and Tamar\u00a0I. Regev. 2024. The language network as a natural kind within the broader landscape of the human brain. Nature Reviews Neuroscience 25 5 (May 2024) 289\u2013312. 10.1038\/s41583-024-00802-4Publisher: Nature Publishing Group.","DOI":"10.1038\/s41583-024-00802-4"},{"key":"e_1_3_3_3_37_2","doi-asserted-by":"publisher","unstructured":"Angela\u00a0D Friederici and Sarah\u00a0Me Gierhan. 2013. The language network. Current Opinion in Neurobiology 23 2 (April 2013) 250\u2013254. 10.1016\/j.conb.2012.10.002","DOI":"10.1016\/j.conb.2012.10.002"},{"key":"e_1_3_3_3_38_2","doi-asserted-by":"publisher","unstructured":"James\u00a0S. Gao Alexander\u00a0G. Huth Mark\u00a0D. Lescroart and Jack\u00a0L. Gallant. 2015. Pycortex: an interactive surface visualizer for fMRI. Frontiers in Neuroinformatics 9 (Sept. 2015). 10.3389\/fninf.2015.00023","DOI":"10.3389\/fninf.2015.00023"},{"key":"e_1_3_3_3_39_2","doi-asserted-by":"publisher","unstructured":"Marc-Oliver Gewaltig and Robert Cannon. 2014. Current practice in software development for computational neuroscience and how to improve it. PLOS Computational Biology 10 1 (Jan. 2014) e1003376. 10.1371\/journal.pcbi.1003376Publisher: Public Library of Science.","DOI":"10.1371\/journal.pcbi.1003376"},{"key":"e_1_3_3_3_40_2","doi-asserted-by":"publisher","unstructured":"Rick\u00a0O. Gilmore Michele\u00a0T. Diaz Brad\u00a0A. Wyble and Tal Yarkoni. 2017. Progress toward openness transparency and reproducibility in cognitive neuroscience. Annals of the New York Academy of Sciences 1396 1 (May 2017) 5\u201318. 10.1111\/nyas.13325","DOI":"10.1111\/nyas.13325"},{"key":"e_1_3_3_3_41_2","doi-asserted-by":"publisher","unstructured":"Krzysztof\u00a0J. Gorgolewski Tibor Auer Vince\u00a0D. Calhoun R.\u00a0Cameron Craddock Samir Das Eugene\u00a0P. Duff Guillaume Flandin Satrajit\u00a0S. Ghosh Tristan Glatard Yaroslav\u00a0O. Halchenko Daniel\u00a0A. Handwerker Michael Hanke David Keator Xiangrui Li Zachary Michael Camille Maumet B.\u00a0Nolan Nichols Thomas\u00a0E. Nichols John Pellman Jean-Baptiste Poline Ariel Rokem Gunnar Schaefer Vanessa Sochat William Triplett Jessica\u00a0A. Turner Ga\u00ebl Varoquaux and Russell\u00a0A. Poldrack. 2016. The brain imaging data structure a format for organizing and describing outputs of neuroimaging experiments. Scientific Data 3 1 (June 2016) 1\u20139. 10.1038\/sdata.2016.44Number: 1 Publisher: Nature Publishing Group.","DOI":"10.1038\/sdata.2016.44"},{"key":"e_1_3_3_3_42_2","doi-asserted-by":"publisher","unstructured":"Qing Guo Melissa Parlar Wanda Truong Geoffrey Hall Lehana Thabane Margaret McKinnon Ron Goeree and Eleanor Pullenayegum. 2014. The reporting of observational clinical functional magnetic resonance imaging studies: A systematic review. PLOS ONE 9 4 (April 2014) e94412. 10.1371\/journal.pone.0094412Publisher: Public Library of Science.","DOI":"10.1371\/journal.pone.0094412"},{"key":"e_1_3_3_3_43_2","doi-asserted-by":"publisher","unstructured":"Peter Hagoort. 2019. The neurobiology of language beyond single-word processing. Science 366 6461 (Oct. 2019) 55\u201358. 