diff --git a/swh.bib b/swh.bib index 2e3e7e3..cd2f576 100644 --- a/swh.bib +++ b/swh.bib @@ -1,1874 +1,1951 @@ -@Article{ 2017whitt, - author = {Whitt, Richard S.}, - title = {"Through A Glass, Darkly" Technical, Policy, and Financial - Actions to Avert the Coming Digital Dark Ages}, - journal = {Santa Clara High Tech. L.J.}, - year = 2017, - volume = 33, - number = 2, - pages = 117, - month = jan, - note = {Available at: - http://digitalcommons.law.scu.edu/chtlj/vol33/iss2/1} -} - @Article{ 1999-beagle-in-commons, - title = {Conceptualizing an information commons}, - author = {Beagle, Donald}, - journal = {The Journal of Academic Librarianship}, - volume = {25}, - number = {2}, - pages = {82--89}, - year = {1999}, - publisher = {Elsevier} + Title = {Conceptualizing an information commons}, + Author = {Beagle, Donald}, + Journal = {The Journal of Academic Librarianship}, + Volume = {25}, + Number = {2}, + Pages = {82--89}, + Year = {1999}, + Publisher = {Elsevier} } @Article{ 2002-lerner-foss-economics, - title = {Some simple economics of open source}, - author = {Lerner, Josh and Tirole, Jean}, - journal = {The journal of industrial economics}, - volume = {50}, - number = {2}, - pages = {197--234}, - year = {2002}, - publisher = {Wiley Online Library} + Title = {Some simple economics of open source}, + Author = {Lerner, Josh and Tirole, Jean}, + Journal = {The journal of industrial economics}, + Volume = {50}, + Number = {2}, + Pages = {197--234}, + Year = {2002}, + Publisher = {Wiley Online Library} } @InProceedings{ 2004-dyba-ese, - title = {Evidence-based software engineering}, - author = {Kitchenham, Barbara A and Dyba, Tore and Jorgensen, + Title = {Evidence-based software engineering}, + Author = {Kitchenham, Barbara A and Dyba, Tore and Jorgensen, Magne}, - booktitle = {Software Engineering, 2004. ICSE 2004. Proceedings. 26th + BookTitle = {Software Engineering, 2004. ICSE 2004. Proceedings. 26th International Conference on}, - pages = {273--281}, - year = {2004}, - organization = {IEEE} + Pages = {273--281}, + Year = {2004}, + Organization = {IEEE} } @InProceedings{ 2006-zeller-msr, - title = {Mining metrics to predict component failures}, - author = {Nagappan, Nachiappan and Ball, Thomas and Zeller, + Title = {Mining metrics to predict component failures}, + Author = {Nagappan, Nachiappan and Ball, Thomas and Zeller, Andreas}, - booktitle = {Proceedings of the 28th international conference on + BookTitle = {Proceedings of the 28th international conference on Software engineering}, - pages = {452--461}, - year = {2006}, - organization = {ACM} + Pages = {452--461}, + Year = {2006}, + Organization = {ACM} } @InProceedings{ 2007-mockus-reuse, - title = {Large-scale code reuse in open source software}, - author = {Mockus, Audris}, - booktitle = {FLOOS'07: 1st International Workshop on Emerging Trends in + Title = {Large-scale code reuse in open source software}, + Author = {Mockus, Audris}, + BookTitle = {FLOOS'07: 1st International Workshop on Emerging Trends in {FLOSS} Research and Development}, - year = {2007}, - organization = {IEEE} + Year = {2007}, + Organization = {IEEE} } @Article{ 2008-paskin-doi, - title = {Digital object identifier ({DOI}) system}, - author = {Paskin, Norman}, - journal = {Encyclopedia of library and information sciences}, - volume = {3}, - pages = {1586--1592}, - year = {2008}, - publisher = {Taylor \& Francis} + Title = {Digital object identifier ({DOI}) system}, + Author = {Paskin, Norman}, + Journal = {Encyclopedia of library and information sciences}, + Volume = {3}, + Pages = {1586--1592}, + Year = {2008}, + Publisher = {Taylor \& Francis} } @InCollection{ 2008-riehle-foss-growth, - title = {The total growth of open source}, - author = {Deshpande, Amit and Riehle, Dirk}, - booktitle = {Open Source Development, Communities and Quality}, - pages = {197--209}, - year = {2008}, - publisher = {Springer} + Title = {The total growth of open source}, + Author = {Deshpande, Amit and Riehle, Dirk}, + BookTitle = {Open Source Development, Communities and Quality}, + Pages = {197--209}, + Year = {2008}, + Publisher = {Springer} } @Article{ 2011-cerf-bitrot, - author = {Cerf, Vinton G.}, - journal = {Proceedings of the IEEE}, - title = {Avoiding "Bit Rot": Long-Term Preservation of Digital + Author = {Cerf, Vinton G.}, + Journal = {Proceedings of the IEEE}, + Title = {Avoiding "Bit Rot": Long-Term Preservation of Digital Information [Point of View]}, - year = {2011}, - month = {June}, - volume = {99}, - number = {6}, - pages = {915-916}, - abstract = {This paper discusses about the long term preservation of + Year = {2011}, + Month = {June}, + Volume = {99}, + Number = {6}, + Pages = {915-916}, + Abstract = {This paper discusses about the long term preservation of digital information. There is something ultimately satisfying about keeping information in digital form. It does not take up much space. It can be replicated for resilient preservation. It can be searched mechanically. It can be used to combine with other material using digital power tools. But this blissful outlook may not comport with the reality of digital information preservation and interpretation.}, - keywords = {information storage;software engineering;bit rot;digital + Keywords = {information storage;software engineering;bit rot;digital information interpretation;digital power tool;resilient preservation;Content management;Data storage systems;Digital systems;Information management;Information retrieval;Libraries;Software;Standards}, - doi = {10.1109/JPROC.2011.2124190}, - issn = {0018-9219} + DOI = {10.1109/JPROC.2011.2124190}, + ISSN = {0018-9219} } @Article{ 2011-peng-reproducible-computations, - title = {Reproducible research in computational science}, - author = {Peng, Roger D}, - journal = {Science}, - volume = {334}, - number = {6060}, - pages = {1226}, - year = {2011}, - publisher = {NIH Public Access} + Title = {Reproducible research in computational science}, + Author = {Peng, Roger D}, + Journal = {Science}, + Volume = {334}, + Number = {6060}, + Pages = {1226}, + Year = {2011}, + Publisher = {NIH Public Access} } @Article{ 2013-gent-recomputation-manifesto, - author = {Ian P. Gent}, - title = {The Recomputation Manifesto}, - journal = {CoRR}, - year = {2013}, - volume = {abs/1304.3674}, - note = {\url{http://www.software.ac.uk/blog/2013-07-09-recomputation-manifesto}} + Author = {Ian P. Gent}, + Title = {The Recomputation Manifesto}, + Journal = {CoRR}, + Year = {2013}, + Volume = {abs/1304.3674}, + Note = {\url{http://www.software.ac.uk/blog/2013-07-09-recomputation-manifesto}} } @InProceedings{ 2013-kirschenbaum-history-exe, - author = {Matthew Kirschenbaum}, - title = {History.exe: How can we preserve the software of today for + Author = {Matthew Kirschenbaum}, + Title = {History.exe: How can we preserve the software of today for historians of tomorrow?}, - crossref = {2013-preserving-exe}, - note = {\url{http://www.slate.com/articles/arts/culturebox/2013/07/how_will_historians_of_the_future_run_ms_word_97_how_can_we_save_it_for.single.html}} + CrossRef = {2013-preserving-exe}, + Note = {\url{http://www.slate.com/articles/arts/culturebox/2013/07/how_will_historians_of_the_future_run_ms_word_97_how_can_we_save_it_for.single.html}} } @Proceedings{ 2013-preserving-exe, - editor = {Trevor Owens}, - title = {Preserving.exe Report: Toward a [US] National Strategy for + Editor = {Trevor Owens}, + Title = {Preserving.exe Report: Toward a [US] National Strategy for Preserving Software}, - year = {2013}, - month = jul, - note = {\url{http://blogs.loc.gov/digitalpreservation/2013/10/preserving-exe-report-toward-a-national-strategy-for-preserving-software/}} + Year = {2013}, + Month = jul, + Note = {\url{http://blogs.loc.gov/digitalpreservation/2013/10/preserving-exe-report-toward-a-national-strategy-for-preserving-software/}} } @Proceedings{ 2014-digital-preservation, - editor = {Erin Engle}, - title = {Digital Preservation 2014: annual meeting of the [US] + Editor = {Erin Engle}, + Title = {Digital Preservation 2014: annual meeting of the [US] National Digital Information Infrastructure and Preservation Program and the [US] National Digital Stewardship Alliance}, - year = {2014}, - month = jul, - note = {\url{http://www.digitalpreservation.gov/meetings/ndiipp14.html}} + Year = {2014}, + Month = jul, + Note = {\url{http://www.digitalpreservation.gov/meetings/ndiipp14.html}} } @Article{ 2014-fursin-collectivemind, - author = {Grigori Fursin and Renato Miceli and Anton Lokhmotov and + Author = {Grigori Fursin and Renato Miceli and Anton Lokhmotov and Michael Gerndt and Marc Baboulin and Allen D. Malony and Zbigniew Chamski and Diego Novillo and Davide Del Vento}, - title = {Collective mind: Towards practical and collaborative + Title = {Collective mind: Towards practical and collaborative auto-tuning}, - journal = {Scientific Programming}, - year = {2014}, - volume = {22}, - number = {4}, - pages = {309--329}, - url = {http://dx.doi.org/10.3233/SPR-140396}, - doi = {10.3233/SPR-140396}, + Journal = {Scientific Programming}, + Year = {2014}, + Volume = {22}, + Number = {4}, + Pages = {309--329}, + URL = {http://dx.doi.org/10.3233/SPR-140396}, + DOI = {10.3233/SPR-140396}, timestamp = {Tue, 30 Sep 2014 17:29:46 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/journals/sp/FursinMLGBMCNV14}, bibsource = {dblp computer science bibliography, http://dblp.org} } @InProceedings{ 2014-kirschenbaum-software-thing, - author = {Matthew Kirschenbaum}, - title = {Software, It's a Thing}, - crossref = {2014-digital-preservation}, - note = {\url{https://medium.com/@mkirschenbaum/software-its-a-thing-a550448d0ed3}} + Author = {Matthew Kirschenbaum}, + Title = {Software, It's a Thing}, + CrossRef = {2014-digital-preservation}, + Note = {\url{https://medium.com/@mkirschenbaum/software-its-a-thing-a550448d0ed3}} } @TechReport{ 2014-rousseau-tempsdulogiciel, - title = {Le temps du logiciel}, - author = {Magali Fitzgibbon and Luc Grateau and Guillaume Rousseau}, - institution = {Institut National de la Propriété Industrielle}, - year = {2014} + Title = {Le temps du logiciel}, + Author = {Magali Fitzgibbon and Luc Grateau and Guillaume Rousseau}, + Institution = {Institut National de la Propriété Industrielle}, + Year = {2014} +} + +@Article{ 2017whitt, + Author = {Whitt, Richard S.}, + Title = {"Through A Glass, Darkly" Technical, Policy, and Financial + Actions to Avert the Coming Digital Dark Ages}, + Journal = {Santa Clara High Tech. L.J.}, + Year = 2017, + Volume = 33, + Number = 2, + Pages = 117, + Month = jan, + Note = {Available at: + http://digitalcommons.law.scu.edu/chtlj/vol33/iss2/1} } @Article{ anderson2015digital, - title = {The digital dark age}, - author = {Anderson, David}, - journal = {Communications of the ACM}, - volume = {58}, - number = {12}, - pages = {20--23}, - year = {2015}, - publisher = {ACM} + Title = {The digital dark age}, + Author = {Anderson, David}, + Journal = {Communications of the ACM}, + Volume = {58}, + Number = {12}, + Pages = {20--23}, + Year = {2015}, + Publisher = {ACM} } @Misc{ ark, - author = {The California Digital Library}, - title = {Archival Resource Key}, - url = {http://n2t.net/e/ark_ids.html}, - year = {2001} + Author = {The California Digital Library}, + Title = {Archival Resource Key}, + URL = {http://n2t.net/e/ark_ids.html}, + Year = {2001} } @Article{ Arms01, - author = {William Y. Arms}, - title = {Uniform resource names: handles, PURLs, and digital object + Author = {William Y. Arms}, + Title = {Uniform resource names: handles, PURLs, and digital object identifiers}, - journal = {Commun. {ACM}}, - volume = {44}, - number = {5}, - pages = {68}, - year = {2001}, - url = {http://doi.acm.org/10.1145/374308.375358}, - doi = {10.1145/374308.375358}, + Journal = {Commun. {ACM}}, + Volume = {44}, + Number = {5}, + Pages = {68}, + Year = {2001}, + URL = {http://doi.acm.org/10.1145/374308.375358}, + DOI = {10.1145/374308.375358}, timestamp = {Thu, 20 Nov 2003 13:05:23 +0100}, biburl = {http://dblp2.uni-trier.de/rec/bib/journals/cacm/Arms01}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Article{ armscacm2001, - author = {Arms, William Y.}, - title = {Uniform Resource Names: Handles, PURLs, and Digital Object + Author = {Arms, William Y.