{"7f281edbd2f7ba5d5ae07a239810e68chermann":{"DOI":"","ISBN":"978-1-4920-8276-7","ISSN":"","URL":"","abstract":"","annote":"","author":[{"family":"Winters","given":"Titus"},{"family":"Manshreck","given":"Tom"},{"family":"Hyrum","given":"Wright"}],"citation-label":"Winters2020Softwareengineering","collection-editor":[],"collection-title":"","container-author":[],"container-title":"","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2020"]],"literal":"2020"},"event-place":"Beijing","id":"7f281edbd2f7ba5d5ae07a239810e68chermann","interhash":"5db5f91bf9bab54fe6a2e4aa2185e9ee","intrahash":"7f281edbd2f7ba5d5ae07a239810e68c","issue":"","issued":{"date-parts":[["2020"]],"literal":"2020"},"keyword":"documentation software diss","misc":{"isbn":"978-1-4920-8276-7","language":"Englisch"},"note":"1 Online Ressource (xxv, 571 pages)","number":"","page":"","page-first":"","publisher":"O'Reilly","publisher-place":"Beijing","status":"","title":"Software engineering at Google: lessons learned from programming over time","type":"book","username":"hermann","version":"","volume":""},"3210e1ffc832fafc1dca203bc6d8869dhermann":{"DOI":"10.1007/978-1-4842-7217-6","ISBN":"","ISSN":"","URL":"https://doi.org/10.1007%2F978-1-4842-7217-6","abstract":"","annote":"","author":[{"family":"Bhatti","given":"Jared"},{"family":"Corleissen","given":"Zachary Sarah"},{"family":"Lambourne","given":"Jen"},{"family":"Nunez","given":"David"},{"family":"Waterhouse","given":"Heidi"}],"citation-label":"bhatti2021developers","collection-editor":[],"collection-title":"","container-author":[],"container-title":"","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2021"]],"literal":"2021"},"event-place":"","id":"3210e1ffc832fafc1dca203bc6d8869dhermann","interhash":"a3e47a18268aab24f08bfe75e91190cb","intrahash":"3210e1ffc832fafc1dca203bc6d8869d","issue":"","issued":{"date-parts":[["2021"]],"literal":"2021"},"keyword":"documentation workflow diss","misc":{"doi":"10.1007/978-1-4842-7217-6"},"note":"","number":"","page":"","page-first":"","publisher":"Apress","publisher-place":"","status":"","title":"Docs for Developers","type":"book","username":"hermann","version":"","volume":""},"2f2ee5301ce94996363f6f8863bfdf6ehermann":{"DOI":"","ISBN":"9781848728912; 1848728913","ISSN":"","URL":"http://swbplus.bsz-bw.de/bsz33072066Xinh.htm","abstract":"","annote":"","author":[{"family":"Bjork","given":"R.A."}],"citation-label":"Bjork2011successful","collection-editor":[{"family":"Benjamin","given":"Aaron S."},{"family":"Bjork","given":"Robert A."}],"collection-title":"","container-author":[{"family":"Benjamin","given":"Aaron S."},{"family":"Bjork","given":"Robert A."}],"container-title":"Successful remembering and successful forgetting : a Festschrift in honor of Robert A. Bjork","documents":[],"edition":"","editor":[{"family":"Benjamin","given":"Aaron S."},{"family":"Bjork","given":"Robert A."}],"event-date":{"date-parts":[["2011"]],"literal":"2011"},"event-place":"New York, NY [u.a.]","id":"2f2ee5301ce94996363f6f8863bfdf6ehermann","interhash":"550af74d59660f47da7b019637fecfa6","intrahash":"2f2ee5301ce94996363f6f8863bfdf6e","issue":"","issued":{"date-parts":[["2011"]],"literal":"2011"},"keyword":"documentation Gedächtnis lernen","misc":{"isbn":"9781848728912; 1848728913"},"note":"Literaturangaben; Mit Reg.; \"In January 2009, the University of California, Los Angeles hosted a conference in which only a small portion of the many friends, mentors, colleagues, and students of Robert Bjork came together to discuss current research on human memory and to celebrate together the many traditions and friendships that mark Bob's career.