10.1126\/science.aax0289","DOI":"10.1126\/science.aax0289"},{"key":"e_1_3_3_3_44_2","doi-asserted-by":"publisher","unstructured":"Yaroslav Halchenko Kyle Meyer Benjamin Poldrack Debanjum Solanky Adina Wagner Jason Gors Dave MacFarlane Dorian Pustina Vanessa Sochat Satrajit Ghosh Christian M\u00f6nch Christopher Markiewicz Laura Waite Ilya Shlyakhter Alejandro De\u00a0La\u00a0Vega Soichi Hayashi Christian H\u00e4usler Jean-Baptiste Poline Tobias Kadelka Kusti Skyt\u00e9n Dorota Jarecka David Kennedy Ted Strauss Matt Cieslak Peter Vavra Horea-Ioan Ioanas Robin Schneider Mika Pfl\u00fcger James Haxby Simon Eickhoff and Michael Hanke. 2021. DataLad: distributed system for joint management of code data and their relationship. Journal of Open Source Software 6 63 (July 2021) 3262. 10.21105\/joss.03262","DOI":"10.21105\/joss.03262"},{"key":"e_1_3_3_3_45_2","doi-asserted-by":"publisher","unstructured":"Tom\u00a0E. Hardwicke Manuel Bohn Kyle MacDonald Emily Hembacher Mich\u00e8le\u00a0B. Nuijten Benjamin\u00a0N. Peloquin Benjamin\u00a0E. deMayo Bria Long Erica\u00a0J. Yoon and Michael\u00a0C. Frank. 2021. Analytic reproducibility in articles receiving open data badges at the journal Psychological Science : an observational study. Royal Society Open Science 8 1 (Jan. 2021) 201494. 10.1098\/rsos.201494","DOI":"10.1098\/rsos.201494"},{"key":"e_1_3_3_3_46_2","doi-asserted-by":"publisher","unstructured":"Charles\u00a0R. Harris K.\u00a0Jarrod Millman St\u00e9fan\u00a0J. Van Der\u00a0Walt Ralf Gommers Pauli Virtanen David Cournapeau Eric Wieser Julian Taylor Sebastian Berg Nathaniel\u00a0J. Smith Robert Kern Matti Picus Stephan Hoyer Marten\u00a0H. Van\u00a0Kerkwijk Matthew Brett Allan Haldane Jaime\u00a0Fern\u00e1ndez Del\u00a0R\u00edo Mark Wiebe Pearu Peterson Pierre G\u00e9rard-Marchant Kevin Sheppard Tyler Reddy Warren Weckesser Hameer Abbasi Christoph Gohlke and Travis\u00a0E. Oliphant. 2020. Array programming with NumPy. Nature 585 7825 (Sept. 2020) 357\u2013362. 10.1038\/s41586-020-2649-2","DOI":"10.1038\/s41586-020-2649-2"},{"key":"e_1_3_3_3_47_2","doi-asserted-by":"publisher","unstructured":"Soichi Hayashi Bradley\u00a0A. Caron Anibal\u00a0S\u00f3lon Heinsfeld Sophia Vinci-Booher Brent McPherson Daniel\u00a0N. Bullock Giulia Bert\u00f2 Guiomar Niso Sandra Hanekamp Daniel Levitas Kimberly Ray Anne MacKenzie Paolo Avesani Lindsey Kitchell Josiah\u00a0K. Leong Filipi Nascimento-Silva Serge Koudoro Hanna Willis Jasleen\u00a0K. Jolly Derek Pisner Taylor\u00a0R. Zuidema Jan\u00a0W. Kurzawski Kyriaki Mikellidou Aurore Bussalb Maximilien Chaumon Nathalie George Christopher Rorden Conner Victory Dheeraj Bhatia Dogu\u00a0Baran Aydogan Fang-Cheng\u00a0F. Yeh Franco Delogu Javier Guaje Jelle Veraart Jeremy Fischer Joshua Faskowitz Ricardo Fabrega David Hunt Shawn McKee Shawn\u00a0T. Brown Stephanie Heyman Vittorio Iacovella Amanda\u00a0F. Mejia Daniele Marinazzo R.\u00a0Cameron Craddock Emanuale Olivetti Jamie\u00a0L. Hanson Eleftherios Garyfallidis Dan Stanzione James Carson Robert Henschel David\u00a0Y. Hancock Craig\u00a0A. Stewart David Schnyer Damian\u00a0O. Eke Russell\u00a0A. Poldrack Steffen Bollmann Ashley Stewart Holly Bridge Ilaria Sani Winrich\u00a0A. Freiwald Aina Puce Nicholas\u00a0L. Port and Franco Pestilli. 2024. brainlife.io: a decentralized and open-source cloud platform to support neuroscience research. Nature Methods 21 5 (May 2024) 809\u2013813. 10.1038\/s41592-024-02237-2Publisher: Nature Publishing Group.","DOI":"10.1038\/s41592-024-02237-2"},{"key":"e_1_3_3_3_48_2","doi-asserted-by":"publisher","unstructured":"Gregory Hickok and David Poeppel. 2007. The cortical organization of speech processing. Nature Reviews Neuroscience 8 5 (May 2007) 393\u2013402. 