}, + Title = {Uniform Resource Names: Handles, PURLs, and Digital Object Identifiers}, - journal = {Commun. ACM}, + Journal = {Commun. ACM}, issue_date = {May 2001}, - volume = {44}, - number = {5}, - month = may, - year = {2001}, - issn = {0001-0782}, - pages = {68--}, - url = {http://doi.acm.org/10.1145/374308.375358}, - doi = {10.1145/374308.375358}, + Volume = {44}, + Number = {5}, + Month = may, + Year = {2001}, + ISSN = {0001-0782}, + Pages = {68--}, + URL = {http://doi.acm.org/10.1145/374308.375358}, + DOI = {10.1145/374308.375358}, acmid = {375358}, - publisher = {ACM}, - address = {New York, NY, USA} + Publisher = {ACM}, + Address = {New York, NY, USA} } @InProceedings{ arnab2006, - author = {Arnab, Alapan and Hutchison, Andrew}, - title = {Verifiable Digital Object Identity System}, - booktitle = {Proceedings of the ACM Workshop on Digital Rights + Author = {Arnab, Alapan and Hutchison, Andrew}, + Title = {Verifiable Digital Object Identity System}, + BookTitle = {Proceedings of the ACM Workshop on Digital Rights Management}, - series = {DRM '06}, - year = {2006}, - isbn = {1-59593-555-X}, - location = {Alexandria, Virginia, USA}, - pages = {19--26}, + Series = {DRM '06}, + Year = {2006}, + ISBN = {1-59593-555-X}, + Location = {Alexandria, Virginia, USA}, + Pages = {19--26}, numpages = {8}, - url = {http://doi.acm.org/10.1145/1179509.1179514}, - doi = {10.1145/1179509.1179514}, + URL = {http://doi.acm.org/10.1145/1179509.1179514}, + DOI = {10.1145/1179509.1179514}, acmid = {1179514}, - publisher = {ACM}, - address = {New York, NY, USA}, - keywords = {data identity, digital signatures, handle system, + Publisher = {ACM}, + Address = {New York, NY, USA}, + Keywords = {data identity, digital signatures, handle system, identifier, identity verification, vdoi} } +@Article{ Baker2016, + DOI = {10.1038/533452a}, + URL = {https://doi.org/10.1038/533452a}, + Year = {2016}, + Month = {may}, + Publisher = {Springer Nature}, + Volume = {533}, + Number = {7604}, + Pages = {452--454}, + Author = {Monya Baker}, + Title = {1, 500 scientists lift the lid on reproducibility}, + Journal = {Nature} +} + +@Article{ Biagioli2016, + Author = {Biagioli, Mario}, + Year = {2016}, + Month = {07}, + Pages = {201-201}, + Title = {Watch out for cheats in citation game}, + Volume = {535}, + Journal = {Nature}, + DOI = {10.1038/535201a} +} + @Misc{ bitcoin, - author = {Satoshi Nakamoto}, - title = {Bitcoin: A Peer-to-Peer Electronic Cash System}, - url = {https://bitcoin.org/bitcoin.pdf}, - year = {2010}, - note = {retrieved 09 April 2018} + Author = {Satoshi Nakamoto}, + Title = {Bitcoin: A Peer-to-Peer Electronic Cash System}, + URL = {https://bitcoin.org/bitcoin.pdf}, + Year = {2010}, + Note = {retrieved 09 April 2018} } @Article{ bizer2009linked-data, - title = {Linked data-the story so far}, - author = {Bizer, Christian and Heath, Tom and Berners-Lee, Tim}, - journal = {Semantic services, interoperability and web applications: + Title = {Linked data-the story so far}, + Author = {Bizer, Christian and Heath, Tom and Berners-Lee, Tim}, + Journal = {Semantic services, interoperability and web applications: emerging concepts}, - pages = {205--227}, - year = {2009} + Pages = {205--227}, + Year = {2009} +} + +@Article{ Borgman2012, + Author = {Christine L. Borgman and Jillian C. Wallis and Matthew S. + Mayernik}, + Title = {Who's Got the Data? Interdependencies in Science and + Technology Collaborations}, + Journal = {Computer Supported Cooperative Work}, + Volume = {21}, + Number = {6}, + Pages = {485--523}, + Year = {2012}, + URL = {https://doi.org/10.1007/s10606-012-9169-z}, + DOI = {10.1007/s10606-012-9169-z}, + timestamp = {Mon, 05 Jun 2017 20:44:38 +0200}, + biburl = {https://dblp.org/rec/bib/journals/cscw/BorgmanWM12}, + bibsource = {dblp computer science bibliography, https://dblp.org} } @Article{ BugRepair2017, - author = {Matias Martinez and Thomas Durieux and Romain Sommerard + Author = {Matias Martinez and Thomas Durieux and Romain Sommerard and Jifeng Xuan and Martin Monperrus}, - title = {Automatic repair of real bugs in java: a large-scale + Title = {Automatic repair of real bugs in java: a large-scale experiment on the defects4j dataset}, - journal = {Empirical Software Engineering}, - volume = {22}, - number = {4}, - pages = {1936--1964}, - year = {2017}, - url = {https://doi.org/10.1007/s10664-016-9470-4}, - doi = {10.1007/s10664-016-9470-4}, + Journal = {Empirical Software Engineering}, + Volume = {22}, + Number = {4}, + Pages = {1936--1964}, + Year = {2017}, + URL = {https://doi.org/10.1007/s10664-016-9470-4}, + DOI = {10.1007/s10664-016-9470-4}, timestamp = {Sat, 16 Sep 2017 12:05:10 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/journals/ese/MartinezDSXM17}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Article{ cacm:wikidata, - title = {Wikidata: a free collaborative knowledgebase}, - author = {Vrande{\v{c}}i{\'c}, Denny and Kr{\"o}tzsch, Markus}, - journal = {Communications of the ACM}, - volume = {57}, - number = {10}, - pages = {78--85}, - year = {2014}, - publisher = {ACM} + Title = {Wikidata: a free collaborative knowledgebase}, + Author = {Vrande{\v{c}}i{\'c}, Denny and Kr{\"o}tzsch, Markus}, + Journal = {Communications of the ACM}, + Volume = {57}, + Number = {10}, + Pages = {78--85}, + Year = {2014}, + Publisher = {ACM} } @InProceedings{ Candoia2016, - author = {Nitin M. Tiwari and Ganesha Upadhyaya and Hridesh Rajan}, - title = {Candoia: a platform and ecosystem for mining software + Author = {Nitin M. Tiwari and Ganesha Upadhyaya and Hridesh Rajan}, + Title = {Candoia: a platform and ecosystem for mining software repositories tools}, - booktitle = {Proceedings of the 38th International Conference on + BookTitle = {Proceedings of the 38th International Conference on Software Engineering, {ICSE} 2016}, - pages = {759--764}, - year = {2016}, - crossref = {DBLP:conf/icse/2016c}, - url = {http://doi.acm.org/10.1145/2889160.2892662}, - doi = {10.1145/2889160.2892662}, + Pages = {759--764}, + Year = {2016}, + CrossRef = {DBLP:conf/icse/2016c}, + URL = {http://doi.acm.org/10.1145/2889160.2892662}, + DOI = {10.1145/2889160.2892662}, timestamp = {Fri, 24 Mar 2017 09:33:29 +0100}, biburl = {http://dblp.uni-trier.de/rec/bib/conf/icse/TiwariUR16}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Article{ castagne2013consider, - title = {Consider the Source: The Value of Source Code to Digital + Title = {Consider the Source: The Value of Source Code to Digital Preservation Strategies}, - author = {Castagn{\'e}, Michel}, - journal = {SLIS Student Research Journal}, - volume = {2}, - number = {2}, - pages = {5}, - year = {2013} + Author = {Castagn{\'e}, Michel}, + Journal = {SLIS Student Research Journal}, + Volume = {2}, + Number = {2}, + Pages = {5}, + Year = {2013} } @Article{ cerf2011avoiding, - title = {Avoiding" Bit Rot": Long-Term Preservation of Digital + Title = {Avoiding" Bit Rot": Long-Term Preservation of Digital Information [Point of View]}, - author = {Cerf, Vinton G}, - journal = {Proceedings of the IEEE}, - volume = {99}, - number = {6}, - pages = {915--916}, - year = {2011}, - publisher = {IEEE} + Author = {Cerf, Vinton G}, + Journal = {Proceedings of the IEEE}, + Volume = {99}, + Number = {6}, + Pages = {915--916}, + Year = {2011}, + Publisher = {IEEE} +} + +@Book{ CGAL, + Title = {{CGAL} User and Reference Manual}, + Author = {{The CGAL Project}}, + Publisher = {{CGAL Editorial Board}}, + Edition = {{4.14}}, + Year = 2019, + URL = {https://doc.cgal.org/4.14/Manual/packages.html} +} + +@Article{ Collberg2016, + DOI = {10.1145/2812803}, + URL = {https://doi.org/10.1145/2812803}, + Year = {2016}, + Month = {feb}, + Publisher = {Association for Computing Machinery ({ACM})}, + Volume = {59}, + Number = {3}, + Pages = {62--69}, + Author = {Christian Collberg and Todd A. Proebsting}, + Title = {Repeatability in computer systems research}, + Journal = {Communications of the {ACM}} } @Article{ CollbergCACM2016, - author = {Christian S. Collberg and Todd A. Proebsting}, - title = {Repeatability in computer systems research}, - journal = {Commun. {ACM}}, - volume = {59}, - number = {3}, - pages = {62--69}, - year = {2016}, - url = {http://doi.acm.org/10.1145/2812803}, - doi = {10.1145/2812803}, + Author = {Christian S. Collberg and Todd A. Proebsting}, + Title = {Repeatability in computer systems research}, + Journal = {Commun. {ACM}}, + Volume = {59}, + Number = {3}, + Pages = {62--69}, + Year = {2016}, + URL = {http://doi.acm.org/10.1145/2812803}, + DOI = {10.1145/2812803}, timestamp = {Thu, 25 Feb 2016 18:39:51 +0100}, biburl = {http://dblp.uni-trier.de/rec/bib/journals/cacm/CollbergP16}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Misc{ credit, - author = "CASRAI", - title = "The CRediT Taxonomy", - year = "2015", - url = "https://casrai.org/credit/", - note = "retrieved January 2019" + Author = "CASRAI", + Title = "The CRediT Taxonomy", + Year = "2015", + URL = "https://casrai.org/credit/", + Note = "retrieved January 2019" } @Misc{ crossref, - author = "Crossref", - title = "DOI Fees", - year = "2017", - url = "https://web.archive.org/web/20180129114723/https://www.crossref.org/fees/", - note = "Online; retrieved 09 April 2018" + Author = "Crossref", + Title = "DOI Fees", + Year = "2017", + URL = "https://web.archive.org/web/20180129114723/https://www.crossref.org/fees/", + Note = "Online; retrieved 09 April 2018" +} + +@Article{ Dagstuhl-Artefacts-2016, + Author = {Bruce R. Childers and Grigori Fursin and Shriram + Krishnamurthi and Andreas Zeller}, + Title = {{Artifact Evaluation for Publications (Dagstuhl + Perspectives Workshop 15452)}}, + Pages = {29--35}, + Journal = {Dagstuhl Reports}, + ISSN = {2192-5283}, + Year = {2016}, + Volume = {5}, + Number = {11}, + Editor = {Bruce R. Childers and Grigori Fursin and Shriram + Krishnamurthi and Andreas Zeller}, + Publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik}, + Address = {Dagstuhl, Germany}, + URL = {http://drops.dagstuhl.de/opus/volltexte/2016/5762}, + urn = {urn:nbn:de:0030-drops-57620}, + DOI = {10.4230/DagRep.5.11.29}, + Annote = {Keywords: Computer systems, artifacts, reproducibility, + archive} } @Article{ DagstuhlArtifactEvaluation, - author = {Bruce R. Childers and Grigori Fursin and Shriram + Author = {Bruce R. Childers and Grigori Fursin and Shriram Krishnamurthi and Andreas Zeller}, - title = {{Artifact Evaluation for Publications (Dagstuhl + Title = {{Artifact Evaluation for Publications (Dagstuhl Perspectives Workshop 15452)}}, - pages = {29--35}, - journal = {Dagstuhl Reports}, - issn = {2192-5283}, - year = {2016}, - volume = {5}, - number = {11}, - editor = {Bruce R. Childers and Grigori Fursin and Shriram + Pages = {29--35}, + Journal = {Dagstuhl Reports}, + ISSN = {2192-5283}, + Year = {2016}, + Volume = {5}, + Number = {11}, + Editor = {Bruce R. Childers and Grigori Fursin and Shriram Krishnamurthi and Andreas Zeller}, - publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik}, - address = {Dagstuhl, Germany}, - url = {http://drops.dagstuhl.de/opus/volltexte/2016/5762}, + Publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik}, + Address = {Dagstuhl, Germany}, + URL = {http://drops.dagstuhl.de/opus/volltexte/2016/5762}, urn = {urn:nbn:de:0030-drops-57620}, - doi = {10.4230/DagRep.5.11.29}, - annote = {Keywords: Computer systems, artifacts, reproducibility, + DOI = {10.4230/DagRep.5.11.29}, + Annote = {Keywords: Computer systems, artifacts, reproducibility, archive} } @Article{ DagstuhlEngineeringResearchSoftware, - author = {Alice Allen and Cecilia R. Aragon and Christoph Becker and + Author = {Alice Allen and Cecilia R. Aragon and Christoph Becker and Jeffrey Carver and Andrei Chis and Beno{\^{\i}}t Combemale and Mike Croucher and Kevin Crowston and Daniel Garijo and Ashish Gehani and Carole A. Goble and Robert Haines and Robert Hirschfeld and James Howison and Kathryn D. Huff and Caroline Jay and Daniel S. Katz and Claude Kirchner and Katie Kuksenok and Ralf L{\"{a}}mmel and Oscar Nierstrasz and Matthew Turk and Rob van Nieuwpoort and Matthew Vaughn and Jurgen J. Vinju}, - title = {Engineering Academic Software (Dagstuhl Perspectives + Title = {Engineering Academic Software (Dagstuhl Perspectives Workshop 16252)}, - journal = {Dagstuhl Manifestos}, - volume = {6}, - number = {1}, - pages = {1--20}, - year = {2017}, - url = {https://doi.org/10.4230/DagMan.6.1.1}, - doi = {10.4230/DagMan.6.1.1}, + Journal = {Dagstuhl Manifestos}, + Volume = {6}, + Number = {1}, + Pages = {1--20}, + Year = {2017}, + URL = {https://doi.org/10.4230/DagMan.6.1.1}, + DOI = {10.4230/DagMan.6.1.1}, timestamp = {Wed, 02 Aug 2017 20:15:49 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/journals/dagstuhl-manifestos/AllenABCCCCCGGG17}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Article{ dappert, - author = {Dappert, A. et al.}, - title = {Connecting the Persistent Identifier Ecosystem: Building + Author = {Dappert, A. et al.}, + Title = {Connecting the Persistent Identifier Ecosystem: Building the Technical and Human Infrastructure for Open Research}, - journal = {Data Science Journal}, - volume = {16}, - pages = {28}, - year = 2017, + Journal = {Data Science Journal}, + Volume = {16}, + Pages = {28}, + Year = 2017, id = {10.5334/dsj-2017-028}, - url = {http://doi.org/10.5334/dsj-2017-028} + URL = {http://doi.org/10.5334/dsj-2017-028} } @Article{ davidson2006, - author = {Davidson, J}, - title = {Persistent Identifiers}, - journal = {DCC Briefing Papers: Introduction to Curation. Edinburgh: + Author = {Davidson, J}, + Title = {Persistent Identifiers}, + Journal = {DCC Briefing Papers: Introduction to Curation. Edinburgh: Digital Curation Centre. Handle: 1842/3368.