\" (Preface, p. XI)Erscheint: 01. November 2010; On the symbiosis of remembering, forgetting, and learning; Intricacies of spaced retrieval : a resolution; Distributed learning and the size of memory : a 50-year spacing odyssey; The causes and consequences of reminding; Retrieval-induced forgetting and the resolution of competition; On the relationship between interference and inhibition in cognition; Sleep, retrieval inhibition, and the resolving power of human memory; Blocking out blocks : adaptive forgetting of fixation in memory, problem solving, and creative ideation; A contextual framework for understanding when difficulties are desirable; Testing, generation, and spacing applied to education : past, present, and future; Learning from and for tests; Can desirable difficulties overcome deceptive clarity in scientific visualizations?; Desirable difficulties and studying in the region of proximal learning; Data entry : a window to principles of training; An output-bound perspective on false memories : the case of the Deese Roediger McDermott (DRM) paradigm; How should we define and differentiate metacognitions?; Learning from the consequences of retrieval : another test effect; Failing to predict future changes in memory : a stability bias yields long-term overconfidence; Relying on other people's metamemory; Multidimensional models for item recognition and source identification; Pursuing a general model of recall and recognition; Memory for pictures : sometimes a picture is not worth a single word; Administration of dehydroepiandrosterone (DHEA) increases serum levels of androgens and estrogens but does not enhance recognition memory in postmenopausal women; On the fruitful relationship between functional neuroimaging and cognitive theories of human learning and memory; Age-related changes in the episodic simulation of past and future events","number":"","page":"","page-first":"","publisher":"Psychology Press","publisher-place":"New York, NY [u.a.]","status":"","title":"On the Symbiosis of Remembering, Forgetting and Learning","type":"chapter","username":"hermann","version":"","volume":""},"4c6417d0d82be245a908bfd13c0b1e78hermann":{"DOI":"10.12688/f1000research.11407.1","ISBN":"","ISSN":"","URL":"https://doi.org/10.12688%2Ff1000research.11407.1","abstract":"","annote":"","author":[{"family":"Jiménez","given":"Rafael C."},{"family":"Kuzak","given":"Mateusz"},{"family":"Alhamdoosh","given":"Monther"},{"family":"Barker","given":"Michelle"},{"family":"Batut","given":"Bérénice"},{"family":"Borg","given":"Mikael"},{"family":"Capella-Gutierrez","given":"Salvador"},{"family":"Hong","given":"Neil Chue"},{"family":"Cook","given":"Martin"},{"family":"Corpas","given":"Manuel"},{"family":"Flannery","given":"Madison"},{"family":"Garcia","given":"Leyla"},{"family":"Gelp\\'ı","given":"Josep Ll."},{"family":"Gladman","given":"Simon"},{"family":"Goble","given":"Carole"},{"family":"Ferreiro","given":"Montserrat González"},{"family":"Gonzalez-Beltran","given":"Alejandra"},{"family":"Griffin","given":"Philippa C."},{"family":"Grüning","given":"Björn"},{"family":"Hagberg","given":"Jonas"},{"family":"Holub","given":"Petr"},{"family":"Hooft","given":"Rob"},{"family":"Ison","given":"Jon"},{"family":"Katz","given":"Daniel S."},{"family":"Leskosek","given":"Brane"},{"family":"Gómez","given":"Federico López"},{"family":"Oliveira","given":"Luis J."},{"family":"Mellor","given":"David"},{"family":"Mosbergen","given":"Rowland"},{"family":"Mulder","given":"Nicola"},{"family":"Perez-Riverol","given":"Yasset"},{"family":"Pergl","given":"Robert"},{"family":"Pichler","given":"Horst"},{"family":"Pope","given":"Bernard"},{"family":"Sanz","given":"Ferran"},{"family":"Schneider","given":"Maria V."