10.1038\/nrn2113","DOI":"10.1038\/nrn2113"},{"key":"e_1_3_3_3_49_2","doi-asserted-by":"publisher","unstructured":"J.\u00a0D. Hunter. 2007. Matplotlib: A 2D graphics environment. Computing in Science & Engineering 9 3 (2007) 90\u201395. 10.1109\/MCSE.2007.55Publisher: IEEE COMPUTER SOC.","DOI":"10.1109\/MCSE.2007.55"},{"key":"e_1_3_3_3_50_2","doi-asserted-by":"publisher","unstructured":"Alexander\u00a0G. Huth Wendy A.\u00a0de Heer Thomas\u00a0L. Griffiths Fr\u00e9d\u00e9ric\u00a0E. Theunissen and Jack\u00a0L. Gallant. 2016. Natural speech reveals the semantic maps that tile human cerebral cortex. Nature 532 7600 (April 2016) 453. 10.1038\/nature17637","DOI":"10.1038\/nature17637"},{"key":"e_1_3_3_3_51_2","doi-asserted-by":"publisher","unstructured":"Anna\u00a0A Ivanova Martin Schrimpf Stefano Anzellotti Noga Zaslavsky Evelina Fedorenko and Leyla Isik. 2022. Beyond linear regression: mapping models in cognitive neuroscience should align with research goals. Neurons Behavior Data analysis and Theory 1 (Aug. 2022). 10.51628\/001c.37507","DOI":"10.51628\/001c.37507"},{"key":"e_1_3_3_3_52_2","doi-asserted-by":"publisher","unstructured":"Erik\u00a0C. Johnson Thinh\u00a0T. Nguyen Benjamin\u00a0K. Dichter Frank Zappulla Montgomery Kosma Kabilar Gunalan Yaroslav\u00a0O. Halchenko Shay\u00a0Q. Neufeld Kristen Ratan Nicholas\u00a0J. Edwards Susanne Ressl Sarah\u00a0R. Heilbronner Michael Schirner Petra Ritter Brock Wester Satrajit Ghosh Maryann\u00a0E. Martone Franco Pestilli and Dimitri Yatsenko. 2024. SciOps: Achieving productivity and reliability in data-intensive research. 10.48550\/arXiv.2401.00077arXiv:https:\/\/arXiv.org\/abs\/2401.00077 [q-bio].","DOI":"10.48550\/arXiv.2401.00077"},{"key":"e_1_3_3_3_53_2","doi-asserted-by":"publisher","unstructured":"Anita\u00a0S. Jwa and Russell\u00a0A. Poldrack. 2022. The spectrum of data sharing policies in neuroimaging data repositories. Human Brain Mapping 43 8 (2022) 2707\u20132721. 10.1002\/hbm.25803_eprint: https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/hbm.25803.","DOI":"10.1002\/hbm.25803"},{"key":"e_1_3_3_3_54_2","doi-asserted-by":"publisher","unstructured":"Agah Karakuzu Elizabeth DuPre Loic Tetrel Patrick Bermudez Mathieu Boudreau Mary Chin Jean-Baptiste Poline Samir Das Lune Bellec and Nikola Stikov. 2022. NeuroLibre : A preprint server for full-fledged reproducible neuroscience. 10.31219\/osf.io\/h89js","DOI":"10.31219\/osf.io\/h89js"},{"key":"e_1_3_3_3_55_2","doi-asserted-by":"publisher","unstructured":"Nikolaus Kriegeskorte and Pamela\u00a0K. Douglas. 2018. Cognitive computational neuroscience. Nature Neuroscience 21 9 (Sept. 2018) 1148\u20131160. 10.1038\/s41593-018-0210-5","DOI":"10.1038\/s41593-018-0210-5"},{"key":"e_1_3_3_3_56_2","doi-asserted-by":"publisher","unstructured":"Nikolaus Kriegeskorte and Pamela\u00a0K Douglas. 2019. Interpreting encoding and decoding models. Current Opinion in Neurobiology 55 (April 2019) 167\u2013179. 10.1016\/j.conb.2019.04.002","DOI":"10.1016\/j.conb.2019.04.002"},{"key":"e_1_3_3_3_57_2","doi-asserted-by":"publisher","unstructured":"Arjun Krishna Erick Galinkin Leon Derczynski and Jeffrey Martin. 2025. Importing Phantoms: Measuring LLM Package Hallucination Vulnerabilities. 