}, - year = 2006, + Year = 2006, id = {Handle: 1842/3368}, - url = {http://www.dcc.ac.uk/resources/briefing-papers/introduction-curation} + URL = {http://www.dcc.ac.uk/resources/briefing-papers/introduction-curation} } @Proceedings{ DBLP:conf/crypto/1987, - editor = {Carl Pomerance}, - title = {Advances in Cryptology - {CRYPTO} '87, {A} Conference on + Editor = {Carl Pomerance}, + Title = {Advances in Cryptology - {CRYPTO} '87, {A} Conference on the Theory and Applications of Cryptographic Techniques, Santa Barbara, California, USA, August 16-20, 1987, Proceedings}, - series = {Lecture Notes in Computer Science}, - volume = {293}, - publisher = {Springer}, - year = {1988}, - url = {https://doi.org/10.1007/3-540-48184-2}, - doi = {10.1007/3-540-48184-2}, - isbn = {3-540-18796-0}, + Series = {Lecture Notes in Computer Science}, + Volume = {293}, + Publisher = {Springer}, + Year = {1988}, + URL = {https://doi.org/10.1007/3-540-48184-2}, + DOI = {10.1007/3-540-48184-2}, + ISBN = {3-540-18796-0}, timestamp = {Fri, 19 May 2017 13:10:47 +0200}, biburl = {https://dblp.org/rec/bib/conf/crypto/1987}, bibsource = {dblp computer science bibliography, https://dblp.org} } +@Proceedings{ DBLP:conf/crypto/1987, + Editor = {Carl Pomerance}, + Title = {Advances in Cryptology - {CRYPTO} '87, {A} Conference on + the Theory and Applications of Cryptographic Techniques}, + Series = {Lecture Notes in Computer Science}, + Volume = {293}, + Publisher = {Springer}, + Year = {1988}, + URL = {https://doi.org/10.1007/3-540-48184-2}, + DOI = {10.1007/3-540-48184-2}, + ISBN = {3-540-18796-0}, + timestamp = {Fri, 19 May 2017 13:10:47 +0200}, + biburl = {https://dblp.org/rec/bib/conf/crypto/1987}, + bibsource = {dblp computer science bibliography, https://dblp.org} +} + +@Proceedings{ DBLP:conf/icms/2018, + Editor = {James H. Davenport and Manuel Kauers and George Labahn and + Josef Urban}, + Title = {Mathematical Software - {ICMS} 2018 - 6th International + Conference, South Bend, IN, USA, July 24-27, 2018, + Proceedings}, + Series = {Lecture Notes in Computer Science}, + Volume = {10931}, + Publisher = {Springer}, + Year = {2018}, + URL = {https://doi.org/10.1007/978-3-319-96418-8}, + DOI = {10.1007/978-3-319-96418-8}, + ISBN = {978-3-319-96417-1}, + timestamp = {Tue, 17 Jul 2018 12:46:33 +0200}, + biburl = {https://dblp.org/rec/bib/conf/icms/2018}, + bibsource = {dblp computer science bibliography, https://dblp.org} +} + @Proceedings{ DBLP:conf/icse/2016c, - editor = {Laura K. Dillon and Willem Visser and Laurie Williams}, - title = {Proceedings of the 38th International Conference on + Editor = {Laura K. Dillon and Willem Visser and Laurie Williams}, + Title = {Proceedings of the 38th International Conference on Software Engineering, {ICSE} 2016, Austin, TX, USA, May 14-22, 2016 - Companion Volume}, - publisher = {{ACM}}, - year = {2016}, - url = {http://dl.acm.org/citation.cfm?id=2889160}, - isbn = {978-1-4503-4205-6}, + Publisher = {{ACM}}, + Year = {2016}, + URL = {http://dl.acm.org/citation.cfm?id=2889160}, + ISBN = {978-1-4503-4205-6}, timestamp = {Fri, 24 Mar 2017 09:33:29 +0100}, biburl = {http://dblp.uni-trier.de/rec/bib/conf/icse/2016c}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Proceedings{ DBLP:conf/msr/2012, - editor = {Michele Lanza and Massimiliano Di Penta and Tao Xie}, - title = {9th {IEEE} Working Conference of Mining Software + Editor = {Michele Lanza and Massimiliano Di Penta and Tao Xie}, + Title = {9th {IEEE} Working Conference of Mining Software Repositories, {MSR} 2012, June 2-3, 2012, Zurich, Switzerland}, - publisher = {{IEEE} Computer Society}, - year = {2012}, - url = {http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6220358}, - isbn = {978-1-4673-1761-0}, + Publisher = {{IEEE} Computer Society}, + Year = {2012}, + URL = {http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6220358}, + ISBN = {978-1-4673-1761-0}, timestamp = {Wed, 13 May 2015 17:45:20 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/conf/msr/2012}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Proceedings{ DBLP:conf/msr/2017, - editor = {Jes{\'{u}}s M. Gonzalez{-}Barahona and Abram Hindle and + Editor = {Jes{\'{u}}s M. Gonzalez{-}Barahona and Abram Hindle and Lin Tan}, - title = {Proceedings of the 14th International Conference on Mining + Title = {Proceedings of the 14th International Conference on Mining Software Repositories, {MSR} 2017, Buenos Aires, Argentina, May 20-28, 2017}, - publisher = {{IEEE} Computer Society}, - year = {2017}, - url = {http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=7959735}, - isbn = {978-1-5386-1544-7}, + Publisher = {{IEEE} Computer Society}, + Year = {2017}, + URL = {http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=7959735}, + ISBN = {978-1-5386-1544-7}, timestamp = {Fri, 07 Jul 2017 14:06:35 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/conf/msr/2017}, bibsource = {dblp computer science bibliography, http://dblp.org} } @InProceedings{ debsources-esem-2014, - author = {Caneill, Matthieu and Stefano Zacchiroli}, - title = {Debsources: Live and Historical Views on Macro-Level + Author = {Caneill, Matthieu and Stefano Zacchiroli}, + Title = {Debsources: Live and Historical Views on Macro-Level Software Evolution}, - publisher = {ACM}, - year = {2014}, - isbn = {978-1-4503-2774-9}, - doi = {10.1145/2652524.2652528}, - booktitle = {ESEM 2014: 8th International Symposium on Empirical + Publisher = {ACM}, + Year = {2014}, + ISBN = {978-1-4503-2774-9}, + DOI = {10.1145/2652524.2652528}, + BookTitle = {ESEM 2014: 8th International Symposium on Empirical Software Engineering and Measurement}, - note = {\url{http://sources.debian.net}} + Note = {\url{http://sources.debian.net}} } @Misc{ didw3c, - author = "the Contributors to the Decentralized Identifiers (DIDs)", - title = "Decentralized Identifiers (DIDs) v0.9", - year = "2018", - url = "https://w3c-ccg.github.io/did-spec/", - note = "Online; Draft Community Group Report 02 April 2018" + Author = "the Contributors to the Decentralized Identifiers (DIDs)", + Title = "Decentralized Identifiers (DIDs) v0.9", + Year = "2018", + URL = "https://w3c-ccg.github.io/did-spec/", + Note = "Online; Draft Community Group Report 02 April 2018" } @Article{ dns, - author = {J. Charles}, - journal = {IEEE Software}, - title = {Web interests tangle over DNS proposal}, - year = {1997}, - volume = {14}, - number = {4}, - pages = {100-105}, - keywords = {Contracts;Domain Name System;IP networks;Job shop + Author = {J. Charles}, + Journal = {IEEE Software}, + Title = {Web interests tangle over DNS proposal}, + Year = {1997}, + Volume = {14}, + Number = {4}, + Pages = {100-105}, + Keywords = {Contracts;Domain Name System;IP networks;Job shop scheduling;Proposals;Registers;Stability;Trademarks;US Government;Web and internet services}, - doi = {10.1109/MS.1997.595968}, - issn = {0740-7459}, - month = {July} + DOI = {10.1109/MS.1997.595968}, + ISSN = {0740-7459}, + Month = {July} } @Article{ doi, - title = {Digital object identifier ({DOI}) system}, - author = {Paskin, Norman}, - journal = {Encyclopedia of library and information sciences}, - volume = {3}, - pages = {1586--1592}, - year = {2008}, - publisher = {Taylor \& Francis} + Title = {Digital object identifier ({DOI}) system}, + Author = {Paskin, Norman}, + Journal = {Encyclopedia of library and information sciences}, + Volume = {3}, + Pages = {1586--1592}, + Year = {2008}, + Publisher = {Taylor \& Francis} } @Misc{ earkproject, key = {E-ARK}, - title = {E-ARK (European Archival Records and Knowledge + Title = {E-ARK (European Archival Records and Knowledge Preservation) Project}, - year = {2014}, - howpublished = {\url{http://www.eark-project.com/}} + Year = {2014}, + HowPublished = {\url{http://www.eark-project.com/}} +} + +@InProceedings{ edos2006wsl, + Address = {Porto Alegre, Brazil}, + Author = {Boender, Jaap and Di Cosmo, Roberto and Durak, Berke and + Leroy, Xavier and Mancinelli, Fabio and Morgado, Mario and + Pinheiro, David and Treinen, Ralf and Trezentos, Paulo and + Vouillon, J{\'e}r{\^o}me}, + BookTitle = {{P}roceedings of the 7th {I}nternational {W}orkshop on + {F}ree {S}oftware ({IWFS}'06)}, + Editor = {Berger, Olivier}, + Month = apr, + x-topic = "softeng", + Title = {News from the {EDOS} project: improving the maintenance of + free software distributions}, + urllocal = {http://www.dicosmo.org/Articles/wsl06.pdf}, + URL = {http://www.dicosmo.org/Articles/wsl06.pdf}, + Year = {2006}, + dmi-category = {autc}, + Pages = {199 -- 207}, + ISBN = {857669066-7} } @Article{ FLOSSmole, - author = {James Howison and Megan Conklin and Kevin Crowston}, - title = {FLOSSmole: {A} Collaborative Repository for {FLOSS} + Author = {James Howison and Megan Conklin and Kevin Crowston}, + Title = {FLOSSmole: {A} Collaborative Repository for {FLOSS} Research Data and Analyses}, - journal = {{IJITWE}}, - volume = {1}, - number = {3}, - pages = {17--26}, - year = {2006}, - url = {http://dx.doi.org/10.4018/jitwe.2006070102}, - doi = {10.4018/jitwe.2006070102}, + Journal = {{IJITWE}}, + Volume = {1}, + Number = {3}, + Pages = {17--26}, + Year = {2006}, + URL = {http://dx.doi.org/10.4018/jitwe.2006070102}, + DOI = {10.4018/jitwe.2006070102}, timestamp = {Fri, 09 Nov 2012 14:42:08 +0100}, biburl = {http://dblp.uni-trier.de/rec/bib/journals/ijitwe/HowisonCC06}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Article{ force11citationprinciples, - author = {Smith AM and Katz DS and Niemeyer KE}, - institution = {FORCE11 Software Citation Working Group}, - year = 2016, - title = "Software citation principles", - journal = {PeerJ Computer Science}, - volume = {2:e86}, - doi = "https://doi.org/10.7717/peerj-cs.86" + Author = {Smith AM and Katz DS and Niemeyer KE}, + Institution = {FORCE11 Software Citation Working Group}, + Year = 2016, + Title = "Software citation principles", + Journal = {PeerJ Computer Science}, + Volume = {2:e86}, + DOI = "https://doi.org/10.7717/peerj-cs.86" } @InProceedings{ GHTorrent, - author = {Georgios Gousios and Diomidis Spinellis}, - title = {GHTorrent: Github's data from a firehose}, - booktitle = {9th {IEEE} Working Conference of Mining Software + Author = {Georgios Gousios and Diomidis Spinellis}, + Title = {GHTorrent: Github's data from a firehose}, + BookTitle = {9th {IEEE} Working Conference of Mining Software Repositories, {MSR}}, - pages = {12--21}, - year = {2012}, - crossref = {DBLP:conf/msr/2012}, - url = {http://dx.doi.org/10.1109/MSR.2012.6224294}, - doi = {10.1109/MSR.2012.6224294}, + Pages = {12--21}, + Year = {2012}, + CrossRef = {DBLP:conf/msr/2012}, + URL = {http://dx.doi.org/10.1109/MSR.2012.6224294}, + DOI = {10.1109/MSR.2012.6224294}, timestamp = {Wed, 13 May 2015 17:45:20 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/conf/msr/GousiosS12}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Article{ gil2016, - author = {Gil, Yolanda and H. David, Cédric and Demir, Ibrahim and + Author = {Gil, Yolanda and H. David, Cédric and Demir, Ibrahim and Essawy, Bakinam and Fulweiler, Wally and Goodall, Jonathan and Karlstrom, Leif and Lee, Huikyo and Mills, Heath and Oh, Ji-Hyun and Pierce, Suzanne and Pope, Allen and Tzeng, Mimi and Villamizar, Sandra and Yu, Xuan}, - year = {2016}, - month = {07}, - pages = {}, - title = {Towards the Geoscience Paper of the Future: Best Practices + Year = {2016}, + Month = {07}, + Pages = {}, + Title = {Towards the Geoscience Paper of the Future: Best Practices for Documenting and Sharing Research from Data to Software to Provenance: Geoscience Paper of the Future}, - volume = {3}, - journal = {Earth and Space Science}, - doi = {10.1002/2015EA000136} + Volume = {3}, + Journal = {Earth and Space Science}, + DOI = {10.1002/2015EA000136} } @Misc{ git, - author = {Git community}, - title = "Git version control system", - year = "2005", - url = "https://git-scm.com/", - note = "retrieved 09 April 2018" + Author = {Git community}, + Title = "Git version control system", + Year = "2005", + URL = "https://git-scm.com/", + Note = "retrieved 09 April 2018" } @Misc{ gitorious-shutdown, - author = {GitLab}, - title = {GitLab acquires Gitorious to bolster its on premises code + Author = {GitLab}, + Title = {GitLab acquires Gitorious to bolster its on premises code collaboration platform}, - year = {2015}, - howpublished = {\url{https://about.gitlab.com/2015/03/03/gitlab-acquires-gitorious/}} + Year = {2015}, + HowPublished = {\url{https://about.gitlab.com/2015/03/03/gitlab-acquires-gitorious/}} } @Misc{ gnu:gpl2, - author = {GNU}, - title = "GNU General Public License, version 2", - year = "1991", - url = "https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html", - note = "retrieved September 2015" + Author = {GNU}, + Title = "GNU General Public License, version 2", + Year = "1991", + URL = "https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html", + Note = "retrieved September 2015" } @Misc{ google-code-shutdown, - author = {Google Project Hosting}, - title = {Bidding farewell to Google Code}, - year = {2015}, - howpublished = {\url{https://opensource.googleblog.com/2015/03/farewell-to-google-code.html}} + Author = {Google Project Hosting}, + Title = {Bidding farewell to Google Code}, + Year = {2015}, + HowPublished = {\url{https://opensource.googleblog.com/2015/03/farewell-to-google-code.html}} } @Misc{ GPLCompliance, - title = "A Practical Guide to {GPL} Compliance", - author = "Bradley M. Kuhn and Aaron Williamson and Karen M. Sandler", - month = aug, - year = 2008, - howpublished = "\url{https://www.softwarefreedom.org/resources/2008/compliance-guide.html}" + Title = "A Practical Guide to {GPL} Compliance", + Author = "Bradley M. Kuhn and Aaron Williamson and Karen M. Sandler", + Month = aug, + Year = 2008, + HowPublished = "\url{https://www.softwarefreedom.org/resources/2008/compliance-guide.html}" +} + +@TechReport{ halswdepositguidelines, + Title = {{Create software deposit}}, + Author = {Gruenpeter, Morane and Sadowska, Jozefina}, + URL = {https://hal.inria.fr/hal-01872189}, + Type = {Technical Report}, + Institution = {{Inria ; CCSD ; Software Heritage}}, + Year = {2018}, + Keywords = {Reproductibility ; Source code ; Open / free software ; + pr{\'e}servation du patrimoine logiciel ; D{\'e}p{\^o}t ; + Guide ; Logiciel open source ; code source ; Archivage ; + reproductibilit{\'e} num{\'e}rique}, + hal_id = {hal-01872189}, + hal_version = {v1} +} + +@TechReport{ halswmoderationguidelines, + Title = {{La mod{\'e}ration d'un d{\'e}p{\^o}t logiciel}}, + Author = {Gruenpeter, Morane and Sadowska, Jozefina}, + URL = {https://hal.inria.fr/hal-01876705}, + Type = {Technical Report}, + Institution = {{Inria ; CCSD ; Software Heritage}}, + Year = {2018}, + Keywords = {code source ; pr{\'e}servation du patrimoine logiciel ; + reproductibilit{\'e} num{\'e}rique ; Archivage ; Guide ; + D{\'e}p{\^o}t ; Mod{\'e}ration ; Logiciel ; Logiciel open + source}, + hal_id = {hal-01876705}, + hal_version = {v1} } @InProceedings{ hassan2008road, - title = {The road ahead for mining software repositories}, - author = {Hassan, Ahmed E}, - booktitle = {Frontiers of Software Maintenance, 2008. FoSM 2008.