},{"family":"Stodden","given":"Victoria"},{"family":"Suchecki","given":"Radosław"},{"family":"Vareková","given":"Radka Svobodová"},{"family":"Talvik","given":"Harry-Anton"},{"family":"Todorov","given":"Ilian"},{"family":"Treloar","given":"Andrew"},{"family":"Tyagi","given":"Sonika"},{"family":"van Gompel","given":"Maarten"},{"family":"Vaughan","given":"Daniel"},{"family":"Via","given":"Allegra"},{"family":"Wang","given":"Xiaochuan"},{"family":"Watson-Haigh","given":"Nathan S."},{"family":"Crouch","given":"Steve"}],"citation-label":"jimenez2017simple","collection-editor":[],"collection-title":"","container-author":[],"container-title":"F1000Research","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2017","06"]],"literal":"2017"},"event-place":"","id":"4c6417d0d82be245a908bfd13c0b1e78hermann","interhash":"fef517974b15bda533222611846ebee7","intrahash":"4c6417d0d82be245a908bfd13c0b1e78","issue":"","issued":{"date-parts":[["2017","06"]],"literal":"2017"},"keyword":"forschungsdaten documentation software","misc":{"doi":"10.12688/f1000research.11407.1"},"note":"","number":"","page":"876","page-first":"876","publisher":"F1000 Research Ltd","publisher-place":"","status":"","title":"Four simple recommendations to encourage best practices in research software","type":"article-journal","username":"hermann","version":"","volume":"6"},"c339bc95af1451e1bfa414d3e063f714hermann":{"DOI":"10.1186/2047-217X-3-31","ISBN":"","ISSN":"","URL":"","abstract":"Research in the context of data-driven science requires a backbone of\r\n   well-written software, but scientific researchers are typically not\r\n   trained at length in software engineering, the principles for creating\r\n   better software products. To address this gap, in particular for young\r\n   researchers new to programming, we give ten recommendations to ensure\r\n   the usability, sustainability and practicality of research software.","annote":"","author":[{"family":"Hastings","given":"Janna"},{"family":"Haug","given":"Kenneth"},{"family":"Steinbeck","given":"Christoph"}],"citation-label":"hastings2014recommendations","collection-editor":[],"collection-title":"","container-author":[],"container-title":"GIGASCIENCE","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2014","DEC 4"]],"literal":"2014"},"event-place":"236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND","id":"c339bc95af1451e1bfa414d3e063f714hermann","interhash":"f3537561d112ec6aa23e044f853131f4","intrahash":"c339bc95af1451e1bfa414d3e063f714","issue":"","issued":{"date-parts":[["2014","DEC 4"]],"literal":"2014"},"keyword":"forschungsdaten documentation software recommendation diss","misc":{"author-email":"{hastings@ebi.ac.uk}","language":"{English}","researcherid-numbers":"{Haug, Ove Kenneth/O-3809-2019\r\n   Haug, Kenneth/AAD-4241-2019\r\n   Haug, Ove Kenneth/D-8694-2017\r\n   }","oa":"{DOAJ Gold, Green Published}","affiliation":"{Hastings, J (Corresponding Author), European Bioinformat Inst, European Mol Biol Lab, Cheminformat \\& Metab, Wellcome Trust Genome Campus, Hinxton CB10 1SD, England.\r\n   Hastings, Janna; Haug, Kenneth; Steinbeck, Christoph, European Bioinformat Inst, European Mol Biol Lab, Cheminformat \\& Metab, Hinxton CB10 1SD, England.}","usage-count-last-180-days":"{0}","web-of-science-categories":"{Biology; Multidisciplinary Sciences}","article-number":"{31}","number-of-cited-references":"{12}","research-areas":"{Life Sciences \\& Biomedicine - Other Topics; Science \\& Technology -\r\n   Other Topics}","eissn":"{2047-217X}","times-cited":"{4}","orcid-numbers":"{Haug, Ove Kenneth/0000-0003-3168-4145\r\n   Hastings, Janna/0000-0002-3469-4923\r\n   Steinbeck, Christoph/0000-0001-6966-0814}","usage-count-since-2013":"{8}","doc-delivery-number":"{CX4HC}","da":"{2021-05-27}","journal-iso":"{GigaScience}","unique-id":"{ISI:000365658900002}","doi":"{10.1186/2047-217X-3-31}"},"note":"","number":"","page":"","page-first":"","publisher":"BIOMED