10.48550\/arXiv.2501.19012arXiv:https:\/\/arXiv.org\/abs\/2501.19012 [cs].","DOI":"10.48550\/arXiv.2501.19012"},{"key":"e_1_3_3_3_58_2","doi-asserted-by":"publisher","unstructured":"Amanda LeBel Lauren Wagner Shailee Jain Aneesh Adhikari-Desai Bhavin Gupta Allyson Morgenthal Jerry Tang Lixiang Xu and Alexander\u00a0G. Huth. 2023. An fMRI dataset during a passive natural language listening task. 10.18112\/OPENNEURO.DS003020.V2.0.0","DOI":"10.18112\/OPENNEURO.DS003020.V2.0.0"},{"key":"e_1_3_3_3_59_2","doi-asserted-by":"publisher","unstructured":"Amanda LeBel Lauren Wagner Shailee Jain Aneesh Adhikari-Desai Bhavin Gupta Allyson Morgenthal Jerry Tang Lixiang Xu and Alexander\u00a0G. Huth. 2023. A natural language fMRI dataset for voxelwise encoding models. Scientific Data 10 1 (Aug. 2023) 555. 10.1038\/s41597-023-02437-zPublisher: Nature Publishing Group.","DOI":"10.1038\/s41597-023-02437-z"},{"key":"e_1_3_3_3_60_2","doi-asserted-by":"publisher","unstructured":"Nikos\u00a0K. Logothetis. 2003. The underpinnings of the BOLD functional magnetic resonance imaging signal. The Journal of Neuroscience 23 10 (May 2003) 3963\u20133971. 10.1523\/JNEUROSCI.23-10-03963.2003","DOI":"10.1523\/JNEUROSCI.23-10-03963.2003"},{"key":"e_1_3_3_3_61_2","unstructured":"Eric\u00a0J. Ma. 2024. The human dimension to clean distributable and documented data science code. Eric J. Ma\u2019s Blog (Oct. 2024). https:\/\/ericmjl.github.io\/blog\/2024\/10\/25\/the-human-dimension-to-clean-distributable-and-documented-data-science-code"},{"key":"e_1_3_3_3_62_2","doi-asserted-by":"publisher","unstructured":"Christopher\u00a0J Markiewicz Krzysztof\u00a0J Gorgolewski Franklin Feingold Ross Blair Yaroslav\u00a0O Halchenko Eric Miller Nell Hardcastle Joe Wexler Oscar Esteban Mathias Goncavles Anita Jwa and Russell Poldrack. 2021. The OpenNeuro resource for sharing of neuroscience data. eLife 10 (Oct. 2021) e71774. 10.7554\/eLife.71774","DOI":"10.7554\/eLife.71774"},{"key":"e_1_3_3_3_63_2","volume-title":"Clean code: a handbook of agile software craftsmanship (repr. ed.)","author":"Martin Robert\u00a0C.","year":"2012","unstructured":"Robert\u00a0C. Martin. 2012. Clean code: a handbook of agile software craftsmanship (repr. ed.). Prentice Hall, Upper Saddle River, NJ Munich."},{"key":"e_1_3_3_3_64_2","doi-asserted-by":"publisher","unstructured":"Erin\u00a0C. McKiernan Lorena Barba Philip\u00a0E. Bourne Caitlin Carter Zach Chandler Sayeed Choudhury Stephen Jacobs Daniel\u00a0S. Katz Stefanie Lieggi Beth Plale and Greg Tananbaum. 2023. Policy recommendations to ensure that research software is openly accessible and reusable. PLOS Biology 21 7 (July 2023) e3002204. 10.1371\/journal.pbio.3002204","DOI":"10.1371\/journal.pbio.3002204"},{"key":"e_1_3_3_3_65_2","doi-asserted-by":"publisher","DOI":"10.25080\/Majora-92bf1922-00a"},{"key":"e_1_3_3_3_66_2","doi-asserted-by":"publisher","unstructured":"David Moreau Kristina Wiebels and Carl Boettiger. 2023. Containers for computational reproducibility. Nature Reviews Methods Primers 3 1 (July 2023) 1\u201316. 10.1038\/s43586-023-00236-9Publisher: Nature Publishing Group.","DOI":"10.1038\/s43586-023-00236-9"},{"key":"e_1_3_3_3_67_2","doi-asserted-by":"publisher","unstructured":"Andrew Morin Jennifer Urban and Piotr Sliz. 2012. A quick guide to software licensing for the scientist-programmer. PLOS Computational Biology 8 7 (July 2012) e1002598. 