[ { "key": "PN5TI3EP", "version": 1218, "library": { "type": "group", "id": 177188, "name": "Reproducible Research", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproducible_research", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/177188/items/PN5TI3EP", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproducible_research/items/PN5TI3EP", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2984591, "username": "khinsen", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/khinsen", "type": "text/html" } } }, "creatorSummary": "Winter et al.", "parsedDate": "2022-11-07", "numChildren": 0 }, "data": { "key": "PN5TI3EP", "version": 1218, "itemType": "conferencePaper", "title": "A retrospective study of one decade of artifact evaluations", "creators": [ { "creatorType": "author", "firstName": "Stefan", "lastName": "Winter" }, { "creatorType": "author", "firstName": "Christopher S.", "lastName": "Timperley" }, { "creatorType": "author", "firstName": "Ben", "lastName": "Hermann" }, { "creatorType": "author", "firstName": "Jürgen", "lastName": "Cito" }, { "creatorType": "author", "firstName": "Jonathan", "lastName": "Bell" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Hilton" }, { "creatorType": "author", "firstName": "Dirk", "lastName": "Beyer" } ], "abstractNote": "", "proceedingsTitle": "Proceedings of the 30th ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering", "conferenceName": "ESEC/FSE '22: 30th ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering", "publisher": "ACM", "place": "Singapore Singapore", "date": "2022-11-07", "eventPlace": "", "volume": "", "issue": "", "numberOfVolumes": "", "pages": "145-156", "series": "", "seriesNumber": "", "DOI": "10.1145/3540250.3549172", "ISBN": "978-1-4503-9413-0", "citationKey": "winterRetrospectiveStudyOne2022", "url": "https://dl.acm.org/doi/10.1145/3540250.3549172", "accessDate": "2026-03-05T09:17:41Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "DOI.org (Crossref)", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "XEI6GA9C" ], "relations": {}, "dateAdded": "2026-03-05T09:19:40Z", "dateModified": "2026-03-05T09:19:40Z" } }, { "key": "MQ2UPEW9", "version": 1216, "library": { "type": "group", "id": 177188, "name": "Reproducible Research", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproducible_research", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/177188/items/MQ2UPEW9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproducible_research/items/MQ2UPEW9", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2984591, "username": "khinsen", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/khinsen", "type": "text/html" } } }, "creatorSummary": "Chatelain et al.", "parsedDate": "2026-01-09", "numChildren": 0 }, "data": { "key": "MQ2UPEW9", "version": 1216, "itemType": "preprint", "title": "The practical impact of numerical variability on structural MRI measures of Parkinson’s disease", "creators": [ { "creatorType": "author", "firstName": "Yohan", "lastName": "Chatelain" }, { "creatorType": "author", "firstName": "Andrzej", "lastName": "Soko-lowski" }, { "creatorType": "author", "firstName": "Madeleine", "lastName": "Sharp" }, { "creatorType": "author", "firstName": "Jean-Baptiste", "lastName": "Poline" }, { "creatorType": "author", "firstName": "Tristan", "lastName": "Glatard" } ], "abstractNote": "Numerical variability is rarely quantified in neuroimaging despite many biomarkers relying on subtle morphometric differences across individuals. We instrumented FreeSurfer, a widely used neuroimaging pipeline, to simulate numerical differences across computational environments, and used it to measure numerical variability in MRI analyses of Parkinson’s disease patients and controls. In multiple cortical and subcortical regions, numerical variation reached nearly one-third of the population variability, altering statistical conclusions about group differences and clinical associations. To address this, we developed a practical tool that estimates the Numerical-Population Variability Ratio (NPVR), enabling researchers to assess the impact of numerical noise in existing studies. By applying this framework to thirteen previously published studies reporting MRI measures of Parkinson’s disease, we quantified the probability of numerically induced false positives in the literature, highlighting a substantial impact of numerical variability on MRI measures of Parkinson’s disease. These results underscore the importance of systematically evaluating numerical stability in neuroimaging.", "genre": "", "repository": "bioRxiv", "archiveID": "", "place": "", "date": "2026-01-09", "series": "", "seriesNumber": "", "DOI": "10.64898/2026.01.09.698203", "citationKey": "chatelainPracticalImpactNumerical2026", "url": "https://www.biorxiv.org/content/10.64898/2026.01.09.698203v1", "accessDate": "2026-01-13T08:00:23Z", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "bioRxiv", "callNumber": "", "rights": "© 2026, Posted by openRxiv. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/", "extra": "ISSN: 2692-8205\nPages: 2026.01.09.698203\nSection: New Results", "tags": [], "collections": [ "R6RSF2NH" ], "relations": {}, "dateAdded": "2026-01-13T08:01:04Z", "dateModified": "2026-02-16T09:49:31Z" } }, { "key": "FCMU44LF", "version": 1216, "library": { "type": "group", "id": 177188, "name": "Reproducible Research", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproducible_research", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/177188/items/FCMU44LF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproducible_research/items/FCMU44LF", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2984591, "username": "khinsen", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/khinsen", "type": "text/html" } } }, "creatorSummary": "Yehudi et al.", "parsedDate": "2025-12-15", "numChildren": 0 }, "data": { "key": "FCMU44LF", "version": 1216, "itemType": "journalArticle", "title": "Research Software Lifecycles and Stages", "creators": [ { "creatorType": "author", "firstName": "Yo", "lastName": "Yehudi" }, { "creatorType": "author", "firstName": "Mikaela", "lastName": "Cashman" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Goedicke" }, { "creatorType": "author", "firstName": "Wilhelm", "lastName": "Hasselbring" }, { "creatorType": "author", "firstName": "Daniel S.", "lastName": "Katz" }, { "creatorType": "author", "firstName": "Sebastian", "lastName": "Müller" }, { "creatorType": "author", "firstName": "Carole", "lastName": "Goble" }, { "creatorType": "author", "firstName": "Caroline", "lastName": "Jay" } ], "abstractNote": "Research software is usually developed by researchers themselves or by software developers working closely with researchers. It is typically developed to meet specific research needs. We develop and evaluate a comprehensive and flexible software lifecycle framework that reflects the unique challenges of research software. In review of related work on commercial and open-source software lifecycles, we observed limitations in addressing the heterogeneous, irregular development patterns, and longitudinal and cyclical nature of many research software projects. An initial model, which was based on case-study research of thirty-eight open-source projects was refined through collaborative discussion at a Dagstuhl seminar, introducing additional state transitions, and expanding details on blocked and active development stages for the specific context of research software. We highlight the overlap and extensions in the new model compared to prior literature and present the evaluation with the research software community. We derive the research software stages from our lifecycle model to categorise research software accordingly.", "publicationTitle": "Electronic Communications of the EASST", "publisher": "", "place": "", "date": "2025-12-15", "volume": "85", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.14279/eceasst.v85.2693", "citationKey": "yehudiResearchSoftwareLifecycles2025", "url": "https://eceasst.org/index.php/eceasst/article/view/2693", "accessDate": "2025-12-16T09:04:27Z", "PMID": "", "PMCID": "", "ISSN": "1863-2122", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "eceasst.org", "callNumber": "", "rights": "Copyright (c) 2025 Yo Yehudi, Mikaela Cashman, Michael Goedicke, Wilhelm Hasselbring, Daniel S. Katz, Sebastian Müller, Carole Goble, Caroline Jay", "extra": "", "tags": [ { "tag": "Development Stage", "type": 1 }, { "tag": "Research Software Engineering", "type": 1 }, { "tag": "Software Lifecyle", "type": 1 }, { "tag": "Software Maturity", "type": 1 } ], "collections": [ "XEI6GA9C" ], "relations": {}, "dateAdded": "2025-12-16T09:05:42Z", "dateModified": "2026-02-16T09:49:31Z" } }, { "key": "LXWPEEAB", "version": 1216, "library": { "type": "group", "id": 177188, "name": "Reproducible Research", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproducible_research", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/177188/items/LXWPEEAB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproducible_research/items/LXWPEEAB", "type": "text/html" } }, "meta": { "createdByUser": { "id": 2984591, "username": "khinsen", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/khinsen", "type": "text/html" } } }, "creatorSummary": "Damerow et al.", "parsedDate": "2025-01-01", "numChildren": 0 }, "data": { "key": "LXWPEEAB", "version": 1216, "itemType": "journalArticle", "title": "Code review in digital humanities", "creators": [ { "creatorType": "author", "firstName": "Julia", "lastName": "Damerow" }, { "creatorType": "author", "firstName": "Rebecca Sutton", "lastName": "Koeser" }, { "creatorType": "author", "firstName": "Jeffrey C", "lastName": "Carver" }, { "creatorType": "author", "firstName": "Malte", "lastName": "Vogl" } ], "abstractNote": "Software and computational methods offer tremendous possibilities for digital humanities research, both accelerating existing work and opening up entirely new questions. However, software also has the potential to introduce new kinds of errors into the research workflow. How do we know that the software developed for a digital humanities project is error free and does what we think it does? Code review is a widespread technique to improve software quality and reduce the number of flaws, where a programmer other than the author reviews and comments on the source code. However, given that many digital humanities developers work in developer teams of one, code review is often not possible. 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In the publication system, several actions reflect this increased attention to rigor. Initiatives by major research funding agencies also emphasize rigor. The U.S. National Science Foundation (NSF), for example, has fostered efforts to promote strategies to increase rigor and transparency in the reporting of results of qualitative research. Here, we offer a brief panorama, permeated by transformations that include increasing initiatives to promote open science. 