CENTRAL LTD","publisher-place":"236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND","status":"","title":"Ten recommendations for software engineering in research","type":"article-journal","username":"hermann","version":"","volume":"3"},"b3444488cffac8a5783daba56155426ahermann":{"DOI":"10.1371/journal.pcbi.1005412","ISBN":"","ISSN":"","URL":"https://doi.org/10.1371/journal.pcbi.1005412","abstract":"Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer’s computer. We present ten simple rules to make such software robust enough to be run by anyone, anywhere, and thereby delight your users and collaborators.","annote":"","author":[{"family":"Taschuk","given":"Morgan"},{"family":"Wilson","given":"Greg"}],"citation-label":"taschuk2017simple","collection-editor":[],"collection-title":"","container-author":[],"container-title":"PLOS Computational Biology","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2017","04"]],"literal":"2017"},"event-place":"","id":"b3444488cffac8a5783daba56155426ahermann","interhash":"5a71f8c7107551d18a1a9903e96ddc4d","intrahash":"b3444488cffac8a5783daba56155426a","issue":"4","issued":{"date-parts":[["2017","04"]],"literal":"2017"},"keyword":"forschungsdaten documentation software recommendation diss","misc":{"doi":"10.1371/journal.pcbi.1005412"},"note":"","number":"4","number-of-pages":"9","page":"1-10","page-first":"1","publisher":"Public Library of Science","publisher-place":"","status":"","title":"Ten simple rules for making research software more robust","type":"article-journal","username":"hermann","version":"","volume":"13"},"6d2f38b8cd5017445fc76985fb30e93dhermann":{"DOI":"10.1093/bib/bbw134","ISBN":"","ISSN":"1467-5463","URL":"","abstract":"Investing in documenting your bioinformatics software well can increase\r\n   its impact and save your time. To maximize the effectiveness of your\r\n   documentation, we suggest following a few guidelines we propose here. We\r\n   recommend providing multiple avenues for users to use your research\r\n   software, including a navigable HTML interface with a quick start,\r\n   useful help messages with detailed explanation and thorough examples for\r\n   each feature of your software. By following these guidelines, you can\r\n   assure that your hard work maximally benefits yourself and others.","annote":"","author":[{"family":"Karimzadeh","given":"Mehran"},{"family":"Hoffman","given":"Michael M."}],"citation-label":"karimzadeh2018considerations","collection-editor":[],"collection-title":"","container-author":[],"container-title":"BRIEFINGS IN BIOINFORMATICS","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2018","JUL"]],"literal":"2018"},"event-place":"GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND","id":"6d2f38b8cd5017445fc76985fb30e93dhermann","interhash":"1ddaff170b5ac569bfdcbb3c06dad363","intrahash":"6d2f38b8cd5017445fc76985fb30e93d","issue":"4","issued":{"date-parts":[["2018","JUL"]],"literal":"2018"},"keyword":"forschungsdaten documentation software","misc":{"author-email":"{michael.hoffman@utoronto.ca}","language":"{English}","researcherid-numbers":"{Hoffman, Michael M./I-1924-2012\r\n   }","oa":"{Green Published, Green Accepted, Other Gold}","affiliation":"{Hoffman, MM (Corresponding Author), Princess Margaret Canc Ctr, Toronto Med Discovery Tower 11-311,101 Coll St, Toronto, ON M5G 1L7, Canada.\r\n   Hoffman, Michael M., Princess Margaret Canc Ctr, Toronto Med Discovery Tower 11-311,101 Coll St, Toronto, ON M5G 1L7, Canada.\r\n   Karimzadeh, Mehran; Hoffman, Michael M., Univ Toronto, Dept Med Biophys, Toronto, ON, Canada.