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We present solutions for RDM developed within the DFG-Funded Cluster of Excellence EXC2075 Data-Integrated Simulation Science (SimTech). After an introduction to the scientific context and challenges faced by simulation scientists, we outline the general data management infrastructure and present tools that address these challenges. Exemplary domain applications demonstrate the use and benefits of the proposed data management software solutions. 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Katz","Anna-Lena Lamprecht","Michelle Barker","Axel Loewe","Anne Fouilloux","Jane Wyngaard","Daniel Garijo","Javier Moldon","Leyla Jael Castro","Daniel Wheeler","Joost Rutger Demian Albers","Allen Lee" ], "authors": [ {"first" : "Carlos", "last" : "Martinez-Ortiz"}, {"first" : "Daniel S.", "last" : "Katz"}, {"first" : "Anna-Lena", "last" : "Lamprecht"}, {"first" : "Michelle", "last" : "Barker"}, {"first" : "Axel", "last" : "Loewe"}, {"first" : "Anne", "last" : "Fouilloux"}, {"first" : "Jane", "last" : "Wyngaard"}, {"first" : "Daniel", "last" : "Garijo"}, {"first" : "Javier", "last" : "Moldon"}, {"first" : "Leyla Jael", "last" : "Castro"}, {"first" : "Daniel", "last" : "Wheeler"}, {"first" : "Joost Rutger Demian", "last" : "Albers"}, {"first" : "Allen", "last" : "Lee"} ], "doi" : "10.5281/zenodo.6258366", "bibtexKey": "martinezortiz2022fair4rs" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/27b2cc465640c5b356122749c8f4c2e95/hermann", "tags" : [ "diss","fair","forschungsdaten","software" ], "intraHash" : "7b2cc465640c5b356122749c8f4c2e95", "interHash" : "4575232a7fd1022905db2698a5cb39b0", "label" : "A Survey on Adoption Guidelines for the FAIR4RS \r\n Principles", "user" : "hermann", "description" : "", "date" : "2022-06-28 06:40:41", "changeDate" : "2022-06-28 04:40:41", "count" : 1, "pub-type": "misc", "publisher":"Zenodo", "year": "2022", "url": "https://doi.org/10.5281/zenodo.6374598", "author": [ "Paula Andrea Martinez","Michelle Barker","Alexander Struck","Leyla Jael Castro","Christopher Erdmann","Daniel Garijo","Sandra Gesing","Axel Loewe","Javier Moldón" ], "authors": [ {"first" : "Paula Andrea", "last" : "Martinez"}, {"first" : "Michelle", "last" : "Barker"}, {"first" : "Alexander", "last" : "Struck"}, {"first" : "Leyla Jael", "last" : "Castro"}, {"first" : "Christopher", "last" : "Erdmann"}, {"first" : "Daniel", "last" : "Garijo"}, {"first" : "Sandra", "last" : "Gesing"}, {"first" : "Axel", "last" : "Loewe"}, {"first" : "Javier", "last" : "Moldón"} ], "doi" : "10.5281/zenodo.6374598", "bibtexKey": "martinez2022survey" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2f8395701c149e4aca7e2ad980ae12d79/hermann", "tags" : [ "diss","fair","forschungsdaten","software" ], "intraHash" : "f8395701c149e4aca7e2ad980ae12d79", "interHash" : "97ccca1e8c8fc6ae48e893220d32a75e", "label" : "A Survey on Adoption Guidelines for the FAIR4RS \r\n Principles: Dataset", "user" : "hermann", "description" : "", "date" : "2022-06-28 06:38:58", "changeDate" : "2022-06-28 04:38:58", "count" : 1, "pub-type": "dataset", "publisher":"Zenodo", "year": "2022", "url": "https://doi.org/10.5281/zenodo.6375540", "author": [ "Paula Andrea Martinez","Alexander Struck","Leyla Jael Castro","Daniel Garijo","Axel Loewe","Sandra Gesing","Michelle Barker","Neil Chue Hong","Christopher Erdmann","Carlos Martinez-Ortiz","Susanna-Assunta Sansone" ], "authors": [ {"first" : "Paula Andrea", "last" : "Martinez"}, {"first" : "Alexander", "last" : "Struck"}, {"first" : "Leyla