10.1371\/journal.pcbi.1002598Publisher: Public Library of Science.","DOI":"10.1371\/journal.pcbi.1002598"},{"key":"e_1_3_3_3_68_2","doi-asserted-by":"publisher","unstructured":"Thomas Naselaris Danielle\u00a0S. Bassett Alyson\u00a0K. Fletcher Konrad Kording Nikolaus Kriegeskorte Hendrikje Nienborg Russell\u00a0A. Poldrack Daphna Shohamy and Kendrick Kay. 2018. Cognitive computational neuroscience: A new conference for an emerging discipline. Trends in Cognitive Sciences (Feb. 2018). 10.1016\/j.tics.2018.02.008","DOI":"10.1016\/j.tics.2018.02.008"},{"key":"e_1_3_3_3_69_2","doi-asserted-by":"publisher","unstructured":"Thomas Naselaris Kendrick\u00a0N. Kay Shinji Nishimoto and Jack\u00a0L. Gallant. 2011. Encoding and decoding in fMRI. NeuroImage 56 2 (May 2011) 400\u2013410. 10.1016\/j.neuroimage.2010.07.073","DOI":"10.1016\/j.neuroimage.2010.07.073"},{"key":"e_1_3_3_3_70_2","doi-asserted-by":"publisher","DOI":"10.17226\/25303"},{"key":"e_1_3_3_3_71_2","unstructured":"Alondra Nelson. 2022. Ensuring free immediate and equitable access to federally funded research. https:\/\/bidenwhitehouse.archives.gov\/wp-content\/uploads\/2022\/08\/08-2022-OSTP-Public-Access-Memo.pdf"},{"key":"e_1_3_3_3_72_2","doi-asserted-by":"publisher","unstructured":"Tien Nguyen Waris Gill and Muhammad\u00a0Ali Gulzar. 2025. Are the majority of public computational notebooks pathologically non-executable?10.48550\/arXiv.2502.04184arXiv:https:\/\/arXiv.org\/abs\/2502.04184 [cs].","DOI":"10.48550\/arXiv.2502.04184"},{"key":"e_1_3_3_3_73_2","unstructured":"Brian Nosek. 2019. Strategy for culture change. https:\/\/www.cos.io\/blog\/strategy-for-culture-change"},{"key":"e_1_3_3_3_74_2","doi-asserted-by":"publisher","unstructured":"Jonas Obleser and Frank Eisner. 2009. Pre-lexical abstraction of speech in the auditory cortex. Trends in Cognitive Sciences 13 1 (Jan. 2009) 14\u201319. 10.1016\/j.tics.2008.09.005Publisher: Elsevier.","DOI":"10.1016\/j.tics.2008.09.005"},{"key":"e_1_3_3_3_75_2","doi-asserted-by":"publisher","unstructured":"Open Science Collaboration. 2015. Estimating the reproducibility of psychological science. Science 349 6251 (Aug. 2015) aac4716. 10.1126\/science.aac4716","DOI":"10.1126\/science.aac4716"},{"key":"e_1_3_3_3_76_2","unstructured":"F. Pedregosa G. Varoquaux A. Gramfort V. Michel B. Thirion O. Grisel M. Blondel P. Prettenhofer R. Weiss V. Dubourg J. Vanderplas A. Passos D. Cournapeau M. Brucher M. Perrot and E. Duchesnay. 2011. Scikit-learn: Machine learning in python. Journal of Machine Learning Research 12 (2011) 2825\u20132830."},{"key":"e_1_3_3_3_77_2","doi-asserted-by":"publisher","unstructured":"Roger\u00a0D. Peng. 2009. Reproducible research and biostatistics. Biostatistics 10 3 (July 2009) 405\u2013408. 10.1093\/biostatistics\/kxp014","DOI":"10.1093\/biostatistics\/kxp014"},{"key":"e_1_3_3_3_78_2","doi-asserted-by":"publisher","unstructured":"Roger\u00a0D. Peng. 2011. Reproducible research in computational science. Science 334 6060 (Dec. 2011) 1226\u20131227. 10.1126\/science.1213847Publisher: American Association for the Advancement of Science.","DOI":"10.1126\/science.1213847"},{"key":"e_1_3_3_3_79_2","doi-asserted-by":"publisher","DOI":"10.1109\/MSR.2019.00077"},{"key":"e_1_3_3_3_80_2","unstructured":"Joelle Pineau Philippe Vincent-Lamarre Koustuv Sinha Vincent Lariviere Alina Beygelzimer Florence d\u2019Alche Buc Emily Fox and Hugo Larochelle. 