\r\n   Hoffman, Michael M., Univ Toronto, Dept Comp Sci, Toronto, ON, Canada.}","usage-count-last-180-days":"{0}","web-of-science-categories":"{Biochemical Research Methods; Mathematical \\& Computational Biology}","number-of-cited-references":"{40}","research-areas":"{Biochemistry \\& Molecular Biology; Mathematical \\& Computational Biology}","eissn":"{1477-4054}","funding-text":"{The Canadian Cancer Society (703827 to M.M.H.), the Ontario Institute\r\n   for Cancer Research (OICR), the Natural Sciences and Engineering\r\n   Research Council of Canada (RGPIN-2015-03948 to M.M.H.), the Ontario\r\n   Ministry of Research, Innovation and Science (ER-15-11-223 to M.M.H.),\r\n   the University of Toronto McLaughlin Centre (MC-2015-16 to M.M.H.) and\r\n   the Princess Margaret Cancer Foundation.}","funding-acknowledgement":"{Canadian Cancer SocietyCanadian Cancer Society (CCS) {[}703827]; Ontario\r\n   Institute for Cancer Research (OICR); Natural Sciences and Engineering\r\n   Research Council of CanadaNatural Sciences and Engineering Research\r\n   Council of Canada (NSERC)CGIAR {[}RGPIN-2015-03948]; Ontario Ministry of\r\n   Research, Innovation and Science {[}ER-15-11-223]; University of Toronto\r\n   McLaughlin Centre {[}MC-2015-16]; Princess Margaret Cancer\r\n   FoundationUniversity of Toronto}","times-cited":"{7}","issn":"{1467-5463}","orcid-numbers":"{Hoffman, Michael M./0000-0002-4517-1562\r\n   Karimzadeh, Mehran/0000-0002-7324-6074}","usage-count-since-2013":"{2}","doc-delivery-number":"{GP9NI}","da":"{2021-05-27}","journal-iso":"{Brief. Bioinform.}","keywords-plus":"{DIFFERENTIAL EXPRESSION ANALYSIS; READ ALIGNMENT; SEQUENCE;\r\n   BIOCONDUCTOR; GENERATION; BENEFITS; QUALITY; SUITE; TOOL; DNA}","unique-id":"{ISI:000441243300014}","doi":"{10.1093/bib/bbw134}"},"note":"","number":"4","number-of-pages":"6","page":"693-699","page-first":"693","publisher":"OXFORD UNIV PRESS","publisher-place":"GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND","status":"","title":"Top considerations for creating bioinformatics software documentation","type":"article-journal","username":"hermann","version":"","volume":"19"},"35c906e6e0ed8af37317e03e45d8d101hermann":{"DOI":"","ISBN":"","ISSN":"","URL":"http://arxiv.org/abs/1702.01715","abstract":"","annote":"","author":[{"family":"Henderson","given":"Fergus"}],"citation-label":"henderson2017software","collection-editor":[],"collection-title":"","container-author":[],"container-title":"CoRR","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2017"]],"literal":"2017"},"event-place":"","id":"35c906e6e0ed8af37317e03e45d8d101hermann","interhash":"e7cf2e3e9da28d4a81f902d6e27553c5","intrahash":"35c906e6e0ed8af37317e03e45d8d101","issue":"","issued":{"date-parts":[["2017"]],"literal":"2017"},"keyword":"forschungsdaten documentation software diss quality","misc":{"eprint":"1702.01715","bibsource":"dblp computer science bibliography, https://dblp.org","archiveprefix":"arXiv"},"note":"","number":"","page":"","page-first":"","publisher":"","publisher-place":"","status":"","title":"Software Engineering at Google","type":"article-journal","username":"hermann","version":"","volume":"abs/1702.01715"},"b1b8a9aa87b52be1c120d24b6fe67fb9hermann":{"DOI":"10.1109/MCSE.2018.021651343","ISBN":"","ISSN":"1558-366X","URL":"https://ieeexplore.ieee.org/document/8317991/","abstract":"Despite the increasing importance of in silico experiments to the scientific discovery process, state-of-the-art software engineering practices are rarely adopted in computational science. To understand the underlying causes for this situation and to identify ways to improve it, the authors conducted a literature survey on software engineering practices in