Jael", "last" : "Castro"}, {"first" : "Daniel", "last" : "Garijo"}, {"first" : "Axel", "last" : "Loewe"}, {"first" : "Sandra", "last" : "Gesing"}, {"first" : "Michelle", "last" : "Barker"}, {"first" : "Neil", "last" : "Chue Hong"}, {"first" : "Christopher", "last" : "Erdmann"}, {"first" : "Carlos", "last" : "Martinez-Ortiz"}, {"first" : "Susanna-Assunta", "last" : "Sansone"} ], "version" : "1.0", "doi" : "10.5281/zenodo.6375540", "bibtexKey": "martinez2022survey" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2288bb009be4a6bd36143a17de976c378/hermann", "tags" : [ "diss","fair","forschungsdaten","software" ], "intraHash" : "288bb009be4a6bd36143a17de976c378", "interHash" : "38235a238d5b5cf937a0cfaa08fb368a", "label" : "FAIR Principles for Research Software (FAIR4RS Principles)", "user" : "hermann", "description" : "", "date" : "2022-06-28 06:34:26", "changeDate" : "2022-06-28 04:34:26", "count" : 3, "pub-type": "article", "publisher":"Research Data Alliance", "year": "2021", "url": "https://zenodo.org/record/6623556#.YqCJTJNBwlw", "author": [ "Neil P. Chue Hong","Daniel S. Katz","Michelle Barker","Anna-Lena Lamprecht","Carlos Martinez","Fotis E. Psomopoulos","Jen Harrow","Leyla Jael Castro","Morane Gruenpeter","Paula Andrea Martinez","Tom Honeyman" ], "authors": [ {"first" : "Neil P.", "last" : "Chue Hong"}, {"first" : "Daniel S.", "last" : "Katz"}, {"first" : "Michelle", "last" : "Barker"}, {"first" : "Anna-Lena", "last" : "Lamprecht"}, {"first" : "Carlos", "last" : "Martinez"}, {"first" : "Fotis E.", "last" : "Psomopoulos"}, {"first" : "Jen", "last" : "Harrow"}, {"first" : "Leyla Jael", "last" : "Castro"}, {"first" : "Morane", "last" : "Gruenpeter"}, {"first" : "Paula Andrea", "last" : "Martinez"}, {"first" : "Tom", "last" : "Honeyman"} ], "copyright" : "Creative Commons Attribution 4.0 International", "language" : "en", "doi" : "10.15497/RDA00068", "bibtexKey": "chuehong2021principles" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/29be418a20571f58f3c4b903e781e0b17/hermann", "tags" : [ "development","diss","forschungsdaten","software","success" ], "intraHash" : "9be418a20571f58f3c4b903e781e0b17", "interHash" : "b430f17889ce35afca879683f8c5230b", "label" : "Scientific software production", "user" : "hermann", "description" : "", "date" : "2021-07-19 08:38:08", "changeDate" : "2021-07-19 06:38:08", "count" : 1, "pub-type": "inproceedings", "booktitle": "Proceedings of the ACM 2011 conference on Computer supported cooperative work - CSCW \\textquotesingle11","publisher":"ACM Press", "year": "2011", "url": "https://doi.org/10.1145%2F1958824.1958904", "author": [ "James Howison","James D. Herbsleb" ], "authors": [ {"first" : "James", "last" : "Howison"}, {"first" : "James D.", "last" : "Herbsleb"} ], "doi" : "10.1145/1958824.1958904", "bibtexKey": "howison2011scientific" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/29bacc77fb04a9d2a48996d64c0918d88/hermann", "tags" : [ "development","diss","forschungsdaten","software","success" ], "intraHash" : "9bacc77fb04a9d2a48996d64c0918d88", "interHash" : "cd090c2e63080ddd5a96a8806ba31c4d", "label" : "How to Scale a Code in the Human Dimension", "user" : "hermann", "description" : "", "date" : "2021-07-19 08:36:21", "changeDate" : "2021-07-19 06:36:21", "count" : 2, "pub-type": "article", "journal": "CoRR", "year": "2013", "url": "http://dblp.uni-trier.de/db/journals/corr/corr1301.html#abs-1301-7064", "author": [ "Matthew J. Turk" ], "authors": [ {"first" : "Matthew J.", "last" : "Turk"} ], "volume": "abs/1301.7064", "ee" : "http://arxiv.org/abs/1301.7064", "bibtexKey": "turk2013scale" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2fb13147c5d49c991179550f33cb3ebde/hermann", "tags" : [ "diss","forschungsdaten","recommendation","software" ], "intraHash" : "fb13147c5d49c991179550f33cb3ebde", "interHash" : "c7e73a48cc16904acd7afeb243f9bb1f", "label" : "Top considerations for creating bioinformatics software documentation", "user" : "hermann", "description" : "", "date" : "2021-06-05 17:44:14", "changeDate" : "2021-06-05 15:44:14", "count" : 1, "pub-type": "article", "journal": "Briefings in Bioinformatics", "year": "2017", "url": "https://doi.org/10.1093/bib/bbw134", "author": [ "Mehran Karimzadeh","Michael M Hoffman" ], "authors": [ {"first" : "Mehran", "last" : "Karimzadeh"}, {"first" : "Michael M", "last" : "Hoffman"} ], "volume": "19","number": "4","pages": "693-699","abstract": "Investing in documenting your bioinformatics software well can increase its impact and save your time. To maximize the effectiveness of your documentation, we suggest following a few guidelines we propose here. We recommend providing multiple avenues for users to use your research software, including a navigable HTML interface with a quick start, useful help messages with detailed explanation and thorough examples for each feature of your software. By following these guidelines, you can assure that your hard work maximally benefits yourself and others.", "eprint" : "https://academic.oup.com/bib/article-pdf/19/4/693/25193101/bbw134.pdf", "issn" : "1477-4054", "doi" : "10.1093/bib/bbw134", "bibtexKey": "karimzadeh2017considerations" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/24c6417d0d82be245a908bfd13c0b1e78/hermann", "tags" : [ "documentation","forschungsdaten","software" ], "intraHash" : "4c6417d0d82be245a908bfd13c0b1e78", "interHash" : "fef517974b15bda533222611846ebee7", "label" : "Four simple recommendations to encourage best practices in research software", "user" : "hermann", "description" : "", "date" : "2021-05-27 14:40:06", "changeDate" : "2021-06-05 15:11:18", "count" : 1, "pub-type": "article", "journal": "F1000Research","publisher":"F1000 Research Ltd", "year": "2017", "url": "https://doi.org/10.12688%2Ff1000research.11407.1", "author": [ "Rafael C. Jiménez","Mateusz Kuzak","Monther Alhamdoosh","Michelle Barker","Bérénice Batut","Mikael Borg","Salvador Capella-Gutierrez","Neil Chue Hong","Martin Cook","Manuel Corpas","Madison Flannery","Leyla Garcia","Josep Ll. Gelp\\'ı","Simon Gladman","Carole Goble","Montserrat González Ferreiro","Alejandra Gonzalez-Beltran","Philippa C. Griffin","Björn Grüning","Jonas Hagberg","Petr Holub","Rob Hooft","Jon Ison","Daniel S. Katz","Brane Leskosek","Federico López Gómez","Luis J. Oliveira","David Mellor","Rowland Mosbergen","Nicola Mulder","Yasset Perez-Riverol","Robert Pergl","Horst Pichler","Bernard Pope","Ferran Sanz","Maria V. Schneider","Victoria Stodden","Radosław Suchecki","Radka Svobodová Vareková","Harry-Anton Talvik","Ilian Todorov","Andrew Treloar","Sonika Tyagi","Maarten van Gompel","Daniel Vaughan","Allegra Via","Xiaochuan Wang","Nathan S. Watson-Haigh","Steve Crouch" ], "authors": [ {"first" : "Rafael C.", "last" : "Jiménez"}, {"first" : "Mateusz", "last" : "Kuzak"}, {"first" : "Monther", "last" : "Alhamdoosh"}, {"first" : "Michelle", "last" : "Barker"}, {"first" : "Bérénice", "last" : "Batut"}, {"first" : "Mikael", "last" : "Borg"}, {"first" : "Salvador", "last" : "Capella-Gutierrez"}, {"first" : "Neil Chue", "last" : "Hong"}, {"first" : "Martin", "last" : "Cook"}, {"first" : "Manuel", "last" : "Corpas"}, {"first" : "Madison", "last" : "Flannery"}, {"first" : "Leyla", "last" : "Garcia"}, {"first" : "Josep