2021. Improving reproducibility in machine learning research. Journal of Machine Learning Research 22 164 (2021) 1\u201320. http:\/\/jmlr.org\/papers\/v22\/20-303.html"},{"key":"e_1_3_3_3_81_2","doi-asserted-by":"publisher","unstructured":"Russell\u00a0A. Poldrack Chris\u00a0I. Baker Joke Durnez Krzysztof\u00a0J. Gorgolewski Paul\u00a0M. Matthews Marcus\u00a0R. Munaf\u00f2 Thomas\u00a0E. Nichols Jean-Baptiste Poline Edward Vul and Tal Yarkoni. 2017. Scanning the horizon: towards transparent and reproducible neuroimaging research. Nature Reviews Neuroscience 18 2 (Feb. 2017) 115\u2013126. 10.1038\/nrn.2016.167Publisher: Nature Publishing Group.","DOI":"10.1038\/nrn.2016.167"},{"key":"e_1_3_3_3_82_2","doi-asserted-by":"publisher","unstructured":"Russell\u00a0A Poldrack and Krzysztof\u00a0J Gorgolewski. 2014. Making big data open: data sharing in neuroimaging. Nature Neuroscience 17 11 (Nov. 2014) 1510\u20131517. 10.1038\/nn.3818","DOI":"10.1038\/nn.3818"},{"key":"e_1_3_3_3_83_2","doi-asserted-by":"publisher","unstructured":"Cathy\u00a0J. Price. 2010. The anatomy of language: a review of 100 fMRI studies published in 2009. Annals of the New York Academy of Sciences 1191 1 (March 2010) 62\u201388. 10.1111\/j.1749-6632.2010.05444.x","DOI":"10.1111\/j.1749-6632.2010.05444.x"},{"key":"e_1_3_3_3_84_2","unstructured":"Richard McElreath. 2020. Science as amateur software development. https:\/\/www.youtube.com\/watch?v=zwRdO9_GGhY"},{"key":"e_1_3_3_3_85_2","doi-asserted-by":"publisher","unstructured":"Ariel Rokem. 2024. Ten simple rules for scientific code review. PLOS Computational Biology 20 9 (Sept. 2024) e1012375. 10.1371\/journal.pcbi.1012375Publisher: Public Library of Science.","DOI":"10.1371\/journal.pcbi.1012375"},{"key":"e_1_3_3_3_86_2","doi-asserted-by":"publisher","unstructured":"Geir\u00a0Kjetil Sandve Anton Nekrutenko James Taylor and Eivind Hovig. 2013. Ten simple rules for reproducible computational research. PLoS Computational Biology 9 10 (Oct. 2013) e1003285. 10.1371\/journal.pcbi.1003285","DOI":"10.1371\/journal.pcbi.1003285"},{"key":"e_1_3_3_3_87_2","doi-asserted-by":"publisher","unstructured":"Terrence\u00a0J. Sejnowski Patricia\u00a0S. Churchland and J.\u00a0Anthony Movshon. 2014. Putting big data to good use in neuroscience. Nature Neuroscience 17 11 (Nov. 2014) 1440\u20131441. 10.1038\/nn.3839Publisher: Nature Publishing Group.","DOI":"10.1038\/nn.3839"},{"key":"e_1_3_3_3_88_2","doi-asserted-by":"publisher","unstructured":"Ilia Shumailov Zakhar Shumaylov Yiren Zhao Nicolas Papernot Ross Anderson and Yarin Gal. 2024. AI models collapse when trained on recursively generated data. Nature 631 8022 (July 2024) 755\u2013759. 10.1038\/s41586-024-07566-yPublisher: Nature Publishing Group.","DOI":"10.1038\/s41586-024-07566-y"},{"key":"e_1_3_3_3_89_2","doi-asserted-by":"publisher","unstructured":"Alexander\u00a0B. Silva Kaylo\u00a0T. Littlejohn Jessie\u00a0R. Liu David\u00a0A. Moses and Edward\u00a0F. Chang. 2024. The speech neuroprosthesis. Nature Reviews Neuroscience 25 7 (July 2024) 473\u2013492. 10.1038\/s41583-024-00819-9Publisher: Nature Publishing Group.","DOI":"10.1038\/s41583-024-00819-9"},{"key":"e_1_3_3_3_90_2","doi-asserted-by":"publisher","unstructured":"Tim Storer. 2017. Bridging the chasm: A survey of software engineering practice in scientific programming. ACM Comput. Surv. 50 4 (Aug. 2017) 47:1\u201347:32. 10.1145\/3084225","DOI":"10.1145\/3084225"},{"key":"e_1_3_3_3_91_2","doi-asserted-by":"publisher","unstructured":"Carol Tenopir Natalie\u00a0M. Rice Suzie Allard Lynn Baird Josh Borycz Lisa Christian Bruce Grant Robert Olendorf and Robert\u00a0J. Sandusky. 