computational science. They identified 13 recurring key characteristics of scientific software development that are the result of the nature of scientific challenges, the limitations of computers, and the cultural environment of scientific software development. Their findings allow them to point out shortcomings of existing approaches for bridging the gap between software engineering and computational science and to provide an outlook on promising research directions that could contribute to improving the current situation.","annote":"","author":[{"family":"Johanson","given":"Arne"},{"family":"Hasselbring","given":"Wilhelm"}],"citation-label":"johanson2018software","collection-editor":[],"collection-title":"","container-author":[],"container-title":"Computing in Science   Engineering","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2018","03"]],"literal":"2018"},"event-place":"","id":"b1b8a9aa87b52be1c120d24b6fe67fb9hermann","interhash":"ebd33778680af00f3b38528ba05f9700","intrahash":"b1b8a9aa87b52be1c120d24b6fe67fb9","issue":"2","issued":{"date-parts":[["2018","03"]],"literal":"2018"},"keyword":"forschungsdaten documentation software diss","misc":{"issn":"1558-366X","doi":"10.1109/MCSE.2018.021651343"},"note":"","number":"2","number-of-pages":"19","page":"90-109","page-first":"90","publisher":"","publisher-place":"","status":"","title":"Software Engineering for Computational Science: Past, Present, Future","type":"article-journal","username":"hermann","version":"","volume":"20"},"af0885a34e9bf1a950b4ccdb3b89bf2chermann":{"DOI":"10.1109/MCSE.2017.18","ISBN":"","ISSN":"1558-366X","URL":"https://ieeexplore.ieee.org/document/7802531/","abstract":"Many of us write code regularly as part of our scientific activity, perhaps even as a full-time job. But even though we write--and use--more and more code, we rarely think about the roles that this code will have in our research, in our publications, and ultimately in the scientific record. In this article, the author outlines some frequent roles of code in computational science. These roles aren't exclusive; in fact, it's common for a piece of code to have several roles, at the same time or as an evolution over time. Thinking about these roles, ideally before starting to write the code, is a good habit to develop.","annote":"","author":[{"family":"Hinsen","given":"Konrad"}],"citation-label":"hinsen2017roles","collection-editor":[],"collection-title":"","container-author":[],"container-title":"Computing in Science   Engineering","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2017","01"]],"literal":"2017"},"event-place":"","id":"af0885a34e9bf1a950b4ccdb3b89bf2chermann","interhash":"3c8beb3be2b3585468268a7eb6ceef7f","intrahash":"af0885a34e9bf1a950b4ccdb3b89bf2c","issue":"1","issued":{"date-parts":[["2017","01"]],"literal":"2017"},"keyword":"forschungsdaten documentation software diss","misc":{"issn":"1558-366X","doi":"10.1109/MCSE.2017.18"},"note":"","number":"1","number-of-pages":"4","page":"78-82","page-first":"78","publisher":"","publisher-place":"","status":"","title":"The Roles of Code in Computational Science","type":"article-journal","username":"hermann","version":"","volume":"19"},"89ca6df04bbf38567e94cb2e05fed0c4hermann":{"DOI":"10.1016/j.infsof.2015.09.006","ISBN":"","ISSN":"","URL":"https://doi.org/10.1016%2Fj.infsof.2015.09.006","abstract":"","annote":"","author":[{"family":"Febrero","given":"Felipe"},{"family":"Calero","given":"Coral"},{"family":"Moraga","given":"M. Ángeles"}],"citation-label":"Febrero_2016","collection-editor":[],"collection-title":"","container-author":[],"container-title":"Information and Software