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"“Total survey error” is a conceptual framework describing statistical error properties of sample survey statistics. Early in the history of sample surveys, it arose as a tool to focus on implications of various gaps between the conditions under which probability samples yielded unbiased estimates of finite population parameters and practical situations in implementing survey design. While the framework permits design-based estimates of various error components, many of the design burdens to produce those estimates are large, and in practice most surveys do not implement them. Further, the framework does not incorporate other, nonstatistical, dimensions of quality that are commonly utilized in evaluating statistical information. The importation of new modeling tools brings new promise to measuring total survey error components, but also new challenges. A lasting value of the total survey error framework is at the design stage of a survey, to attempt a balance of costs and various errors. Indeed, this framework is the central organizing structure of the field of survey methodology.", "publicationTitle": "Public Opinion Quarterly", "publisher": "", "place": "", "date": "01/01/2010", "volume": "74", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "849-879", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Public Opin Q", "DOI": "10.1093/poq/nfq065", "citationKey": "grovesTotalSurveyError2010", "url": "http://poq.oxfordjournals.org/content/74/5/849", "accessDate": "2014-06-29T05:25:14Z", "PMID": "", "PMCID": "", "ISSN": "0033-362X, 1537-5331", "archive": "", "archiveLocation": "", "shortTitle": "Total Survey Error", "language": "en", "libraryCatalog": "poq.oxfordjournals.org", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "E3WEVVWV", "S56Z8TCJ" ], "relations": {}, "dateAdded": "2014-06-29T05:25:14Z", "dateModified": "2026-02-16T09:49:31Z" } }, { "key": "TC8QU8MU", "version": 1215, "library": { "type": "group", "id": 177188, "name": "Reproducible Research", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproducible_research", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/177188/items/TC8QU8MU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproducible_research/items/TC8QU8MU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1944449, "username": "PaTaylor", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/pataylor", "type": "text/html" } } }, "lastModifiedByUser": { "id": 2984591, "username": "khinsen", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/khinsen", "type": "text/html" } } }, "creatorSummary": "Fanelli", "parsedDate": "2010-04-21", "numChildren": 2 }, "data": { "key": "TC8QU8MU", "version": 1215, "itemType": "journalArticle", "title": "Do Pressures to Publish Increase Scientists' Bias? An Empirical Support from US States Data", "creators": [ { "creatorType": "author", "firstName": "Daniele", "lastName": "Fanelli" } ], "abstractNote": "The growing competition and “publish or perish” culture in academia might conflict with the objectivity and integrity of research, because it forces scientists to produce “publishable” results at all costs. Papers are less likely to be published and to be cited if they report “negative” results (results that fail to support the tested hypothesis). Therefore, if publication pressures increase scientific bias, the frequency of “positive” results in the literature should be higher in the more competitive and “productive” academic environments. This study verified this hypothesis by measuring the frequency of positive results in a large random sample of papers with a corresponding author based in the US. Across all disciplines, papers were more likely to support a tested hypothesis if their corresponding authors were working in states that, according to NSF data, produced more academic papers per capita. The size of this effect increased when controlling for state's per capita R&D expenditure and for study characteristics that previous research showed to correlate with the frequency of positive results, including discipline and methodology. Although the confounding effect of institutions' prestige could not be excluded (researchers in the more productive universities could be the most clever and successful in their experiments), these results support the hypothesis that competitive academic environments increase not only scientists' productivity but also their bias. The same phenomenon might be observed in other countries where academic competition and pressures to publish are high.", "publicationTitle": "PLoS ONE", "publisher": "", "place": "", "date": "April 21, 2010", "volume": "5", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "e10271", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS ONE", "DOI": "10.1371/journal.pone.0010271", "citationKey": "fanelliPressuresPublishIncrease2010a", "url": "http://dx.doi.org/10.1371/journal.pone.0010271", "accessDate": "2014-06-29T05:18:47Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Do Pressures to Publish Increase Scientists' Bias?", "language": "", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "53JAB2JV", "S56Z8TCJ" ], "relations": {}, "dateAdded": "2014-06-29T05:18:47Z", "dateModified": "2026-02-16T09:49:31Z" } }, { "key": "9VPZCUXU", 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"creators": [ { "creatorType": "author", "firstName": "Steven M.", "lastName": "Cuss" } ], "abstractNote": "", "publicationTitle": "Proceedings of the National Academy of Sciences", "publisher": "", "place": "", "date": "2014-06-11", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "201407402", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PNAS", "DOI": "10.1073/pnas.1407402111", "citationKey": "cussSystemicFlawsCannot2014", "url": "http://www.pnas.org/content/early/2014/05/30/1407402111", "accessDate": "2014-06-29T05:17:10Z", "PMID": "24920597", "PMCID": "", "ISSN": "0027-8424, 