2020. Data sharing management use and reuse: Practices and perceptions of scientists worldwide. PLOS ONE 15 3 (March 2020) e0229003. 10.1371\/journal.pone.0229003Publisher: Public Library of Science.","DOI":"10.1371\/journal.pone.0229003"},{"key":"e_1_3_3_3_92_2","doi-asserted-by":"publisher","unstructured":"The Matplotlib Development Team. 2024. Matplotlib: Visualization with Python. 10.5281\/ZENODO.13308876","DOI":"10.5281\/ZENODO.13308876"},{"key":"e_1_3_3_3_93_2","doi-asserted-by":"publisher","unstructured":"The Pandas Development Team. 2024. pandas-dev\/pandas: Pandas. 10.5281\/zenodo.10957263","DOI":"10.5281\/zenodo.10957263"},{"key":"e_1_3_3_3_94_2","volume-title":"The pragmatic programmer: your journey to mastery (second edition, 20th anniversary edtion ed.)","author":"Thomas David","year":"2020","unstructured":"David Thomas and Andrew Hunt. 2020. The pragmatic programmer: your journey to mastery (second edition, 20th anniversary edtion ed.). Addison-Wesley, Boston."},{"key":"e_1_3_3_3_95_2","doi-asserted-by":"publisher","unstructured":"US Research Software Engineer Association and IEEE Computer Society. 2023. Research software engineers: Creating a career path\u2014and a career. 10.5281\/ZENODO.10073232","DOI":"10.5281\/ZENODO.10073232"},{"key":"e_1_3_3_3_96_2","doi-asserted-by":"publisher","unstructured":"Anusha\u00a0M Vable Scott\u00a0F Diehl and M\u00a0Maria Glymour. 2021. Code review as a simple trick to enhance reproducibility accelerate learning and improve the quality of your team\u2019s research. American Journal of Epidemiology 190 10 (Oct. 2021) 2172\u20132177. 10.1093\/aje\/kwab092","DOI":"10.1093\/aje\/kwab092"},{"key":"e_1_3_3_3_97_2","doi-asserted-by":"publisher","unstructured":"Pauli Virtanen Ralf Gommers Travis\u00a0E. Oliphant Matt Haberland Tyler Reddy David Cournapeau Evgeni Burovski Pearu Peterson Warren Weckesser Jonathan Bright St\u00e9fan\u00a0J. van\u00a0der Walt Matthew Brett Joshua Wilson K.\u00a0Jarrod Millman Nikolay Mayorov Andrew R.\u00a0J. Nelson Eric Jones Robert Kern Eric Larson C\u00a0J Carey \u0130lhan Polat Yu Feng Eric\u00a0W. Moore Jake VanderPlas Denis Laxalde Josef Perktold Robert Cimrman Ian Henriksen E.\u00a0A. Quintero Charles\u00a0R. Harris Anne\u00a0M. Archibald Ant\u00f4nio\u00a0H. Ribeiro Fabian Pedregosa Paul van Mulbregt and SciPy 1.0 Contributors. 2020. SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python. Nature Methods 17 (2020) 261\u2013272. 10.1038\/s41592-019-0686-2","DOI":"10.1038\/s41592-019-0686-2"},{"key":"e_1_3_3_3_98_2","doi-asserted-by":"publisher","unstructured":"Marijn\u00a0van Vliet. 2020. Seven quick tips for analysis scripts in neuroimaging. PLOS Computational Biology 16 3 (March 2020) e1007358. 10.1371\/journal.pcbi.1007358Publisher: Public Library of Science.","DOI":"10.1371\/journal.pcbi.1007358"},{"key":"e_1_3_3_3_99_2","volume-title":"Guide to the Software engineering body of knowledge (SWEBOK Guide) (4.0 ed.)","author":"Washizaki Hironori","year":"2024","unstructured":"Hironori Washizaki. 2024. Guide to the Software engineering body of knowledge (SWEBOK Guide) (4.0 ed.). IEEE Computer Society. https:\/\/www.computer.org\/education\/bodies-of-knowledge\/software-engineering\/"},{"key":"e_1_3_3_3_100_2","doi-asserted-by":"publisher","unstructured":"Michael\u00a0L. Waskom. 