Technology","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2016","02"]],"literal":"2016"},"event-place":"","id":"89ca6df04bbf38567e94cb2e05fed0c4hermann","interhash":"722f4da160c40f832cecac27e437ab4f","intrahash":"89ca6df04bbf38567e94cb2e05fed0c4","issue":"","issued":{"date-parts":[["2016","02"]],"literal":"2016"},"keyword":"forschungsdaten documentation software diss quality","misc":{"doi":"10.1016/j.infsof.2015.09.006"},"note":"","number":"","number-of-pages":"11","page":"18--29","page-first":"18","publisher":"Elsevier BV","publisher-place":"","status":"","title":"Software reliability modeling based on ISO/IEC SQuaRE","type":"article-journal","username":"hermann","version":"","volume":"70"},"f6dbb3004ea1bb6414aadcce70225900hermann":{"DOI":"10.1002/2015EA000155","ISBN":"","ISSN":"2333-5084","URL":"","abstract":"Integrated modeling of coupled surface-subsurface flow and ensuing role\r\n   in diverse Earth system processes is of current research interest to\r\n   characterize nonlinear rainfall-runoff response and also to understand\r\n   land surface energy balances, biogeochemical processes, geomorphological\r\n   dynamics, etc. A growing number of complex models have been developed\r\n   for water-related research, and many of these are made available to the\r\n   Earth science community. However, relatively few resources have been\r\n   made accessible to the potentially large group of Earth science and\r\n   engineering users. New users have to invest an extraordinary effort to\r\n   study the models. To provide a stimulating experience focusing on the\r\n   learning curve of integrated modeling of coupled surface-subsurface\r\n   flow, we describe use cases of an open source model, the Penn State\r\n   Integrated Hydrologic Model, PIHM. New users were guided through data\r\n   processing and model application by reproducing a numerical benchmark\r\n   problem and a real-world watershed simulation. Specifically, we document\r\n   the PIHM application and its computational workflow to enable intuitive\r\n   understanding of coupled surface-subsurface flow processes. In addition,\r\n   we describe the user experience as important evidence of the\r\n   significance of reusability. The interaction shows that documentation of\r\n   data, software, and computational workflow in research papers is a\r\n   promising method to foster open scientific collaboration and reuse. This\r\n   study demonstrates how open science practice in research papers would\r\n   promote the utility of open source software. Addressing such open\r\n   science practice in publications would promote the utility of journal\r\n   papers. Further, popularization of such practice will require\r\n   coordination among research communities, funding agencies, and journals.","annote":"","author":[{"family":"Yu","given":"Xuan"},{"family":"Duffy","given":"Christopher J."},{"family":"Rousseau","given":"Alain N."},{"family":"Bhatt","given":"Gopal"},{"family":"Alvarez","given":"Alvaro Pardo"},{"family":"Charron","given":"Dominique"}],"citation-label":"yu2016science","collection-editor":[],"collection-title":"","container-author":[],"container-title":"EARTH AND SPACE SCIENCE","documents":[],"edition":"","editor":[],"event-date":{"date-parts":[["2016","MAY"]],"literal":"2016"},"event-place":"2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA","id":"f6dbb3004ea1bb6414aadcce70225900hermann","interhash":"3dace87e232cc43887d37e9e3814f0a7","intrahash":"f6dbb3004ea1bb6414aadcce70225900","issue":"5","issued":{"date-parts":[["2016","MAY"]],"literal":"2016"},"keyword":"forschungsdaten documentation software reusability diss","misc":{"author-email":"{xuan@udel.edu}","language":"{English}","researcherid-numbers":"{Yu, Xuan/O-3449-2014\r\n   }","oa":"{DOAJ Gold, Green Accepted}","affiliation":"{Yu, X (Corresponding Author), Univ Delaware, Dept Geol Sci, Newark, DE 19716 USA.