}, - pages = {48--57}, - year = {2008}, - organization = {IEEE} + Title = {The road ahead for mining software repositories}, + Author = {Hassan, Ahmed E}, + BookTitle = {Frontiers of Software Maintenance, 2008. FoSM 2008.}, + Pages = {48--57}, + Year = {2008}, + Organization = {IEEE} +} + +@Article{ Hinsen2013, + Author = {Konrad Hinsen}, + Title = {Software Development for Reproducible Research}, + Journal = {Computing in Science and Engineering}, + Volume = {15}, + Number = {4}, + Pages = {60--63}, + Year = {2013}, + URL = {https://doi.org/10.1109/MCSE.2013.91}, + DOI = {10.1109/MCSE.2013.91}, + timestamp = {Wed, 14 Nov 2018 10:48:30 +0100}, + biburl = {https://dblp.org/rec/bib/journals/cse/Hinsen13a}, + bibsource = {dblp computer science bibliography, https://dblp.org} +} + +@Article{ HowisonBullard2016, + Author = {Howison, James and Bullard, Julia}, + Title = {Software in the scientific literature: Problems with + seeing, finding, and using software mentioned in the + biology literature}, + Journal = {Journal of the Association for Information Science and + Technology}, + Volume = {67}, + Number = {9}, + Pages = {2137-2155}, + Keywords = {biology, journals, bibliographic citations}, + DOI = {10.1002/asi.23538}, + URL = {https://onlinelibrary.wiley.com/doi/abs/10.1002/asi.23538}, + EPrint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/asi.23538}, + Abstract = {Software is increasingly crucial to scholarship, yet the + visibility and usefulness of software in the scientific + record are in question. Just as with data, the visibility + of software in publications is related to incentives to + share software in reusable ways, and so promote efficient + science. In this article, we examine software in + publications through content analysis of a random sample of + 90 biology articles. We develop a coding scheme to identify + software “mentions” and classify them according to + their characteristics and ability to realize the functions + of citations. Overall, we find diverse and problematic + practices: Only between 31\% and 43\% of mentions involve + formal citations; informal mentions are very common, even + in high impact factor journals and across different kinds + of software. Software is frequently inaccessible + (15\%–29\% of packages in any form; between 90\% and 98\% + of specific versions; only between 24\%–40\% provide + source code). Cites to publications are particularly poor + at providing version information, whereas informal mentions + are particularly poor at providing crediting information. + We provide recommendations to improve the practice of + software citation, highlighting recent nascent efforts. + Software plays an increasingly great role in scientific + practice; it deserves a clear and useful place in scholarly + communication.}, + Year = {2016} } @Misc{ hugo, - title = {The HUGO Gene Nomenclature Committee}, - url = {https://www.genenames.org/}, - annote = "[Online; accessed March 1st 2018]" + Title = {The HUGO Gene Nomenclature Committee}, + URL = {https://www.genenames.org/}, + Annote = "[Online; accessed March 1st 2018]" +} + +@Article{ Hwang2017, + Author = {Hwang, Lorraine and Fish, Allison and Soito, Laura and + Smith, MacKenzie and Kellogg, Louise H.}, + Title = {Software and the Scientist: Coding and Citation Practices + in Geodynamics}, + Journal = {Earth and Space Science}, + Volume = {4}, + Number = {11}, + Pages = {670-680}, + Keywords = {attribution, software citation, software best practices, + Computational Infrastructure for Geoduynamics, software + credit, geodynamics}, + DOI = {10.1002/2016EA000225}, + URL = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016EA000225}, + EPrint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2016EA000225}, + Abstract = {Abstract In geodynamics as in other scientific areas, + computation has become a core component of research, + complementing field observation, laboratory analysis, + experiment, and theory. Computational tools for data + analysis, mapping, visualization, modeling, and simulation + are essential for all aspects of the scientific workflow. + Specialized scientific software is often developed by + geodynamicists for their own use, and this effort + represents a distinctive intellectual contribution. Drawing + on a geodynamics community that focuses on developing and + disseminating scientific software, we assess the current + practices of software development and attribution, as well + as attitudes about the need and best practices for software + citation. We analyzed publications by participants in the + Computational Infrastructure for Geodynamics and conducted + mixed method surveys of the solid earth geophysics + community. From this we learned that coding skills are + typically learned informally. Participants considered good + code as trusted, reusable, readable, and not overly complex + and considered a good coder as one that participates in the + community in an open and reasonable manor contributing to + both long- and short-term community projects. Participants + strongly supported citing software reflected by the high + rate a software package was named in the literature and the + high rate of citations in the references. However, lacking + are clear instructions from developers on how to cite and + education of users on what to cite. In addition, citations + did not always lead to discoverability of the resource. A + unique identifier to the software package itself, community + education, and citation tools would contribute to better + attribution practices.}, + Year = {2017} } @Article{ idplos2017, - author = {McMurry, Julie A. AND Juty, Nick AND Blomberg, Niklas AND + Author = {McMurry, Julie A. AND Juty, Nick AND Blomberg, Niklas AND Burdett, Tony AND Conlin, Tom AND Conte, Nathalie AND Courtot, Mélanie AND Deck, John AND Dumontier, Michel AND Fellows, Donal K. AND Gonzalez-Beltran, Alejandra AND Gormanns, Philipp AND Grethe, Jeffrey AND Hastings, Janna AND Hériché, Jean-Karim AND Hermjakob, Henning AND Ison, Jon C. AND Jimenez, Rafael C. AND Jupp, Simon AND Kunze, John AND Laibe, Camille AND Le Novère, Nicolas AND Malone, James AND Martin, Maria Jesus AND McEntyre, Johanna R. AND Morris, Chris AND Muilu, Juha AND Müller, Wolfgang AND Rocca-Serra, Philippe AND Sansone, Susanna-Assunta AND Sariyar, Murat AND Snoep, Jacky L. AND Soiland-Reyes, Stian AND Stanford, Natalie J. AND Swainston, Neil AND Washington, Nicole AND Williams, Alan R. AND Wimalaratne, Sarala M. AND Winfree, Lilly M. AND Wolstencroft, Katherine AND Goble, Carole AND Mungall, Christopher J. AND Haendel, Melissa A. AND Parkinson, Helen}, - journal = {PLOS Biology}, - publisher = {Public Library of Science}, - title = {Identifiers for the 21st century: How to design, + Journal = {PLOS Biology}, + Publisher = {Public Library of Science}, + Title = {Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data}, - year = {2017}, - month = {06}, - volume = {15}, - url = {https://doi.org/10.1371/journal.pbio.2001414}, - pages = {1-18}, - abstract = {In many disciplines, data are highly decentralized across + Year = {2017}, + Month = {06}, + Volume = {15}, + URL = {https://doi.org/10.1371/journal.pbio.2001414}, + Pages = {1-18}, + Abstract = {In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.}, - number = {6}, - doi = {10.1371/journal.pbio.2001414} + Number = {6}, + DOI = {10.1371/journal.pbio.2001414} +} + +@Misc{ ImageJ, + Title = {ImageJ}, + Author = {Rasband, Wayne}, + Address = "US and National Institutes of Health. Bethesda, Maryland, + USA", + Year = {1997--2011}, + URL = {http://imagej.nih.gov/ij/}, + Note = {Retrieved jan 7, 2018} } @InProceedings{ Inoue2017CodeClones, - author = {Takashi Ishio and Yusuke Sakaguchi and Kaoru Ito and + Author = {Takashi Ishio and Yusuke Sakaguchi and Kaoru Ito and Katsuro Inoue}, - title = {Source file set search for clone-and-own reuse analysis}, - booktitle = {Proceedings of the 14th International Conference on Mining + Title = {Source file set search for clone-and-own reuse analysis}, + BookTitle = {Proceedings of the 14th International Conference on Mining Software Repositories, {MSR} 2017, Buenos Aires, Argentina, May 20-28, 2017}, - pages = {257--268}, - year = {2017}, - crossref = {DBLP:conf/msr/2017}, - url = {https://doi.org/10.1109/MSR.2017.19}, - doi = {10.1109/MSR.2017.19}, + Pages = {257--268}, + Year = {2017}, + CrossRef = {DBLP:conf/msr/2017}, + URL = {https://doi.org/10.1109/MSR.2017.19}, + DOI = {10.1109/MSR.2017.19}, timestamp = {Fri, 07 Jul 2017 14:06:35 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/conf/msr/IshioSII17}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Misc{ internet-id, - author = "International DOI Foundation", - title = "Factsheet: DOI System and Internet Identifier + Author = "International DOI Foundation", + Title = "Factsheet: DOI System and Internet Identifier Specifications", - year = "2015", - note = "Online; retrieved 09 April 2018" + Year = "2015", + Note = "Online; retrieved 09 April 2018" } @Misc{ isbn, - title = "What is an ISBN?", - url = "https://www.isbn-international.org/content/what-isbn", - note = "[Online; accessed February 28th 2018]" + Title = "What is an ISBN?", + URL = "https://www.isbn-international.org/content/what-isbn", + Note = "[Online; accessed February 28th 2018]" +} + +@TechReport{ ISO690, + Type = {Standard}, + key = {ISO 690:2010}, + Month = jun, + Year = {2010}, + Title = {Information and documentation -- Guidelines for + bibliographic references and citations to information + resources}, + Volume = {2010}, + Address = {Geneva, CH}, + Institution = {International Organization for Standardization} +} + +@InProceedings{ KatzHong2018, + Author = {Daniel S. Katz and Neil P. Chue Hong}, + Title = {Software Citation in Theory and Practice}, + BookTitle = {Mathematical Software - {ICMS} 2018 - 6th International + Conference, South Bend, IN, USA, July 24-27, 2018, + Proceedings}, + Pages = {289--296}, + Year = {2018}, + CrossRef = {DBLP:conf/icms/2018}, + URL = {https://doi.org/10.1007/978-3-319-96418-8\_34}, + DOI = {10.1007/978-3-319-96418-8\_34}, + timestamp = {Tue, 17 Jul 2018 12:54:15 +0200}, + biburl = {https://dblp.org/rec/bib/conf/icms/KatzH18}, + bibsource = {dblp computer science bibliography, https://dblp.org} } @Misc{ keepproject, key = {European Union}, - title = {KEEP: EU cooperating}, - year = {2000}, - howpublished = {\url{https://www.keep.eu/}} + Title = {KEEP: EU cooperating}, + Year = {2000}, + HowPublished = {\url{https://www.keep.eu/}} } @Book{ knuth1992literate, - title = {Literate Programming}, - author = {Knuth, D.E.}, - isbn = {9780937073810}, + Title = {Literate Programming}, + Author = {Knuth, D.E.}, + ISBN = {9780937073810}, lccn = {lc91039510}, - series = {Center for the Study of Language and Information + Series = {Center for the Study of Language and Information Publication Lecture Notes}, - url = {https://books.google.fr/books?id=vovpQgAACAAJ}, - year = {1992}, - publisher = {Cambridge University Press} + URL = {https://books.google.fr/books?id=vovpQgAACAAJ}, + Year = {1992}, + Publisher = {Cambridge University Press} } @Article{ KnuthLiterate84, - author = {Donald E. Knuth}, - title = {Literate Programming}, - journal = {Comput. J.}, - volume = {27}, - number = {2}, - pages = {97--111}, - year = {1984}, - url = {http://dx.doi.org/10.1093/comjnl/27.2.97}, - doi = {10.1093/comjnl/27.2.97}, + Author = {Donald E. Knuth}, + Title = {Literate Programming}, + Journal = {Comput. J.