Ll.", "last" : "Gelp\\'ı"}, {"first" : "Simon", "last" : "Gladman"}, {"first" : "Carole", "last" : "Goble"}, {"first" : "Montserrat González", "last" : "Ferreiro"}, {"first" : "Alejandra", "last" : "Gonzalez-Beltran"}, {"first" : "Philippa C.", "last" : "Griffin"}, {"first" : "Björn", "last" : "Grüning"}, {"first" : "Jonas", "last" : "Hagberg"}, {"first" : "Petr", "last" : "Holub"}, {"first" : "Rob", "last" : "Hooft"}, {"first" : "Jon", "last" : "Ison"}, {"first" : "Daniel S.", "last" : "Katz"}, {"first" : "Brane", "last" : "Leskosek"}, {"first" : "Federico López", "last" : "Gómez"}, {"first" : "Luis J.", "last" : "Oliveira"}, {"first" : "David", "last" : "Mellor"}, {"first" : "Rowland", "last" : "Mosbergen"}, {"first" : "Nicola", "last" : "Mulder"}, {"first" : "Yasset", "last" : "Perez-Riverol"}, {"first" : "Robert", "last" : "Pergl"}, {"first" : "Horst", "last" : "Pichler"}, {"first" : "Bernard", "last" : "Pope"}, {"first" : "Ferran", "last" : "Sanz"}, {"first" : "Maria V.", "last" : "Schneider"}, {"first" : "Victoria", "last" : "Stodden"}, {"first" : "Radosław", "last" : "Suchecki"}, {"first" : "Radka Svobodová", "last" : "Vareková"}, {"first" : "Harry-Anton", "last" : "Talvik"}, {"first" : "Ilian", "last" : "Todorov"}, {"first" : "Andrew", "last" : "Treloar"}, {"first" : "Sonika", "last" : "Tyagi"}, {"first" : "Maarten", "last" : "van Gompel"}, {"first" : "Daniel", "last" : "Vaughan"}, {"first" : "Allegra", "last" : "Via"}, {"first" : "Xiaochuan", "last" : "Wang"}, {"first" : "Nathan S.", "last" : "Watson-Haigh"}, {"first" : "Steve", "last" : "Crouch"} ], "volume": "6","pages": "876", "doi" : "10.12688/f1000research.11407.1", "bibtexKey": "jimenez2017simple" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2c339bc95af1451e1bfa414d3e063f714/hermann", "tags" : [ "diss","documentation","forschungsdaten","recommendation","software" ], "intraHash" : "c339bc95af1451e1bfa414d3e063f714", "interHash" : "f3537561d112ec6aa23e044f853131f4", "label" : "Ten recommendations for software engineering in research", "user" : "hermann", "description" : "", "date" : "2021-05-27 14:24:06", "changeDate" : "2021-05-27 12:41:49", "count" : 1, "pub-type": "article", "journal": "GIGASCIENCE","publisher":"BIOMED CENTRAL LTD","address":"236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND", "year": "2014", "url": "", "author": [ "Janna Hastings","Kenneth Haug","Christoph Steinbeck" ], "authors": [ {"first" : "Janna", "last" : "Hastings"}, {"first" : "Kenneth", "last" : "Haug"}, {"first" : "Christoph", "last" : "Steinbeck"} ], "volume": "3","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.", "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", "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", "bibtexKey": "hastings2014recommendations" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2b3444488cffac8a5783daba56155426a/hermann", "tags" : [ "diss","documentation","forschungsdaten","recommendation","software" ], "intraHash" : "b3444488cffac8a5783daba56155426a", "interHash" : "5a71f8c7107551d18a1a9903e96ddc4d", "label" : "Ten simple rules for making research software more robust", "user" : "hermann", "description" : "", "date" : "2021-05-27 14:15:39", "changeDate" : "2021-05-27 12:41:59", "count" : 3, "pub-type": "article", "journal": "PLOS Computational Biology","publisher":"Public Library of Science", "year": "2017", "url": "https://doi.org/10.1371/journal.pcbi.1005412", "author": [ "Morgan Taschuk","Greg Wilson" ], "authors": [ {"first" : "Morgan", "last" : "Taschuk"}, {"first" : "Greg", "last" : "Wilson"} ], "volume": "13","number": "4","pages": "1-10","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\u2019s 