\r\n   Yu, Xuan, Univ Delaware, Dept Geol Sci, Newark, DE 19716 USA.\r\n   Duffy, Christopher J.; Bhatt, Gopal, Penn State Univ, Dept Civil \\& Environm Engn, University Pk, PA 16802 USA.\r\n   Rousseau, Alain N.; Alvarez, Alvaro Pardo; Charron, Dominique, Univ Quebec, Inst Natl Rech Sci, Ctr Eau Terre Environm, INRS ETE, Quebec City, PQ, Canada.}","usage-count-last-180-days":"{0}","web-of-science-categories":"{Astronomy \\& Astrophysics; Geosciences, Multidisciplinary}","number-of-cited-references":"{92}","research-areas":"{Astronomy \\& Astrophysics; Geology}","funding-text":"{All data for this paper are properly cited and referred to in the\r\n   reference list. More details of the data are available upon request from\r\n   the corresponding author (xuan@udel.edu). This work was supported by NSF\r\n   grants IIA-1301765, IIS-1344272, ICER-1343800, and ICER-1440323 and\r\n   Shale Hills-Susquehanna Critical Zone Observatory (EAR-0725019,\r\n   EAR-1239285, and EAR-1331726). The authors thank the EarthCube OntoSoft\r\n   leadership for initiating the Geoscience Papers of the Future program\r\n   and the early career advisory committee members. The manuscript\r\n   benefited from conversations facilitated by the EarthCube Distinguished\r\n   Lecturer Program. The authors also thank Yolanda Gil of University of\r\n   Southern California for the insightful discussions and comments on the\r\n   manuscript. We also want to thank Ibrahim Demir from University of Iowa\r\n   and Runjian Wu from University of Arizona for their help with\r\n   proofreading. We are very grateful for the constructive comments from\r\n   reviewer Christopher Hutton and an anonymous reviewer on the earlier\r\n   versions of the manuscript.}","funding-acknowledgement":"{NSFNational Science Foundation (NSF) {[}IIA-1301765, IIS-1344272,\r\n   ICER-1343800, ICER-1440323]; Shale Hills-Susquehanna Critical Zone\r\n   Observatory {[}EAR-0725019, EAR-1239285, EAR-1331726]; Directorate For\r\n   GeosciencesNational Science Foundation (NSF)NSF - Directorate for\r\n   Geosciences (GEO) {[}1331726] Funding Source: National Science\r\n   Foundation; Division Of Earth SciencesNational Science Foundation\r\n   (NSF)NSF - Directorate for Geosciences (GEO) {[}1331726] Funding Source:\r\n   National Science Foundation; Office of Integrative ActivitiesNational\r\n   Science Foundation (NSF)NSF - Office of the Director (OD) {[}1301765]\r\n   Funding Source: National Science Foundation; Office Of The\r\n   DirectorNational Science Foundation (NSF)NSF - Office of the Director\r\n   (OD) {[}1301765] Funding Source: National Science Foundation}","times-cited":"{11}","issn":"{2333-5084}","orcid-numbers":"{Yu, Xuan/0000-0002-9055-7923\r\n   Duffy, Christopher/0000-0003-0080-6445\r\n   Pardo Alvarez, Alvaro/0000-0003-0302-9856\r\n   Rousseau, Alain N./0000-0002-3439-2124\r\n   Charron, Dominique/0000-0002-8494-1152}","usage-count-since-2013":"{11}","doc-delivery-number":"{DU9XO}","da":"{2021-03-01}","journal-iso":"{Earth Space Sci.}","keywords-plus":"{DISTRIBUTED COMPUTING ENVIRONMENT; HYDROLOGIC MODEL; CLIMATE-CHANGE;\r\n   OPPORTUNITIES; SYSTEM; WORKFLOWS; GEOMORPHOLOGY; RESEARCHERS;\r\n   CHALLENGES; FEEDBACKS}","unique-id":"{ISI:000382571700001}","doi":"{10.1002/2015EA000155}"},"note":"","number":"5","number-of-pages":"16","page":"190-206","page-first":"190","publisher":"AMER GEOPHYSICAL UNION","publisher-place":"2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA","status":"","title":"Open science in practice: Learning integrated modeling of coupled\r\n   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