}, + Volume = {27}, + Number = {2}, + Pages = {97--111}, + Year = {1984}, + URL = {http://dx.doi.org/10.1093/comjnl/27.2.97}, + DOI = {10.1093/comjnl/27.2.97}, timestamp = {Tue, 28 Jun 2011 15:15:31 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/journals/cj/Knuth84}, bibsource = {dblp computer science bibliography, http://dblp.org}, citation = "Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a computer what to do, let us concentrate rather on explaining to human beings what we want a computer to do. (page 99)" } @Article{ kranich2008information, - title = {Information Commons}, - author = {Kranich, Nancy and Schement, Jorge Reina}, - journal = {Annual Review of Information Science and Technology}, - volume = {42}, - number = {1}, - pages = {546--591}, - year = {2008}, - publisher = {Wiley} + Title = {Information Commons}, + Author = {Kranich, Nancy and Schement, Jorge Reina}, + Journal = {Annual Review of Information Science and Technology}, + Volume = {42}, + Number = {1}, + Pages = {546--591}, + Year = {2008}, + Publisher = {Wiley} } @Book{ lessig1999code, - title = {Code and other laws of cyberspace}, - author = {Lessig, Lawrence}, - year = {1999}, - publisher = {Basic books} + Title = {Code and other laws of cyberspace}, + Author = {Lessig, Lawrence}, + Year = {1999}, + Publisher = {Basic books} } @TechReport{ mahadev2015olive, - title = {One-Click Time Travel}, - author = {Mahadev Satyanarayanan, Gloriana St Clair and Gilbert, + Title = {One-Click Time Travel}, + Author = {Mahadev Satyanarayanan, Gloriana St Clair and Gilbert, Benjamin and Abe, Yoshihisa and Harkes, Jan and Ryan, Dan and Linke, Erika and Webster, Keith}, - year = {2015}, - institution = {Technical report, Computer Science, Carnegie Mellon + Year = {2015}, + Institution = {Technical report, Computer Science, Carnegie Mellon University} } @Article{ matthews2010framework, - title = {A framework for software preservation}, - author = {Matthews, Brian and Shaon, Arif and Bicarregui, Juan and + Title = {A framework for software preservation}, + Author = {Matthews, Brian and Shaon, Arif and Bicarregui, Juan and Jones, Catherine}, - journal = {International Journal of Digital Curation}, - volume = {5}, - number = {1}, - pages = {91--105}, - year = {2010} + Journal = {International Journal of Digital Curation}, + Volume = {5}, + Number = {1}, + Pages = {91--105}, + Year = {2010} } @InProceedings{ Merkle, - author = {Ralph C. Merkle}, - title = {A Digital Signature Based on a Conventional Encryption + Author = {Ralph C. Merkle}, + Title = {A Digital Signature Based on a Conventional Encryption Function}, - booktitle = {Advances in Cryptology - {CRYPTO} '87, {A} Conference on + BookTitle = {Advances in Cryptology - {CRYPTO} '87, {A} Conference on the Theory and Applications of Cryptographic Techniques, Santa Barbara, California, USA, August 16-20, 1987, Proceedings}, - pages = {369--378}, - year = {1987}, - crossref = {DBLP:conf/crypto/1987}, - url = {https://doi.org/10.1007/3-540-48184-2_32}, - doi = {10.1007/3-540-48184-2_32}, + Pages = {369--378}, + Year = {1987}, + CrossRef = {DBLP:conf/crypto/1987}, + URL = {https://doi.org/10.1007/3-540-48184-2_32}, + DOI = {10.1007/3-540-48184-2_32}, timestamp = {Fri, 19 May 2017 13:10:47 +0200}, biburl = {https://dblp.org/rec/bib/conf/crypto/Merkle87}, bibsource = {dblp computer science bibliography, https://dblp.org} } -@proceedings{DBLP:conf/crypto/1987, - editor = {Carl Pomerance}, - title = {Advances in Cryptology - {CRYPTO} '87, {A} Conference on the Theory - and Applications of Cryptographic Techniques}, - series = {Lecture Notes in Computer Science}, - volume = {293}, - publisher = {Springer}, - year = {1988}, - url = {https://doi.org/10.1007/3-540-48184-2}, - doi = {10.1007/3-540-48184-2}, - isbn = {3-540-18796-0}, - timestamp = {Fri, 19 May 2017 13:10:47 +0200}, - biburl = {https://dblp.org/rec/bib/conf/crypto/1987}, - bibsource = {dblp computer science bibliography, https://dblp.org} -} - @InProceedings{ merkle1987digital, - title = {A digital signature based on a conventional encryption + Title = {A digital signature based on a conventional encryption function}, - author = {Merkle, Ralph C}, - booktitle = {Conference on the Theory and Application of Cryptographic + Author = {Merkle, Ralph C}, + BookTitle = {Conference on the Theory and Application of Cryptographic Techniques}, - pages = {369--378}, - year = {1987}, - organization = {Springer} + Pages = {369--378}, + Year = {1987}, + Organization = {Springer} +} + +@Book{ Mysql5, + Author = {Michael Kofler}, + Title = {The Definitive Guide to MySQL5}, + Publisher = {Apress}, + Year = {2005} } @Article{ NatureTop, - author = {Van Noorden, Richard and Brendan Maher and Regina Nuzzo}, - title = {The top 100 papers}, - journal = {Nature}, - year = 2014, - pages = {550-553}, - month = oct # 4, - doi = "10.1038/514550a" + Author = {Van Noorden, Richard and Brendan Maher and Regina Nuzzo}, + Title = {The top 100 papers}, + Journal = {Nature}, + Year = 2014, + Pages = {550-553}, + Month = oct # 4, + DOI = "10.1038/514550a" } @Unpublished{ nsrl2006, - author = {Steve Mead}, - title = {Unique File Identification in the National Software + Author = {Steve Mead}, + Title = {Unique File Identification in the National Software Reference Library}, - note = {National Institute of Standards and Technology}, - year = {2006}, - url = {https://www.nist.gov/sites/default/files/draft-060530.pdf} + Note = {National Institute of Standards and Technology}, + Year = {2006}, + URL = {https://www.nist.gov/sites/default/files/draft-060530.pdf} +} + +@Article{ NumbersGame2007, + Author = {Parnas, David Lorge}, + Title = {Stop the Numbers Game}, + Journal = {Commun. ACM}, + issue_date = {November 2007}, + Volume = {50}, + Number = {11}, + Month = nov, + Year = {2007}, + ISSN = {0001-0782}, + Pages = {19--21}, + numpages = {3}, + URL = {http://doi.acm.org/10.1145/1297797.1297815}, + DOI = {10.1145/1297797.1297815}, + acmid = {1297815}, + Publisher = {ACM}, + Address = {New York, NY, USA} } @Manual{ OAIS2002, added-at = {2008-09-12T12:15:29.000+0200}, - author = {}, + Author = {}, biburl = {https://www.bibsonomy.org/bibtex/29a3071d3a754f11b547d8daa8d439fa1/hansgeorgbecker}, interhash = {d81d1990c6a25e93776de70fd39e8237}, intrahash = {9a3071d3a754f11b547d8daa8d439fa1}, - keywords = {OAIS Referenzmodell reference.model}, - month = {January}, - organization = {CCSDS - Consultative Committee for Space Data Systems}, + Keywords = {OAIS Referenzmodell reference.model}, + Month = {January}, + Organization = {CCSDS - Consultative Committee for Space Data Systems}, timestamp = {2008-09-12T12:15:29.000+0200}, - title = {Reference Model for an Open Archival Information System + Title = {Reference Model for an Open Archival Information System (OAIS), Blue Book, Issue 1}, - url = {http://public.ccsds.org/publications/archive/650x0b1.pdf}, - year = 2002 + URL = {http://public.ccsds.org/publications/archive/650x0b1.pdf}, + Year = 2002 } @Article{ osullivan2009making, - title = {Making sense of revision-control systems}, - author = {O'Sullivan, Bryan}, - journal = {Communications of the ACM}, - volume = {52}, - number = {9}, - pages = {56--62}, - year = {2009}, - publisher = {ACM} + Title = {Making sense of revision-control systems}, + Author = {O'Sullivan, Bryan}, + Journal = {Communications of the ACM}, + Volume = {52}, + Number = {9}, + Pages = {56--62}, + Year = {2009}, + Publisher = {ACM} +} + +@Article{ Parmap2012, + Author = {Marco Danelutto and Di Cosmo, Roberto}, + Title = {A "{M}inimal {D}isruption" Skeleton Experiment: Seamless + Map {\&} Reduce Embedding in {OC}aml}, + Journal = {Procedia CS}, + Volume = {9}, + Year = {2012}, + Pages = {1837-1846}, + ee = {http://dx.doi.org/10.1016/j.procs.2012.04.202}, + DOI = {http://dx.doi.org/10.1016/j.procs.2012.04.202}, + urllocal = {http://www.dicosmo.org/Articles/2012-DaneluttoDiCosmo-Pcs.pdf}, + dmi-category = {intc}, + x-topic = "parallel", + bibsource = {DBLP, http://dblp.uni-trier.de} } @Article{ paskin2005digital, - title = {Digital object identifiers for scientific data}, - author = {Paskin, Norman}, - journal = {Data Science Journal}, - volume = {4}, - pages = {12--20}, - year = {2005}, - publisher = {CODATA} + Title = {Digital object identifiers for scientific data}, + Author = {Paskin, Norman}, + Journal = {Data Science Journal}, + Volume = {4}, + Pages = {12--20}, + Year = {2005}, + Publisher = {CODATA} } @Article{ paskin2010digital, - title = {Digital object identifier (DOI) system}, - author = {Paskin, Norman}, - journal = {Encyclopedia of library and information sciences}, - volume = {3}, - pages = {1586--1592}, - year = {2010}, - publisher = {Taylor \& Francis England} + Title = {Digital object identifier (DOI) system}, + Author = {Paskin, Norman}, + Journal = {Encyclopedia of library and information sciences}, + Volume = {3}, + Pages = {1586--1592}, + Year = {2010}, + Publisher = {Taylor \& Francis England} +} + +@Article{ Peng2015, + Author = {Peng, Roger}, + Title = {The reproducibility crisis in science: A statistical + counterattack}, + Journal = {Significance}, + Volume = {12}, + Number = {3}, + Pages = {30-32}, + DOI = {10.1111/j.1740-9713.2015.00827.x}, + URL = {https://rss.onlinelibrary.wiley.com/doi/abs/10.1111/j.1740-9713.2015.00827.x}, + EPrint = {https://rss.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1740-9713.2015.00827.x}, + Abstract = {More people have more access to data than ever before. But + a comparative lack of analytical skills has resulted in + scientific findings that are neither replicable nor + reproducible. It is time to invest in statistics education, + says Roger Peng}, + Year = {2015} } @Misc{ plan9, - author = "Wikipedia contributors", - title = "Plan 9 from Bell Labs --- Wikipedia{,} The Free + Author = "Wikipedia contributors", + Title = "Plan 9 from Bell Labs --- Wikipedia{,} The Free Encyclopedia", - year = "2018", - url = "https://en.wikipedia.org/w/index.php?title=Plan_9_from_Bell_Labs&oldid=832417303", - note = "retrieved 09 April 2018" + Year = "2018", + URL = "https://en.wikipedia.org/w/index.php?title=Plan_9_from_Bell_Labs&oldid=832417303", + Note = "retrieved 09 April 2018" +} + +@Book{ Popper34, + Author = {Karl R. Popper}, + Title = {Logik der Forschung}, + Publisher = {J.C.B. Mohr}, + Year = {1971}, + ISBN = {316148410X}, + Note = {Reprint of the original 1934 edition} } @Article{ PourLaScience2013, - author = {Di Cosmo, Roberto}, - title = {Organiser le partage pour pr\'eserver les donn\'ees}, - journal = {Pour la {S}cience}, - pages = {86--90}, - year = {2013}, - volume = 433, + Author = {Di Cosmo, Roberto}, + Title = {Organiser le partage pour pr\'eserver les donn\'ees}, + Journal = {Pour la {S}cience}, + Pages = {86--90}, + Year = {2013}, + Volume = 433, dmi-category = {vulg}, - month = nov, + Month = nov, urllocal = {http://www.dicosmo.org/Articles/2013-11-PourLaScience-partage_donnees.pdf}, - url = {http://www.pourlascience.fr/ewb_pages/a/article-32240-organiser-le-partage-pour-preserver-les-donnees.php} + URL = {http://www.pourlascience.fr/ewb_pages/a/article-32240-organiser-le-partage-pour-preserver-les-donnees.php} } @Book{ ProGit2014, - author = {Chacon, Scott and Straub, Ben}, - title = {Pro Git}, - year = {2014}, - isbn = {1484200772, 9781484200773}, - edition = {2nd}, - publisher = {Apress}, - address = {Berkely, CA, USA} + Author = {Chacon, Scott and Straub, Ben}, + Title = {Pro Git}, + Year = {2014}, + ISBN = {1484200772, 9781484200773}, + Edition = {2nd}, + Publisher = {Apress}, + Address = {Berkely, CA, USA} } @Book{ raymond2003art, - title = {The art of Unix programming}, - author = {Raymond, Eric S}, - year = {2003}, - publisher = {Addison-Wesley Professional} + Title = {The art of Unix programming}, + Author = {Raymond, Eric S}, + Year = {2003}, + Publisher = {Addison-Wesley Professional} } @TechReport{ RFC3650, - author = {S. Sun and L. Lannom and B. Boesch}, - title = {Handle System Overview}, - howpublished = {Internet Requests for Comments}, - type = {RFC}, - number = {3650}, - year = {2003}, - month = {November}, - issn = {2070-1721}, - publisher = {RFC Editor}, - institution = {RFC Editor} + Author = {S. Sun and L. Lannom and B. Boesch}, + Title = {Handle System Overview}, + HowPublished = {Internet Requests for Comments}, + Type = {RFC}, + Number = {3650}, + Year = {2003}, + Month = {November}, + ISSN = {2070-1721}, + Publisher = {RFC Editor}, + Institution = {RFC Editor} } @TechReport{ rfc3986, - author = {T. Berners-Lee, R. Fielding, L. Masinter}, - title = {Uniform Resource Identifier (URI): Generic Syntax}, - howpublished = {The Internet Society}, - type = {RFC}, - number = {3986}, - year = {2005}, - month = {January}, - publisher = {RFC Editor}, - institution = {RFC Editor}, - url = {https://tools.ietf.org/html/rfc3986} + Author = {T. Berners-Lee, R. Fielding, L. Masinter}, + Title = {Uniform Resource Identifier (URI): Generic Syntax}, + HowPublished = {The Internet Society}, + Type = {RFC}, + Number = {3986}, + Year = {2005}, + Month = {January}, + Publisher = {RFC Editor}, + Institution = {RFC Editor}, + URL = {https://tools.ietf.org/html/rfc3986} } @Article{ RiehleFLOSSFoundations2010, - author = {Dirk Riehle}, - title = {The Economic Case for Open Source Foundations}, - journal = {{IEEE} Computer}, - volume = {43}, - number = {1}, - pages = {86--90}, - year = {2010}, - url = {https://doi.org/10.1109/MC.2010.24}, - doi = {10.1109/MC.2010.24}, + Author = {Dirk Riehle}, + Title = {The Economic Case for Open Source Foundations}, + Journal = {{IEEE} Computer}, + Volume = {43}, + Number = {1}, + Pages = {86--90}, + Year = {2010}, + URL = {https://doi.org/10.1109/MC.2010.24}, + DOI = {10.1109/MC.2010.24}, timestamp = {Mon, 05 Jun 2017 20:51:35 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/journals/computer/Riehle10}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Misc{ roadsandbridges, - author = "Nadia Eghbal", - year = 2016, - title = "Roads and Bridges: The Unseen Labor Behind Our Digital + Author = "Nadia Eghbal", + Year = 2016, + Title = "Roads and Bridges: The Unseen Labor Behind Our Digital Infrastructure.", - howpublished = "Report from the Ford Foundation" + HowPublished = "Report from the Ford Foundation" } @Article{ rosenthal17, - author = {David S. H. Rosenthal}, - title = {The medium-term prospects for long-term storage systems}, - journal = {Library Hi Tech}, - volume = {35}, - number = {1}, - pages = {11--31}, - year = {2017}, - url = {https://doi.org/10.1108/LHT-11-2016-0128}, - doi = {10.1108/LHT-11-2016-0128}, + Author = {David S. H. Rosenthal}, + Title = {The medium-term prospects for long-term storage systems}, + Journal = {Library Hi Tech}, + Volume = {35}, + Number = {1}, + Pages = {11--31}, + Year = {2017}, + URL = {https://doi.org/10.1108/LHT-11-2016-0128}, + DOI = {10.1108/LHT-11-2016-0128}, timestamp = {Sun, 28 May 2017 13:20:10 +0200}, biburl = {https://dblp.org/rec/bib/journals/lht/Rosenthal17}, bibsource = {dblp computer science bibliography, https://dblp.org} } @Misc{ RosenthalEUDAT, - author = {David Rosenthal and Rob Baxter and Laurence Field}, - title = {Towards a shared vision of sustainability for research and + Author = {David Rosenthal and Rob Baxter and Laurence Field}, + Title = {Towards a shared vision of sustainability for research and e-infrastructures}, - howpublished = {https://www.eudat.eu/news/towards-shared-vision-sustainability-research-and-e-infrastructures}, - month = "24-25 " # sep, - year = 2014, - note = {EUDAT conference} + HowPublished = {https://www.eudat.eu/news/towards-shared-vision-sustainability-research-and-e-infrastructures}, + Month = "24-25 " # sep, + Year = 2014, + Note = {EUDAT conference} } @Book{ schweik2012internet, - title = {Internet success: a study of open-source software + Title = {Internet success: a study of open-source software commons}, - author = {Schweik, Charles M and English, Robert C}, - year = {2012}, - publisher = {MIT Press} + Author = {Schweik, Charles M and English, Robert C}, + Year = {2012}, + Publisher = {MIT Press} } @Article{ seminalhgnc78, - author = {Shows, T.B. and McAlpine, P.J.