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.", "doi" : "10.1371/journal.pcbi.1005412", "bibtexKey": "taschuk2017simple" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/21067f244d259e0508d982198162629cd/hermann", "tags" : [ "diss","forschungsdaten","opensource","software" ], "intraHash" : "1067f244d259e0508d982198162629cd", "interHash" : "6e78586c851511bb216526a592d1da2c", "label" : "Lesson Development for Open Source Software Best Practices Adoption", "user" : "hermann", "description" : "", "date" : "2021-05-27 14:08:47", "changeDate" : "2021-05-27 12:08:47", "count" : 1, "pub-type": "inproceedings", "booktitle": "2018 IEEE 14th International Conference on e-Science (e-Science)", "year": "2018", "url": "https://ieeexplore.ieee.org/document/8588630/", "author": [ "Mateusz Kuzak","Jen Harrow","Rafael C. Jimenez","Paula Andrea Martinez","Fotis E. Psomopoulos","Radka Svobodová Vařeková","Allegra Via" ], "authors": [ {"first" : "Mateusz", "last" : "Kuzak"}, {"first" : "Jen", "last" : "Harrow"}, {"first" : "Rafael C.", "last" : "Jimenez"}, {"first" : "Paula Andrea", "last" : "Martinez"}, {"first" : "Fotis E.", "last" : "Psomopoulos"}, {"first" : "Radka", "last" : "Svobodová Vařeková"}, {"first" : "Allegra", "last" : "Via"} ], "pages": "19-20","abstract": "The \"ELIXIR Training Platform\" is partnering with The Carpentries (Software and Data Carpentry) to train life science researchers in computing and data management skills. The \"ELIXIR Software development best practices\" group, which is part of the ELIXIR Tools Platform, has proposed \"Four simple recommendations to encourage best practices in research software\" aiming to help researchers and developers to adopt Open Source Software (OSS) practices and thus improve the quality and sustainability of research software. In order to encourage researchers and developers to adopt the four recommendations (4OSS) and build FAIR software, we are developing specific and practical training materials, taking advantage of the Carpentries approach and experience in training material development and maintenance.", "doi" : "10.1109/eScience.2018.00011", "bibtexKey": "kuzak2018lesson" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2756885cd7f6a36477c98be240e592a0f/hermann", "tags" : [ "forschungsdaten","software","steward" ], "intraHash" : "756885cd7f6a36477c98be240e592a0f", "interHash" : "9e3fd42a44a385016436c5f92d5d4fa2", "label" : "The Role of Data Stewardship in Software Sustainability and Reproducibility", "user" : "hermann", "description" : "", "date" : "2021-05-27 14:06:05", "changeDate" : "2021-05-27 12:06:05", "count" : 2, "pub-type": "inproceedings", "booktitle": "2018 IEEE 14th International Conference on e-Science (e-Science)", "year": "2018", "url": "https://ieeexplore.ieee.org/document/8588628/", "author": [ "Maria J. Cruz","Shalini Kurapati","Yasemin Turkyilmaz-van der Velden" ], "authors": [ {"first" : "Maria J.", "last" : "Cruz"}, {"first" : "Shalini", "last" : "Kurapati"}, {"first" : "Yasemin", "last" : "Turkyilmaz-van der Velden"} ], "pages": "1-8","abstract": "Software and computational tools are instrumental for scientific investigation in today's digitized research environment. Despite this crucial role, the path towards implementing best practices to achieve reproducibility and sustainability of research software is challenging. Delft University of Technology has begun recently a novel initiative of data stewardship - disciplinary support for research data management, one of