1091-6490", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.pnas.org", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "2M6KJQKA", "S56Z8TCJ" ], "relations": {}, "dateAdded": "2014-06-29T05:17:10Z", "dateModified": "2026-02-16T09:49:31Z" } }, { "key": "AMXRDQXB", 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Tools and strategies for changing the culture", "creators": [ { "creatorType": "author", "firstName": "Ian M.", "lastName": "Mitchell" }, { "creatorType": "author", "firstName": "Randall J.", "lastName": "LeVeque" }, { "creatorType": "author", "firstName": "Victoria", "lastName": "Stodden" } ], "abstractNote": "This article considers the obstacles involved in creating reproducible computational research as well as some efforts and approaches to overcome them.", "publicationTitle": "Computing in Science and Engineering", "publisher": "", "place": "", "date": "2012", "volume": "14", "issue": "4", "pages": "13-17", "ISSN": "1521-9615", "DOI": "", "citationKey": "mitchellReproducibleResearchScientific2012", "url": "", "accessDate": "", "archive": "", "archiveLocation": "", "shortTitle": "Reproducible research for scientific computing", "language": "", "libraryCatalog": "IEEE Computer Society", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "computational complexity", "type": 1 }, { "tag": "computational science and engineering", "type": 1 }, { "tag": "data and code disclosure", "type": 1 }, { "tag": "hidden markov models", "type": 1 }, { "tag": "reproducibility", "type": 1 }, { "tag": "reproducibility of results", "type": 1 }, { "tag": "reproducible research", "type": 1 }, { "tag": "research and development", "type": 1 }, { "tag": "scientific computing", "type": 1 } ], "collections": [ "9BCTVBXA", "S56Z8TCJ" ], "relations": {}, "dateAdded": "2014-06-29T05:41:53Z", "dateModified": "2026-02-16T09:49:31Z" } }, { "key": "MHFQMMKA", "version": 1215, "library": { "type": "group", "id": 177188, "name": "Reproducible Research", "links": { "alternate": { "href": "https://www.zotero.org/groups/reproducible_research", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/177188/items/MHFQMMKA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/reproducible_research/items/MHFQMMKA", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1944449, "username": "PaTaylor", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/pataylor", "type": "text/html" } } }, "lastModifiedByUser": { "id": 2984591, "username": "khinsen", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/khinsen", "type": "text/html" } } }, "creatorSummary": "Gentleman and Temple Lang", "parsedDate": "2007", "numChildren": 2 }, "data": { "key": "MHFQMMKA", "version": 1215, "itemType": "journalArticle", "title": "Statistical Analyses and Reproducible Research", "creators": [ { "creatorType": "author", "firstName": "Robert", "lastName": "Gentleman" }, { "creatorType": "author", "firstName": "Duncan", "lastName": "Temple Lang" } ], "abstractNote": "It is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, and so on with the documents that describe and rely on them. This integration allows readers to both verify and adapt the claims in the documents. Authors can easily reproduce the results in the future, and they can present the document's contents in a different medium, for example, with interactive controls. This article describes a software framework for both authoring and distributing these integrated, dynamic documents that contain text, code, data, and any auxiliary content needed to recreate the computations. The documents are dynamic in that the contents—including figures, tables, and so on—can be recalculated each time a view of the document is generated. Our model treats a dynamic document as a master or “source” document from which one can generate different views in the form of traditional, derived documents for different audiences.We introduce the concept of a compendium as a container for one or more dynamic documents and the different elements needed when processing them, such as code and data. The compendium serves as a means for distributing, managing, and updating the collection.The step from disseminating analyses via a compendium to reproducible research is a small one. By reproducible research, we mean research papers with accompanying software tools that allow the reader to directly reproduce the results and employ the computational methods that are presented in the research paper. Some of the issues involved in paradigms for the production, distribution, and use of such reproducible research are discussed.", "publicationTitle": "Journal of Computational and Graphical Statistics", "publisher": "", "place": "", "date": "2007", "volume": "16", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "1-23", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1198/106186007X178663", "citationKey": "gentlemanStatisticalAnalysesReproducible2007b", "url": "http://dx.doi.org/10.1198/106186007X178663", "accessDate": "2014-06-29T05:34:07Z", "PMID": "", "PMCID": "", "ISSN": "1061-8600", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Taylor and Francis+NEJM", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "9BCTVBXA", "S56Z8TCJ" ], "relations": {}, "dateAdded": "2014-06-29T05:34:07Z", "dateModified": "2026-02-16T09:49:31Z" } }, { "key": "97GN9RVH", 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Our proposal is appropriate for primary studies that involve large-scale searches for rare true positives (i.e. needles in a haystack). Our proposal assigns an $r$-value to each finding; this is the lowest false discovery rate at which the finding can be called replicated. 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