}, - title = {The catalog of human genes and chromosome assignments}, - journal = {Cytogenetic and Genome Research}, - year = 1978, - volume = 22, - number = {1-6}, - pages = {132--145}, - doi = {10.1159/000130925}, - url = {https://www.karger.com/DOI/10.1159/000130925} + Author = {Shows, T.B. and McAlpine, P.J.}, + Title = {The catalog of human genes and chromosome assignments}, + Journal = {Cytogenetic and Genome Research}, + Year = 1978, + Volume = 22, + Number = {1-6}, + Pages = {132--145}, + DOI = {10.1159/000130925}, + URL = {https://www.karger.com/DOI/10.1159/000130925} +} + +@Book{ SemiPar2003, + Author = {David Ruppert}, + Title = {Semiparametric Regression (Cambridge Series in Statistical + and Probabilistic Mathematics)}, + Publisher = {Cambridge University Press}, + Year = {2003}, + ISBN = {9780521785167} } @InCollection{ sep-names, - author = {Cumming, Sam}, - title = {Names}, - booktitle = {The Stanford Encyclopedia of Philosophy}, - editor = {Edward N. Zalta}, - howpublished = {\url{https://plato.stanford.edu/archives/fall2016/entries/names/}}, - year = {2016}, - edition = {Fall 2016}, - publisher = {Metaphysics Research Lab, Stanford University} + Author = {Cumming, Sam}, + Title = {Names}, + BookTitle = {The Stanford Encyclopedia of Philosophy}, + Editor = {Edward N. Zalta}, + HowPublished = {\url{https://plato.stanford.edu/archives/fall2016/entries/names/}}, + Year = {2016}, + Edition = {Fall 2016}, + Publisher = {Metaphysics Research Lab, Stanford University} } @InCollection{ sep-peirce-semiotics, - author = {Atkin, Albert}, - title = {Peirce's Theory of Signs}, - booktitle = {The Stanford Encyclopedia of Philosophy}, - editor = {Edward N. Zalta}, - howpublished = {\url{https://plato.stanford.edu/archives/sum2013/entries/peirce-semiotics/}}, - year = {2013}, - edition = {Summer 2013}, - publisher = {Metaphysics Research Lab, Stanford University} + Author = {Atkin, Albert}, + Title = {Peirce's Theory of Signs}, + BookTitle = {The Stanford Encyclopedia of Philosophy}, + Editor = {Edward N. Zalta}, + HowPublished = {\url{https://plato.stanford.edu/archives/sum2013/entries/peirce-semiotics/}}, + Year = {2013}, + Edition = {Summer 2013}, + Publisher = {Metaphysics Research Lab, Stanford University} } @Article{ SHA1, added-at = {2013-01-27T00:00:00.000+0100}, - author = {Dang, Quynh}, + Author = {Dang, Quynh}, biburl = {http://www.bibsonomy.org/bibtex/2639634f48d1781b5312fdc8f19cf5c43/dblp}, ee = {http://dx.doi.org/10.1080/01611194.2012.687431}, interhash = {aea496907c0a161be8390d0e1b69474f}, intrahash = {639634f48d1781b5312fdc8f19cf5c43}, - journal = {Cryptologia}, - keywords = {dblp}, - number = 1, - pages = {69-73}, + Journal = {Cryptologia}, + Keywords = {dblp}, + Number = 1, + Pages = {69-73}, timestamp = {2013-01-29T11:36:44.000+0100}, - title = {Changes in Federal Information Processing Standard (FIPS) + Title = {Changes in Federal Information Processing Standard (FIPS) 180-4, Secure Hash Standard.}, - volume = 37, - year = 2013 + Volume = 37, + Year = 2013 } @Article{ Shustek06, - author = {Leonard J. Shustek}, - title = {What Should We Collect to Preserve the History of + Author = {Leonard J. Shustek}, + Title = {What Should We Collect to Preserve the History of Software?}, - journal = {{IEEE} Annals of the History of Computing}, - volume = {28}, - number = {4}, - pages = {110--112}, - year = {2006}, - url = {http://dx.doi.org/10.1109/MAHC.2006.78}, - doi = {10.1109/MAHC.2006.78}, + Journal = {{IEEE} Annals of the History of Computing}, + Volume = {28}, + Number = {4}, + Pages = {110--112}, + Year = {2006}, + URL = {http://dx.doi.org/10.1109/MAHC.2006.78}, + DOI = {10.1109/MAHC.2006.78}, timestamp = {Tue, 05 Jan 2016 15:36:44 +0100}, biburl = {http://dblp2.uni-trier.de/rec/bib/journals/annals/Shustek06}, bibsource = {dblp computer science bibliography, http://dblp.org} } @Article{ SoftwareAnalytics2013, - author = {Menzies, Tim and Zimmermann, Thomas}, - journal = {IEEE Software}, - title = {Software Analytics: So What?}, - year = {2013}, - month = {July}, - volume = {30}, - number = {4}, - pages = {31-37}, - abstract = {The guest editors of this special issue of IEEE Software + Author = {Menzies, Tim and Zimmermann, Thomas}, + Journal = {IEEE Software}, + Title = {Software Analytics: So What?}, + Year = {2013}, + Month = {July}, + Volume = {30}, + Number = {4}, + Pages = {31-37}, + Abstract = {The guest editors of this special issue of IEEE Software invited submissions that reflected the benefits (and drawbacks) of software analytics, an area of explosive growth. They had so many excellent submissions that they had to split this special issue into two volumes--you'll see even more content in the September/October issue. They divided the articles on conceptual grounds, so both volumes will feature equally excellent work. The Web extra at http://youtu.be/nO6X0azR0nw is a video interview in which IEEE Software editor in chief Forrest Shull speaks with Tim Menzies about the growing importance of software analytics.}, - keywords = {program diagnostics;software engineering;IEEE + Keywords = {program diagnostics;software engineering;IEEE Software;explosive software growth;software analytics;Data analysis;Data models;Decision making;Software algorithms;Software development;Software engineering;Special issues and sections;analysis;big data;measurement;metrics;software analytics}, - doi = {10.1109/MS.2013.86}, - issn = {0740-7459} + DOI = {10.1109/MS.2013.86}, + ISSN = {0740-7459} } @Article{ SoftwareCitationPrinciples, - author = {Arfon M. Smith and Daniel S. Katz and Kyle E. Niemeyer}, - title = {Software citation principles}, - journal = {PeerJ Computer Science}, - volume = {2}, - pages = {e86}, - year = {2016}, - url = {https://doi.org/10.7717/peerj-cs.86}, - doi = {10.7717/peerj-cs.86}, + Author = {Arfon M. Smith and Daniel S. Katz and Kyle E. Niemeyer}, + Title = {Software citation principles}, + Journal = {PeerJ Computer Science}, + Volume = {2}, + Pages = {e86}, + Year = {2016}, + URL = {https://doi.org/10.7717/peerj-cs.86}, + DOI = {10.7717/peerj-cs.86}, timestamp = {Thu, 08 Jun 2017 09:07:38 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/journals/peerj-cs/SmithKN16}, bibsource = {dblp computer science bibliography, http://dblp.org} } +@Article{ SoftwareCitationPrinciples-2016, + Author = {Arfon M. Smith and Daniel S. Katz and Kyle E. Niemeyer}, + Title = {Software citation principles}, + Journal = {PeerJ Computer Science}, + Volume = {2}, + Pages = {e86}, + Year = {2016}, + URL = {https://doi.org/10.7717/peerj-cs.86}, + DOI = {10.7717/peerj-cs.86}, + timestamp = {Wed, 14 Nov 2018 10:22:40 +0100}, + biburl = {https://dblp.org/rec/bib/journals/peerj-cs/SmithKN16}, + bibsource = {dblp computer science bibliography, https://dblp.org} +} + +@Article{ Soito2016, + Author = {Laura Soito and J Hwang, Lorraine}, + Title = "Citations for Software : Providing Identification, Access + and Recognition for Research Software", + Journal = "International Journal of Digital Curation", + Volume = 11, + Number = 2, + Year = 2016, + DOI = {10.2218/ijdc.v11i2.390}, + URL = "http://www.ijdc.net/index.php/ijdc/article/view/11.2.48/451" +} + @Article{ SpinellisUnix2017, - author = {Diomidis Spinellis}, - title = {A repository of Unix history and evolution}, - journal = {Empirical Software Engineering}, - volume = {22}, - number = {3}, - pages = {1372--1404}, - year = {2017}, - url = {https://doi.org/10.1007/s10664-016-9445-5}, - doi = {10.1007/s10664-016-9445-5}, + Author = {Diomidis Spinellis}, + Title = {A repository of Unix history and evolution}, + Journal = {Empirical Software Engineering}, + Volume = {22}, + Number = {3}, + Pages = {1372--1404}, + Year = {2017}, + URL = {https://doi.org/10.1007/s10664-016-9445-5}, + DOI = {10.1007/s10664-016-9445-5}, timestamp = {Thu, 01 Jun 2017 18:57:39 +0200}, biburl = {http://dblp.uni-trier.de/rec/bib/journals/ese/Spinellis17}, bibsource = {dblp computer science bibliography, http://dblp.org} } @InProceedings{ squire2012describing, - title = {Describing the software forge ecosystem}, - author = {Squire, Megan and Williams, David}, - booktitle = {System Science (HICSS), 2012 45th Hawaii International + Title = {Describing the software forge ecosystem}, + Author = {Squire, Megan and Williams, David}, + BookTitle = {System Science (HICSS), 2012 45th Hawaii International Conference on}, - pages = {3416--3425}, - year = {2012}, - organization = {IEEE} + Pages = {3416--3425}, + Year = {2012}, + Organization = {IEEE} +} + +@Unpublished{ SSIguidelines, + Author = {Mike Jackson}, + Title = {How to cite and describe software}, + Note = {Accessed on December 31st 2018}, + URL = {https://www.software.ac.uk/how-cite-software} } @Article{ stanisicld15, - author = {Luka Stanisic and Arnaud Legrand and Vincent Danjean}, - title = {An Effective Git And Org-Mode Based Workflow For + Author = {Luka Stanisic and Arnaud Legrand and Vincent Danjean}, + Title = {An Effective Git And Org-Mode Based Workflow For Reproducible Research}, - journal = {Operating Systems Review}, - volume = {49}, - number = {1}, - pages = {61--70}, - year = {2015}, - url = {https://doi.org/10.1145/2723872.2723881}, - doi = {10.1145/2723872.2723881}, + Journal = {Operating Systems Review}, + Volume = {49}, + Number = {1}, + Pages = {61--70}, + Year = {2015}, + URL = {https://doi.org/10.1145/2723872.2723881}, + DOI = {10.1145/2723872.2723881}, timestamp = {Tue, 06 Nov 2018 12:51:34 +0100}, biburl = {https://dblp.org/rec/bib/journals/sigops/StanisicLD15}, bibsource = {dblp computer science bibliography, https://dblp.org} } +@Article{ Stodden-reprod-2012, + Author = {Victoria Stodden and Randall J. LeVeque and Ian Mitchell}, + Title = {Reproducible Research for Scientific Computing: Tools and + Strategies for Changing the Culture}, + Journal = {Computing in Science and Engineering}, + Volume = {14}, + Number = {4}, + Pages = {13--17}, + Year = {2012}, + URL = {https://doi.org/10.1109/MCSE.2012.38}, + DOI = {10.1109/MCSE.2012.38}, + timestamp = {Thu, 15 Jun 2017 21:31:58 +0200}, + biburl = {https://dblp.org/rec/bib/journals/cse/StoddenLM12}, + bibsource = {dblp computer science bibliography, https://dblp.org} +} + +@Misc{ swh-hal-deposit-2018, + Author = "Yannick Barborini and Di Cosmo, Roberto and Dumont, + Antoine R. and Morane Gruenpeter and Bruno Marmol and Alain + Monteil and Jozefina Sadowska and Stefano Zacchiroli", + Title = "The creation of a new type of scientific deposit: + Software", + BookTitle = "RDA Eleventh Plenary Meeting", + Year = 2018, + HowPublished = {https://www.rd-alliance.org/rda-11th-plenary-poster-session}, + halid = {hal-01738741} +} + @Article{ swhcacm2018, - author = {Abramatic, Jean-Fran\c{c}ois and Di Cosmo, Roberto and + Author = {Abramatic, Jean-Fran\c{c}ois and Di Cosmo, Roberto and Zacchiroli, Stefano}, - title = {Building the Universal Archive of Source Code}, - journal = {Commun. ACM}, + Title = {Building the Universal Archive of Source Code}, + Journal = {Commun. ACM}, issue_date = {October 2018}, - volume = {61}, - number = {10}, - month = sep, - year = {2018}, - issn = {0001-0782}, - pages = {29--31}, + Volume = {61}, + Number = {10}, + Month = sep, + Year = {2018}, + ISSN = {0001-0782}, + Pages = {29--31}, numpages = {3}, - url = {http://doi.acm.org/10.1145/3183558}, - doi = {10.1145/3183558}, + URL = {http://doi.acm.org/10.1145/3183558}, + DOI = {10.1145/3183558}, acmid = {3183558}, - publisher = {ACM}, - address = {New York, NY, USA} + Publisher = {ACM}, + Address = {New York, NY, USA} } @InProceedings{ swhipres2017, - author = "Di Cosmo, Roberto and Stefano Zacchiroli", - title = "Software Heritage: Why and How to Preserve Software Source + Author = "Di Cosmo, Roberto and Stefano Zacchiroli", + Title = "Software Heritage: Why and How to Preserve Software Source Code", - booktitle = {Proceedings of the 14th International Conference on + BookTitle = {Proceedings of the 14th International Conference on Digital Preservation, iPRES 2017}, - month = sep, - year = {2017} + Month = sep, + Year = {2017} } @InProceedings{ swhipres2018, - author = "Di Cosmo, Roberto and Morane Gruenpeter and Stefano + Author = "Di Cosmo, Roberto and Morane Gruenpeter and Stefano Zacchiroli", - title = "Identifiers for Digital Objects: the Case of Software + Title = "Identifiers for Digital Objects: the Case of Software Source Code Preservation", - booktitle = {Proceedings of the 15th International Conference on + BookTitle = {Proceedings of the 15th International Conference on Digital Preservation, iPRES 2018, Boston, USA}, - month = sep, - year = {2018}, - url = {https://hal.archives-ouvertes.fr/hal-01865790}, + Month = sep, + Year = {2018}, + URL = {https://hal.archives-ouvertes.fr/hal-01865790}, urllocal = {http://www.dicosmo.org/Articles/iPres2018.pdf}, dmi-category = {intc}, x-topic = "preservation", - note = {Available from + Note = {Available from \url{https://hal.archives-ouvertes.fr/hal-01865790}} } @Article{ syeed-2013-oss-evol-review, - author = {M. M. Mahbubul Syeed and Imed Hammouda and Tarja + Author = {M. M. Mahbubul Syeed and Imed Hammouda and Tarja Syst{\"a}}, - title = {Evolution of Open Source Software Projects: A Systematic + Title = {Evolution of Open Source Software Projects: A Systematic Literature Review}, - journal = {JSW}, - volume = {8}, - number = {11}, - year = {2013}, - pages = {2815-2829}, + Journal = {JSW}, + Volume = {8}, + Number = {11}, + Year = {2013}, + Pages = {2815-2829}, ee = {http://dx.doi.org/10.4304/jsw.8.11.2815-2829}, bibsource = {DBLP, http://dblp.uni-trier.de} } @Article{ thain2015, - title = {Techniques for Preserving Scientific Software Executions: + Title = {Techniques for Preserving Scientific Software Executions: Preserve the Mess or Encourage Cleanliness?