the main aims of which is achieving reproducibility of scientific results in general. In this paper, we aim to explore the potential of data stewardship for supporting software reproducibility and sustainability as well. Recently, we gathered the key stakeholders of the topic (i.e. researchers, research software engineers, and data stewards) in a workshop setting to understand the challenges and barriers, the support required to achieve software sustainability and reproducibility, and how all the three parties can efficiently work together. Based on the insights from the workshop, as well as our professional experience as data stewards, we draw conclusions on possible ways forward to achieve the important goal of software reproducibility and sustainability through coordinated efforts of the key stakeholders.", "doi" : "10.1109/eScience.2018.00009", "bibtexKey": "cruz2018stewardship" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/26d2f38b8cd5017445fc76985fb30e93d/hermann", "tags" : [ "documentation","forschungsdaten","software" ], "intraHash" : "6d2f38b8cd5017445fc76985fb30e93d", "interHash" : "1ddaff170b5ac569bfdcbb3c06dad363", "label" : "Top considerations for creating bioinformatics software documentation", "user" : "hermann", "description" : "", "date" : "2021-05-27 14:05:13", "changeDate" : "2021-05-27 12:05:13", "count" : 2, "pub-type": "article", "journal": "BRIEFINGS IN BIOINFORMATICS","publisher":"OXFORD UNIV PRESS","address":"GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND", "year": "2018", "url": "", "author": [ "Mehran Karimzadeh","Michael M. Hoffman" ], "authors": [ {"first" : "Mehran", "last" : "Karimzadeh"}, {"first" : "Michael M.", "last" : "Hoffman"} ], "volume": "19","number": "4","pages": "693-699","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.", "author-email" : "michael.hoffman@utoronto.ca", "language" : "English", "researcherid-numbers" : "Hoffman, Michael M./I-1924-2012", "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", "bibtexKey": "karimzadeh2018considerations" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/24e7ce166ae110b14ab0e7d5ba2be67b0/hermann", "tags" : [ "forschungsdaten","software","survey" ], "intraHash" : "4e7ce166ae110b14ab0e7d5ba2be67b0", "interHash" : "8a147b46ffd2b36f399bd0784c53c857", "label" : "Towards computational reproducibility: researcher perspectives on the use and sharing of software", "user" : "hermann", "description" : "", "date" : "2021-05-27 13:59:05", "changeDate" : "2021-05-27 11:59:05", "count" : 3, "pub-type": "article", "journal": "PeerJ Computer Science","publisher":"PeerJ", "year": "2018", "url": "https://doi.org/10.7717%2Fpeerj-cs.163", "author": [ "Yasmin AlNoamany","John A. Borghi" ], "authors": [ {"first" : "Yasmin", "last" : "AlNoamany"}, {"first" : "John A.", "last" : "Borghi"} ], "volume": "4","pages": "e163", "doi" : "10.7717/peerj-cs.163", "bibtexKey": "alnoamany2018towards" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2703614507797ec5c691ca1a52a028226/hermann", "tags" : [ "diss","forschungsdaten","software","susi","zitieren" ], "intraHash" : "703614507797ec5c691ca1a52a028226", "interHash" : "2543e90db868c76f3dca1d24285985e5", "label" : "Attributing and Referencing (Research) Software: Best Practices and Outlook From Inria", "user" : "hermann", "description" : "", "date" : "2021-05-27 11:02:12", "changeDate" : "2021-05-27 09:02:12", "count" : 1, "pub-type": "article", "journal": "Computing in Science Engineering", "year": "2020", "url": "https://ieeexplore.ieee.org/document/8887228/", "author": [ "Pierre Alliez","Roberto