2021. seaborn: statistical data visualization. Journal of Open Source Software 6 60 (2021) 3021. 10.21105\/joss.03021Publisher: The Open Journal.","DOI":"10.21105\/joss.03021"},{"key":"e_1_3_3_3_101_2","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.13154979"},{"key":"e_1_3_3_3_102_2","doi-asserted-by":"publisher","unstructured":"Sean\u00a0R. Wilkinson Meznah Aloqalaa Khalid Belhajjame Michael\u00a0R. Crusoe Bruno de Paula\u00a0Kinoshita Luiz Gadelha Daniel Garijo Ove Johan\u00a0Ragnar Gustafsson Nick Juty Sehrish Kanwal Farah\u00a0Zaib Khan Johannes K\u00f6ster Karsten Peters-von Gehlen Line Pouchard Randy\u00a0K. Rannow Stian Soiland-Reyes Nicola Soranzo Shoaib Sufi Ziheng Sun Baiba Vilne Merridee\u00a0A. Wouters Denis Yuen and Carole Goble. 2025. Applying the FAIR Principles to computational workflows. Scientific Data 12 1 (Feb. 2025) 328. 10.1038\/s41597-025-04451-9Publisher: Nature Publishing Group.","DOI":"10.1038\/s41597-025-04451-9"},{"key":"e_1_3_3_3_103_2","doi-asserted-by":"publisher","unstructured":"Gregory Wilson. 2006. Where\u2019s the real bottleneck in scientific computing? American Scientist 94 1 (2006) 5. 10.1511\/2006.57.3473","DOI":"10.1511\/2006.57.3473"},{"key":"e_1_3_3_3_104_2","doi-asserted-by":"publisher","unstructured":"Greg Wilson D.\u00a0A. Aruliah C.\u00a0Titus Brown Neil P.\u00a0Chue Hong Matt Davis Richard\u00a0T. Guy Steven H.\u00a0D. Haddock Kathryn\u00a0D. Huff Ian\u00a0M. Mitchell Mark\u00a0D. Plumbley Ben Waugh Ethan\u00a0P. White and Paul Wilson. 2014. Best practices for scientific computing. PLOS Biology 12 1 (Jan. 2014) e1001745. 10.1371\/journal.pbio.1001745Publisher: Public Library of Science.","DOI":"10.1371\/journal.pbio.1001745"},{"key":"e_1_3_3_3_105_2","doi-asserted-by":"publisher","unstructured":"Greg Wilson Jennifer Bryan Karen Cranston Justin Kitzes Lex Nederbragt and Tracy\u00a0K. Teal. 2017. Good enough practices in scientific computing. PLOS Computational Biology 13 6 (June 2017) e1005510. 10.1371\/journal.pcbi.1005510Publisher: Public Library of Science.","DOI":"10.1371\/journal.pcbi.1005510"},{"key":"e_1_3_3_3_106_2","doi-asserted-by":"publisher","unstructured":"Xin Xiong and Ivor Cribben. 2023. The state of play of reproducibility in statistics: An empirical analysis. The American Statistician 77 2 (April 2023) 115\u2013126. 10.1080\/00031305.2022.2131625","DOI":"10.1080\/00031305.2022.2131625"}],"event":{"name":"ACM REP '25: ACM Conference on Reproducibility and Replicability","location":"Vancouver Canada","acronym":"ACM REP '25","sponsor":["EIGREP Emerging Interest Group on Reproducibility and Replicability"]},"container-title":["Proceedings of the 3rd ACM Conference on Reproducibility and Replicability"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3736731.3746147","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3736731.3746147","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T18:05:28Z","timestamp":1767981928000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3736731.3746147"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,29]]},"references-count":105,"alternative-id":["10.1145\/3736731.3746147","10.1145\/3736731"],"URL":"https:\/\/doi.org\/10.1145\/3736731.3746147","relation":{},"subject":[],"published":{"date-parts":[[2025,7,29]]},"assertion":[{"value":"2025-10-21","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}