}, - author = {Douglas Thain and Peter Ivie and Haiyan Meng}, - journal = {Proceedings of the International Conference on Digital + Author = {Douglas Thain and Peter Ivie and Haiyan Meng}, + Journal = {Proceedings of the International Conference on Digital Preservation (iPRES)}, - year = {2015}, - doi = {http://dx.doi.org/doi:10.7274/R0CZ353M} + Year = {2015}, + DOI = {http://dx.doi.org/doi:10.7274/R0CZ353M} } @Misc{ titusbrown2015, - author = "Titus Brown, C.", - title = "Pubwication of software papers, and authorship on them", - year = "2015", - month = sep, - url = "https://ivory.idyll.org/blog/2015-authorship-on-software-papers.html", - note = "retrieved January 2019" + Author = "Titus Brown, C.", + Title = "Pubwication of software papers, and authorship on them", + Year = "2015", + Month = sep, + URL = "https://ivory.idyll.org/blog/2015-authorship-on-software-papers.html", + Note = "retrieved January 2019" } @Article{ treolar2014, - title = {A perspective on Archiving the Scholarly Web}, - author = {Van de Sompel, Herbert and Andrew Treolar}, - journal = {Proceedings of the International Conference on Digital + Title = {A perspective on Archiving the Scholarly Web}, + Author = {Van de Sompel, Herbert and Andrew Treolar}, + Journal = {Proceedings of the International Conference on Digital Preservation (iPRES)}, - pages = {194--198}, - year = {2014} + Pages = {194--198}, + Year = {2014} } @Misc{ UnescoInria2017, - title = "L'UNESCO et INRIA signent un accord sur l'archivage des + Title = "L'UNESCO et INRIA signent un accord sur l'archivage des logiciels en pr\'esence du Pr\'esident Hollande", - howpublished = "\url{http://fr.unesco.org/news/unesco-inria-signent-accord-archivage-logiciels-presence-du-president-hollande}", - year = 2017, - month = apr + HowPublished = "\url{http://fr.unesco.org/news/unesco-inria-signent-accord-archivage-logiciels-presence-du-president-hollande}", + Year = 2017, + Month = apr } @Misc{ unescopersist, key = {UNESCO}, - title = {UNESCO PERSIST Programme}, - year = {2015}, - howpublished = {\url{https://unescopersist.org/}} + Title = {UNESCO PERSIST Programme}, + Year = {2015}, + HowPublished = {\url{https://unescopersist.org/}} } @TechReport{ us-fed-strategy, key = {US Fed}, - title = {Strategy for American Innovation}, - institution = {[US] Federal Register}, - year = {2014}, - note = {\url{https://www.federalregister.gov/articles/2014/07/29/2014-17761/strategy-for-american-innovation}} + Title = {Strategy for American Innovation}, + Institution = {[US] Federal Register}, + Year = {2014}, + Note = {\url{https://www.federalregister.gov/articles/2014/07/29/2014-17761/strategy-for-american-innovation}} } @Misc{ uuid, - author = "P. Leach, M. Mealling, R. Salz", - title = "A Universally Unique IDentifier (UUID) URN Namespace", - doi = "10.17487/RFC4122", - url = "https://www.rfc-editor.org/info/rfc4122", - year = "2005" + Author = "P. Leach, M. Mealling, R. Salz", + Title = "A Universally Unique IDentifier (UUID) URN Namespace", + DOI = "10.17487/RFC4122", + URL = "https://www.rfc-editor.org/info/rfc4122", + Year = "2005" +} + +@Article{ VanNoorden2014, + DOI = {10.1038/514550a}, + URL = {https://doi.org/10.1038/514550a}, + Year = {2014}, + Month = {oct}, + Publisher = {Springer Nature}, + Volume = {514}, + Number = {7524}, + Pages = {550--553}, + Author = {Richard Van Noorden and Brendan Maher and Regina Nuzzo}, + Title = {The top 100 papers}, + Journal = {Nature} } @Misc{ web:arxiv, - title = "ArXiv: e-prints archive", - year = "2017", - url = "\url{https://arxiv.org/}", - note = "retrieved June 2017" + Title = "ArXiv: e-prints archive", + Year = "2017", + URL = "\url{https://arxiv.org/}", + Note = "retrieved June 2017" } @Misc{ web:cines, key = {CINES}, - title = {Centre Informatique National de l'Enseignement + Title = {Centre Informatique National de l'Enseignement Supérieur}, - year = "2014", - url = "\url{https://www.cines.fr/}", - note = "\url{https://www.cines.fr/}" + Year = "2014", + URL = "\url{https://www.cines.fr/}", + Note = "\url{https://www.cines.fr/}" } @Misc{ web:dp-coalition, key = {DPC}, - title = {Digital Preservation Coalition}, - url = "http://www.dpconline.org/", - note = "\url{http://www.dpconline.org/}" + Title = {Digital Preservation Coalition}, + URL = "http://www.dpconline.org/", + Note = "\url{http://www.dpconline.org/}" } @Misc{ web:githubarchive, key = {GitHubArchive}, - title = {GitHub Archive}, - year = "2017", - howpublished = "https://www.githubarchive.org/", - note = "Retrivede March 2017" + Title = {GitHub Archive}, + Year = "2017", + HowPublished = "https://www.githubarchive.org/", + Note = "Retrivede March 2017" } @Misc{ web:gmane, key = {Gmane}, - title = {Gmane}, - year = "2017", - howpublished = "\url{http://gmane.org}" + Title = {Gmane}, + Year = "2017", + HowPublished = "\url{http://gmane.org}" } @Misc{ web:hal, - title = "HAL: Hyper articles en ligne", - year = "2017", - url = "\url{https://hal.archives-ouvertes.fr/}", - note = "retrieved June 2017" + Title = "HAL: Hyper articles en ligne", + Year = "2017", + URL = "\url{https://hal.archives-ouvertes.fr/}", + Note = "retrieved June 2017" } @Misc{ web:internet-archive, key = {InternetArchive}, - title = {Internet Archive: Digital Library of Free Books, Movies, + Title = {Internet Archive: Digital Library of Free Books, Movies, Music \& Wayback Machine}, - url = "https://archive.org", - year = "Retrieved 3/3/2017", - note = "\url{https://archive.org}" + URL = "https://archive.org", + Year = "Retrieved 3/3/2017", + Note = "\url{https://archive.org}" } @Misc{ web:national-sw-ref-library, - author = {NIST}, - title = "{[US]} National Software Reference Library", - year = "2014", - url = "\url{http://www.nsrl.nist.gov}", - note = "\url{http://www.nsrl.nist.gov}" + Author = {NIST}, + Title = "{[US]} National Software Reference Library", + Year = "2014", + URL = "\url{http://www.nsrl.nist.gov}", + Note = "\url{http://www.nsrl.nist.gov}" } @Misc{ web:national-sw-ref-library-hash, - author = {Steve Mead}, - title = "Unique File Identification in the {National Software + Author = {Steve Mead}, + Title = "Unique File Identification in the {National Software Reference Library}", - year = "2014", - howpublished = "\url{http://www.nsrl.nist.gov}", - institution = "National Institute of Standards & Technology", - note = "smead@nist.gov" + Year = "2014", + HowPublished = "\url{http://www.nsrl.nist.gov}", + Institution = "National Institute of Standards & Technology", + Note = "smead@nist.gov" } @Misc{ web:openaire, key = {OpenAIRE}, - title = {OpenAIRE}, - year = "2014", - url = "https://www.openaire.eu/", - note = "\url{https://www.openaire.eu/}" + Title = {OpenAIRE}, + Year = "2014", + URL = "https://www.openaire.eu/", + Note = "\url{https://www.openaire.eu/}" } @Misc{ web:openedition, - title = "Open Edition", - year = "2017", - url = "\url{https://www.openedition.org/}", - note = "retrieved June 2017" + Title = "Open Edition", + Year = "2017", + URL = "\url{https://www.openedition.org/}", + Note = "retrieved June 2017" } @Misc{ web:zenodo, key = {Zenodo}, - title = {Zenodo}, - year = "2013", - howpublished = "\url{https://zenodo.org/}" + Title = {Zenodo}, + Year = "2013", + HowPublished = "\url{https://zenodo.org/}" } @Article{ Whitt2017, - author = {Whitt, Richard S.}, - title = {"Through A Glass, Darkly" Technical, Policy, and Financial + Author = {Whitt, Richard S.}, + Title = {"Through A Glass, Darkly" Technical, Policy, and Financial Actions to Avert the Coming Digital Dark Ages}, - journal = {Santa Clara High Tech. L.J.}, - year = 2017, - volume = 33, - number = 2, - pages = 117, - month = jan, - note = {Available at: + Journal = {Santa Clara High Tech. L.J.}, + Year = 2017, + Volume = 33, + Number = 2, + Pages = 117, + Month = jan, + Note = {Available at: http://digitalcommons.law.scu.edu/chtlj/vol33/iss2/1} } @Misc{ wikipedia:cultural-heritage, - author = "Wikipedia", - title = "Cultural heritage --- {W}ikipedia{,} The Free + Author = "Wikipedia", + Title = "Cultural heritage --- {W}ikipedia{,} The Free Encyclopedia", - year = "2015", - url = "\url{https://en.wikipedia.org/wiki/Cultural_heritage}", - note = "retrieved September 2015" + Year = "2015", + URL = "\url{https://en.wikipedia.org/wiki/Cultural_heritage}", + Note = "retrieved September 2015" } @Misc{ wikipedia:notability, - author = "Wikipedia", - title = "{Wikipedia:Notability} --- {W}ikipedia{,} The Free + Author = "Wikipedia", + Title = "{Wikipedia:Notability} --- {W}ikipedia{,} The Free Encyclopedia", - year = "2015", - url = "\url{https://en.wikipedia.org/wiki/Wikipedia:Notability}", - note = "retrieved November 2015" -} - -@Article{Soito2016, - author = {Laura Soito and J Hwang, Lorraine}, - title = "Citations for Software : Providing Identification, Access and Recognition for Research Software", - journal = "International Journal of Digital Curation", - volume= 11, - number=2, - year=2016, - doi={10.2218/ijdc.v11i2.390}, - url="http://www.ijdc.net/index.php/ijdc/article/view/11.2.48/451" -} - -@article{HowisonBullard2016, -author = {Howison, James and Bullard, Julia}, -title = {Software in the scientific literature: Problems with seeing, finding, and using software mentioned in the biology literature}, -journal = {Journal of the Association for Information Science and Technology}, -volume = {67}, -number = {9}, -pages = {2137-2155}, -keywords = {biology, journals, bibliographic citations}, -doi = {10.1002/asi.23538}, -url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/asi.23538}, -eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/asi.23538}, -abstract = {Software is increasingly crucial to scholarship, yet the visibility and usefulness of software in the scientific record are in question. Just as with data, the visibility of software in publications is related to incentives to share software in reusable ways, and so promote efficient science. In this article, we examine software in publications through content analysis of a random sample of 90 biology articles. We develop a coding scheme to identify software “mentions” and classify them according to their characteristics and ability to realize the functions of citations. Overall, we find diverse and problematic practices: Only between 31\% and 43\% of mentions involve formal citations; informal mentions are very common, even in high impact factor journals and across different kinds of software. Software is frequently inaccessible (15\%–29\% of packages in any form; between 90\% and 98\% of specific versions; only between 24\%–40\% provide source code). Cites to publications are particularly poor at providing version information, whereas informal mentions are particularly poor at providing crediting information. We provide recommendations to improve the practice of software citation, highlighting recent nascent efforts. Software plays an increasingly great role in scientific practice; it deserves a clear and useful place in scholarly communication.