Di Cosmo","Benjamin Guedj","Alain Girault","Mohand-Saïd Hacid","Arnaud Legrand","Nicolas Rougier" ], "authors": [ {"first" : "Pierre", "last" : "Alliez"}, {"first" : "Roberto Di", "last" : "Cosmo"}, {"first" : "Benjamin", "last" : "Guedj"}, {"first" : "Alain", "last" : "Girault"}, {"first" : "Mohand-Saïd", "last" : "Hacid"}, {"first" : "Arnaud", "last" : "Legrand"}, {"first" : "Nicolas", "last" : "Rougier"} ], "volume": "22","number": "1","pages": "39-52","abstract": "Software is a fundamental pillar of modern scientific research, across all fields and disciplines. However, there is a lack of adequate means to cite and reference software due to the complexity of the problem in terms of authorship, roles, and credits. This complexity is further increased when it is considered over the lifetime of a software that can span up to several decades. Building upon the internal experience of Inria, the French research institute for digital sciences, we provide in this article a contribution to the ongoing efforts in order to develop proper guidelines and recommendations for software citation and reference. Namely, we recommend: first, a richer taxonomy for software contributions with a qualitative scale; second, to put humans at the heart of the evaluation; and third, to distinguish citation from reference.", "issn" : "1558-366X", "doi" : "10.1109/MCSE.2019.2949413", "bibtexKey": "alliez2020attributing" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2688d9c5a956800b79b349ee42c2d990f/hermann", "tags" : [ "SAFE","forschungsdaten","software","survey" ], "intraHash" : "688d9c5a956800b79b349ee42c2d990f", "interHash" : "077542f3073f46f9dd9814c783bb57aa", "label" : "How successfully is open-source research software adopted? Results and implications of surveying the users of a sensitivity analysis toolbox", "user" : "hermann", "description" : "", "date" : "2021-05-27 11:01:09", "changeDate" : "2021-05-27 09:01:09", "count" : 1, "pub-type": "article", "journal": "Environmental Modelling & Software","publisher":"Elsevier BV", "year": "2020", "url": "https://doi.org/10.1016%2Fj.envsoft.2019.104579", "author": [ "Francesca Pianosi","Fanny Sarrazin","Thorsten Wagener" ], "authors": [ {"first" : "Francesca", "last" : "Pianosi"}, {"first" : "Fanny", "last" : "Sarrazin"}, {"first" : "Thorsten", "last" : "Wagener"} ], "volume": "124","pages": "104579", "doi" : "10.1016/j.envsoft.2019.104579", "bibtexKey": "pianosi2020successfully" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/244f8b15507cee0655f0584dd884be31a/hermann", "tags" : [ "diss","forschungsdaten","rules","software" ], "intraHash" : "44f8b15507cee0655f0584dd884be31a", "interHash" : "d79c03967a6bb7041fd1bfb1f8a8a216", "label" : "Approaching Software Engineering for Marine Sciences: A Single Development Process for Multiple End-User Applications", "user" : "hermann", "description" : "", "date" : "2021-05-27 10:42:19", "changeDate" : "2021-05-27 08:42:19", "count" : 1, "pub-type": "article", "journal": "Journal of Marine Science and Engineering","publisher":"MDPI AG", "year": "2020", "url": "https://doi.org/10.3390%2Fjmse8050350", "author": [ "Pedro Magaña","Juan Del-Rosal-Salido","Manuel Cobos","Andrea Lira-Loarca","Miguel Ortega-Sánchez" ], "authors": [ {"first" : "Pedro", "last" : "Magaña"}, {"first" : "Juan", "last" : "Del-Rosal-Salido"}, {"first" : "Manuel", "last" : "Cobos"}, {"first" : "Andrea", "last" : "Lira-Loarca"}, {"first" : "Miguel", "last" : "Ortega-Sánchez"} ], "volume": "8","number": "5","pages": "350", "doi" : "10.3390/jmse8050350", "bibtexKey": "magana2020approaching" } ] }