}, -year = {2016} -} - -@article{NumbersGame2007, - author = {Parnas, David Lorge}, - title = {Stop the Numbers Game}, - journal = {Commun. ACM}, - issue_date = {November 2007}, - volume = {50}, - number = {11}, - month = nov, - year = {2007}, - issn = {0001-0782}, - pages = {19--21}, - numpages = {3}, - url = {http://doi.acm.org/10.1145/1297797.1297815}, - doi = {10.1145/1297797.1297815}, - acmid = {1297815}, - publisher = {ACM}, - address = {New York, NY, USA}, -} - -@article{Stodden-reprod-2012, - author = {Victoria Stodden and - Randall J. LeVeque and - Ian Mitchell}, - title = {Reproducible Research for Scientific Computing: Tools and Strategies - for Changing the Culture}, - journal = {Computing in Science and Engineering}, - volume = {14}, - number = {4}, - pages = {13--17}, - year = {2012}, - url = {https://doi.org/10.1109/MCSE.2012.38}, - doi = {10.1109/MCSE.2012.38}, - timestamp = {Thu, 15 Jun 2017 21:31:58 +0200}, - biburl = {https://dblp.org/rec/bib/journals/cse/StoddenLM12}, - bibsource = {dblp computer science bibliography, https://dblp.org} -} - -@article{Borgman2012, - author = {Christine L. Borgman and - Jillian C. Wallis and - Matthew S. Mayernik}, - title = {Who's Got the Data? Interdependencies in Science and Technology Collaborations}, - journal = {Computer Supported Cooperative Work}, - volume = {21}, - number = {6}, - pages = {485--523}, - year = {2012}, - url = {https://doi.org/10.1007/s10606-012-9169-z}, - doi = {10.1007/s10606-012-9169-z}, - timestamp = {Mon, 05 Jun 2017 20:44:38 +0200}, - biburl = {https://dblp.org/rec/bib/journals/cscw/BorgmanWM12}, - bibsource = {dblp computer science bibliography, https://dblp.org} -} - -@article{Hinsen2013, - author = {Konrad Hinsen}, - title = {Software Development for Reproducible Research}, - journal = {Computing in Science and Engineering}, - volume = {15}, - number = {4}, - pages = {60--63}, - year = {2013}, - url = {https://doi.org/10.1109/MCSE.2013.91}, - doi = {10.1109/MCSE.2013.91}, - timestamp = {Wed, 14 Nov 2018 10:48:30 +0100}, - biburl = {https://dblp.org/rec/bib/journals/cse/Hinsen13a}, - bibsource = {dblp computer science bibliography, https://dblp.org} -} - -@Article{Dagstuhl-Artefacts-2016, - author = {Bruce R. Childers and Grigori Fursin and Shriram Krishnamurthi and Andreas Zeller}, - title = {{Artifact Evaluation for Publications (Dagstuhl Perspectives Workshop 15452)}}, - pages = {29--35}, - journal = {Dagstuhl Reports}, - ISSN = {2192-5283}, - year = {2016}, - volume = {5}, - number = {11}, - editor = {Bruce R. Childers and Grigori Fursin and Shriram Krishnamurthi and Andreas Zeller}, - publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik}, - address = {Dagstuhl, Germany}, - URL = {http://drops.dagstuhl.de/opus/volltexte/2016/5762}, - URN = {urn:nbn:de:0030-drops-57620}, - doi = {10.4230/DagRep.5.11.29}, - annote = {Keywords: Computer systems, artifacts, reproducibility, archive} -} - - -@article{SoftwareCitationPrinciples-2016, - author = {Arfon M. Smith and - Daniel S. Katz and - Kyle E. Niemeyer}, - title = {Software citation principles}, - journal = {PeerJ Computer Science}, - volume = {2}, - pages = {e86}, - year = {2016}, - url = {https://doi.org/10.7717/peerj-cs.86}, - doi = {10.7717/peerj-cs.86}, - timestamp = {Wed, 14 Nov 2018 10:22:40 +0100}, - biburl = {https://dblp.org/rec/bib/journals/peerj-cs/SmithKN16}, - bibsource = {dblp computer science bibliography, https://dblp.org} -} - - -@inproceedings{KatzHong2018, - author = {Daniel S. Katz and - Neil P. Chue Hong}, - title = {Software Citation in Theory and Practice}, - booktitle = {Mathematical Software - {ICMS} 2018 - 6th International Conference, - South Bend, IN, USA, July 24-27, 2018, Proceedings}, - pages = {289--296}, - year = {2018}, - crossref = {DBLP:conf/icms/2018}, - url = {https://doi.org/10.1007/978-3-319-96418-8\_34}, - doi = {10.1007/978-3-319-96418-8\_34}, - timestamp = {Tue, 17 Jul 2018 12:54:15 +0200}, - biburl = {https://dblp.org/rec/bib/conf/icms/KatzH18}, - bibsource = {dblp computer science bibliography, https://dblp.org} -} - -@proceedings{DBLP:conf/icms/2018, - editor = {James H. Davenport and - Manuel Kauers and - George Labahn and - Josef Urban}, - title = {Mathematical Software - {ICMS} 2018 - 6th International Conference, - South Bend, IN, USA, July 24-27, 2018, Proceedings}, - series = {Lecture Notes in Computer Science}, - volume = {10931}, - publisher = {Springer}, - year = {2018}, - url = {https://doi.org/10.1007/978-3-319-96418-8}, - doi = {10.1007/978-3-319-96418-8}, - isbn = {978-3-319-96417-1}, - timestamp = {Tue, 17 Jul 2018 12:46:33 +0200}, - biburl = {https://dblp.org/rec/bib/conf/icms/2018}, - bibsource = {dblp computer science bibliography, https://dblp.org} -} - -@techreport{ISO690, -type = {Standard}, -key = {ISO 690:2010}, -month = jun, -year = {2010}, -title = {Information and documentation -- Guidelines for bibliographic references and citations to information resources}, -volume = {2010}, -address = {Geneva, CH}, -institution = {International Organization for Standardization} -} - -@Unpublished{SSIguidelines, - author = {Mike Jackson}, - title = {How to cite and describe software}, - note = {Accessed on December 31st 2018}, - url = {https://www.software.ac.uk/how-cite-software} -} - -@article{Hwang2017, -author = {Hwang, Lorraine and Fish, Allison and Soito, Laura and Smith, MacKenzie and Kellogg, Louise H.}, -title = {Software and the Scientist: Coding and Citation Practices in Geodynamics}, -journal = {Earth and Space Science}, -volume = {4}, -number = {11}, -pages = {670-680}, -keywords = {attribution, software citation, software best practices, Computational Infrastructure for Geoduynamics, software credit, geodynamics}, -doi = {10.1002/2016EA000225}, -url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016EA000225}, -eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2016EA000225}, -abstract = {Abstract In geodynamics as in other scientific areas, computation has become a core component of research, complementing field observation, laboratory analysis, experiment, and theory. Computational tools for data analysis, mapping, visualization, modeling, and simulation are essential for all aspects of the scientific workflow. Specialized scientific software is often developed by geodynamicists for their own use, and this effort represents a distinctive intellectual contribution. Drawing on a geodynamics community that focuses on developing and disseminating scientific software, we assess the current practices of software development and attribution, as well as attitudes about the need and best practices for software citation. We analyzed publications by participants in the Computational Infrastructure for Geodynamics and conducted mixed method surveys of the solid earth geophysics community. From this we learned that coding skills are typically learned informally. Participants considered good code as trusted, reusable, readable, and not overly complex and considered a good coder as one that participates in the community in an open and reasonable manor contributing to both long- and short-term community projects. Participants strongly supported citing software reflected by the high rate a software package was named in the literature and the high rate of citations in the references. However, lacking are clear instructions from developers on how to cite and education of users on what to cite. In addition, citations did not always lead to discoverability of the resource. A unique identifier to the software package itself, community education, and citation tools would contribute to better attribution practices.}, -year = {2017} -} - -@article{Biagioli2016, -author = {Biagioli, Mario}, -year = {2016}, -month = {07}, -pages = {201-201}, -title = {Watch out for cheats in citation game}, -volume = {535}, -journal = {Nature}, -doi = {10.1038/535201a} -} - - -@misc{ImageJ, - title={ImageJ}, - author={Rasband, Wayne}, - address="US and National Institutes of Health. Bethesda, Maryland, USA", - year={1997--2011}, - url={http://imagej.nih.gov/ij/}, - note={Retrieved jan 7, 2018} -} - - -@Book{Mysql5, - author = {Michael Kofler}, - title = {The Definitive Guide to MySQL5}, - publisher = {Apress}, - year = {2005}, -} - -@article{Baker2016, - doi = {10.1038/533452a}, - url = {https://doi.org/10.1038/533452a}, - year = {2016}, - month = {may}, - publisher = {Springer Nature}, - volume = {533}, - number = {7604}, - pages = {452--454}, - author = {Monya Baker}, - title = {1, 500 scientists lift the lid on reproducibility}, - journal = {Nature} -} - -@article{Peng2015, -author = {Peng, Roger}, -title = {The reproducibility crisis in science: A statistical counterattack}, -journal = {Significance}, -volume = {12}, -number = {3}, -pages = {30-32}, -doi = {10.1111/j.1740-9713.2015.00827.x}, -url = {https://rss.onlinelibrary.wiley.com/doi/abs/10.1111/j.1740-9713.2015.00827.x}, -eprint = {https://rss.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1740-9713.2015.00827.x}, -abstract = {More people have more access to data than ever before. But a comparative lack of analytical skills has resulted in scientific findings that are neither replicable nor reproducible. It is time to invest in statistics education, says Roger Peng}, -year = {2015} -} - -@book{Popper34, - Author = {Karl R. Popper}, - Title = {Logik der Forschung}, - Publisher = {J.C.B. Mohr}, - Year = {1971}, - ISBN = {316148410X}, - note = {Reprint of the original 1934 edition} -} - -@article{VanNoorden2014, - doi = {10.1038/514550a}, - url = {https://doi.org/10.1038/514550a}, - year = {2014}, - month = {oct}, - publisher = {Springer Nature}, - volume = {514}, - number = {7524}, - pages = {550--553}, - author = {Richard Van Noorden and Brendan Maher and Regina Nuzzo}, - title = {The top 100 papers}, - journal = {Nature} -} - -@article{Collberg2016, - doi = {10.1145/2812803}, - url = {https://doi.org/10.1145/2812803}, - year = {2016}, - month = {feb}, - publisher = {Association for Computing Machinery ({ACM})}, - volume = {59}, - number = {3}, - pages = {62--69}, - author = {Christian Collberg and Todd A. Proebsting}, - title = {Repeatability in computer systems research}, - journal = {Communications of the {ACM}} -} - -@book{SemiPar2003, - Author = {David Ruppert}, - Title = {Semiparametric Regression (Cambridge Series in Statistical and Probabilistic Mathematics)}, - Publisher = {Cambridge University Press}, - Year = {2003}, - ISBN = {9780521785167} -} - -@article{Parmap2012, - author = {Marco Danelutto and - Di Cosmo, Roberto}, - title = {A "{M}inimal {D}isruption" Skeleton Experiment: Seamless Map - {\&} Reduce Embedding in {OC}aml}, - journal = {Procedia CS}, - volume = {9}, - year = {2012}, - pages = {1837-1846}, - ee = {http://dx.doi.org/10.1016/j.procs.2012.04.202}, - doi = {http://dx.doi.org/10.1016/j.procs.2012.04.202}, - urllocal = {http://www.dicosmo.org/Articles/2012-DaneluttoDiCosmo-Pcs.pdf}, - DMI-CATEGORY = {intc}, - x-topic="parallel", - bibsource = {DBLP, http://dblp.uni-trier.de} -} - -@inproceedings{edos2006wsl, - address = {Porto Alegre, Brazil}, - author = {Boender, Jaap and Di Cosmo, Roberto and Durak, Berke and Leroy, Xavier and Mancinelli, Fabio and Morgado, Mario and Pinheiro, David and Treinen, Ralf and Trezentos, Paulo and Vouillon, J{\'e}r{\^o}me}, - booktitle = {{P}roceedings of the 7th {I}nternational {W}orkshop on {F}ree {S}oftware ({IWFS}'06)}, - editor = {Berger, Olivier}, - month = apr, - x-topic="softeng", - title = {News from the {EDOS} project: improving the maintenance of free software distributions}, - urllocal = {http://www.dicosmo.org/Articles/wsl06.pdf}, - url = {http://www.dicosmo.org/Articles/wsl06.pdf}, - year = {2006}, - DMI-CATEGORY = {autc}, - pages = {199 -- 207}, - isbn = {857669066-7} -} - -@Misc{swh-hal-deposit-2018, -author="Yannick Barborini and Di Cosmo, Roberto and Dumont, Antoine R. and - Morane Gruenpeter and Bruno Marmol and Alain Monteil and - Jozefina Sadowska and Stefano Zacchiroli", -title="The creation of a new type of scientific deposit: Software", -booktitle="RDA Eleventh Plenary Meeting", -year=2018, -howpublished={https://www.rd-alliance.org/rda-11th-plenary-poster-session}, -halid={hal-01738741} -} - -@book{CGAL, - title = {{CGAL} User and Reference Manual}, - author = {{The CGAL Project}}, - publisher = {{CGAL Editorial Board}}, - edition = {{4.14}}, - year = 2019, - url = {https://doc.cgal.org/4.14/Manual/packages.html} -} - -@techreport{halswdepositguidelines, - TITLE = {{Create software deposit}}, - AUTHOR = {Gruenpeter, Morane and Sadowska, Jozefina}, - URL = {https://hal.inria.fr/hal-01872189}, - TYPE = {Technical Report}, - INSTITUTION = {{Inria ; CCSD ; Software Heritage}}, - YEAR = {2018}, - KEYWORDS = {Reproductibility ; Source code ; Open / free software ; pr{\'e}servation du patrimoine logiciel ; D{\'e}p{\^o}t ; Guide ; Logiciel open source ; code source ; Archivage ; reproductibilit{\'e} num{\'e}rique}, - HAL_ID = {hal-01872189}, - HAL_VERSION = {v1}, -} - -@techreport{halswmoderationguidelines, - TITLE = {{La mod{\'e}ration d'un d{\'e}p{\^o}t logiciel}}, - AUTHOR = {Gruenpeter, Morane and Sadowska, Jozefina}, - URL = {https://hal.inria.fr/hal-01876705}, - TYPE = {Technical Report}, - INSTITUTION = {{Inria ; CCSD ; Software Heritage}}, - YEAR = {2018}, - KEYWORDS = {code source ; pr{\'e}servation du patrimoine logiciel ; reproductibilit{\'e} num{\'e}rique ; Archivage ; Guide ; D{\'e}p{\^o}t ; Mod{\'e}ration ; Logiciel ; Logiciel open source}, - HAL_ID = {hal-01876705}, - HAL_VERSION = {v1}, -} - -@Article{Wimalaratne2018, - author={Wimalaratne, Sarala M. and Juty, Nick and Kunze, John and Jan{\'e}e, Greg - and McMurry, Julie A. and Beard, Niall and Jimenez, Rafael - and Grethe, Jeffrey S. and Hermjakob, Henning - and Martone, Maryann E. and Clark, Tim}, - title={Uniform resolution of compact identifiers for biomedical data}, - journal={Scientific Data}, - year=2018, - month={May}, - day=08, - publisher={Nature}, - volume=5, - pages={180029}, - note={Article}, - abstract={We report here on our project to provide robust support for - machine-resolvable, persistent compact identifiers in - biomedical data citation, by harmonizing the Identifiers.org - and N2T.net (Name-To-Thing) meta-resolvers and extending their - capabilities.}, - url={https://doi.org/10.1038/sdata.2018.29} + Year = "2015", + URL = "\url{https://en.wikipedia.org/wiki/Wikipedia:Notability}", + Note = "retrieved November 2015" +} + +@Article{ Wimalaratne2018, + Author = {Wimalaratne, Sarala M. and Juty, Nick and Kunze, John and + Jan{\'e}e, Greg and McMurry, Julie A. and Beard, Niall and + Jimenez, Rafael and Grethe, Jeffrey S. and Hermjakob, + Henning and Martone, Maryann E. and Clark, Tim}, + Title = {Uniform resolution of compact identifiers for biomedical + data}, + Journal = {Scientific Data}, + Year = 2018, + Month = {May}, + day = 08, + Publisher = {Nature}, + Volume = 5, + Pages = {180029}, + Note = {Article}, + Abstract = {We report here on our project to provide robust support + for machine-resolvable, persistent compact identifiers in + biomedical data citation, by harmonizing the + Identifiers.org and N2T.net (Name-To-Thing) meta-resolvers + and extending their capabilities.}, + URL = {https://doi.org/10.1038/sdata.2018.29} } -