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Main challenges are discussed: The Big Data qualities of HPC research data, technical data management, organizational and administrative challenges. Emerging from these challenges, requirements for a feasible HPC research data management are derived and an alternative data life cycle is proposed. The requirement analysis includes recommendations which are based on a modified OAIS architecture: To meet the HPC requirements of a scalable system, metadata and data must not be stored together. Metadata keys are defined and organizational actions are recommended. 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Version 4.1.", "user" : "diglezakis", "description" : "DataCite Schema", "date" : "2017-12-30 14:21:47", "changeDate" : "2018-02-16 08:31:32", "count" : 1, "pub-type": "article", "year": "2017", "url": "", "author": [ "DataCite Metadata Working Group" ], "authors": [ {"first" : "DataCite Metadata Working", "last" : "Group"} ], "editor": [ "DataCite e.V." ], "editors": [ {"first" : "DataCite", "last" : "e.V."} ], "doi" : "10.5438/0015", "bibtexKey": "noauthororeditor" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2760b9f165bd4b612147d7f6cb0f34d20/diglezakis", "tags" : [ "forschungsdaten","dfg","leitlininen","obib" ], "intraHash" : "760b9f165bd4b612147d7f6cb0f34d20", "interHash" : "5cb649d8852d45dca707a84ba6062fb5", "label" : "Leitlinien zum Umgang mit Forschungsdaten", "user" : "diglezakis", "description" : "", "date" : "2017-12-04 12:00:11", "changeDate" : "2018-02-16 08:31:04", "count" : 2, "pub-type": "techreport", "year": "2015", "url": "", "editor": [ "Deutsche Forschungsgemeinschaft (DFG)" ], "editors": [ {"first" : "Deutsche Forschungsgemeinschaft", "last" : "(DFG)"} ], "bibtexKey": "dfg2015leitlinien" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/211b36eb1eb08709dea38db91522cbe05/diglezakis", "tags" : [ "forschungsdaten","obib","fair" ], "intraHash" : "11b36eb1eb08709dea38db91522cbe05", "interHash" : "d3942649973e201b265fbdde29d14453", "label" : "The FAIR Guiding Principles for scientific data management and stewardship", "user" : "diglezakis", "description" : "The FAIR Guiding Principles for scientific data management and stewardship | Scientific Data", "date" : "2017-10-24 14:10:07", "changeDate" : "2018-02-16 08:41:52", "count" : 12, "pub-type": "article", "journal": "Scientific Data","publisher":"Springer Nature", "year": "2016", "url": "http://dx.doi.org/10.1038/sdata.2016.18", "author": [ "Mark D. Wilkinson","Michel Dumontier","IJsbrand Jan Aalbersberg","Gabrielle Appleton","Myles Axton","Arie Baak","Niklas Blomberg","Jan-Willem Boiten","Luiz Bonino da Silva Santos","Philip E. Bourne","Jildau Bouwman","Anthony J. Brookes","Tim Clark","Mercè Crosas","Ingrid Dillo","Olivier Dumon","Scott Edmunds","Chris T. Evelo","Richard Finkers","Alejandra Gonzalez-Beltran","Alasdair J.G Gray","Paul Groth","Carole Goble","Jeffrey S. Grethe","Jaap Heringa","Peter A.C \u2019t Hoen","Rob Hooft","Tobias Kuhn","Ruben Kok","Joost Kok","Scott J. Lusher","Maryann E. Martone","Albert Mons","Abel L. Packer","Bengt Persson","Philippe Rocca-Serra","Marco Roos","Rene van Schaik","Susanna-Assunta Sansone","Erik Schultes","Thierry Sengstag","Ted Slater","George Strawn","Morris A. Swertz","Mark Thompson","Johan van der Lei","Erik van Mulligen","Jan Velterop","Andra Waagmeester","Peter Wittenburg","Katherine Wolstencroft","Jun Zhao","Barend Mons" ], "authors": [ {"first" : "Mark D.", "last" : "Wilkinson"}, {"first" : "Michel", "last" : "Dumontier"}, {"first" : "IJsbrand Jan", "last" : "Aalbersberg"}, {"first" : "Gabrielle", "last" : "Appleton"}, {"first" : "Myles", "last" : "Axton"}, {"first" : "Arie", "last" : "Baak"}, {"first" : "Niklas", "last" : "Blomberg"}, {"first" : "Jan-Willem", "last" : "Boiten"}, {"first" : "Luiz Bonino", "last" : "da Silva Santos"}, {"first" : "Philip E.", "last" : "Bourne"}, {"first" : "Jildau", "last" : "Bouwman"}, {"first" : "Anthony J.", "last" : "Brookes"}, {"first" : "Tim", "last" : "Clark"}, {"first" : "Mercè", "last" : "Crosas"}, {"first" : "Ingrid", "last" : "Dillo"}, {"first" : "Olivier", "last" : "Dumon"}, {"first" : "Scott", "last" : "Edmunds"}, {"first" : "Chris T.", "last" : "Evelo"}, {"first" : "Richard", "last" : "Finkers"}, {"first" : "Alejandra", "last" : "Gonzalez-Beltran"}, {"first" : "Alasdair J.G", "last" : "Gray"}, {"first" : "Paul", "last" : "Groth"}, {"first" : "Carole", "last" : "Goble"}, {"first" : "Jeffrey S.", "last" : "Grethe"}, {"first" : "Jaap", "last" : "Heringa"}, {"first" : "Peter A.C", "last" : "\u2019t Hoen"}, {"first" : "Rob", "last" : "Hooft"}, {"first" : "Tobias", "last" : "Kuhn"}, {"first" : "Ruben", "last" : "Kok"}, {"first" : "Joost", "last" : "Kok"}, {"first" : "Scott J.", "last" : "Lusher"}, {"first" : "Maryann E.", "last" : "Martone"}, {"first" : "Albert", "last" : "Mons"}, {"first" : "Abel L.", "last" : "Packer"}, {"first" : "Bengt", "last" : "Persson"}, {"first" : "Philippe", "last" : "Rocca-Serra"}, {"first" : "Marco", "last" : "Roos"}, {"first" : "Rene", "last" : "van Schaik"}, {"first" : "Susanna-Assunta", "last" : "Sansone"}, {"first" : "Erik", "last" : "Schultes"}, {"first" : "Thierry", "last" : "Sengstag"}, {"first" : "Ted", "last" : "Slater"}, {"first" : "George", "last" : "Strawn"}, {"first" : "Morris A.", "last" : "Swertz"}, {"first" : "Mark", "last" : "Thompson"}, {"first" : "Johan", "last" : "van der Lei"}, {"first" : "Erik", "last" : "van Mulligen"}, {"first" : "Jan", "last" : "Velterop"}, {"first" : "Andra", "last" : "Waagmeester"}, {"first" : "Peter", "last" : "Wittenburg"}, {"first" : "Katherine", "last" : "Wolstencroft"}, {"first" : "Jun", "last" : "Zhao"}, {"first" : "Barend", "last" : "Mons"} ], "volume": "3","pages": "160018--", "bibtexKey": "wilkinson2016guiding" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2af120e2025f2231edbdc559d627cc66e/diglezakis", "tags" : [ "imported","obib","molecularSimulation" ], "intraHash" : "af120e2025f2231edbdc559d627cc66e", "interHash" : "472014159b2ed79400b3c630847c5e0a", "label" : "DCMS: A data analytics and management system for molecular simulation", "user" : "diglezakis", "description" : "", "date" : "2017-09-12 16:48:59", "changeDate" : "2018-02-16 08:32:48", "count" : 1, "pub-type": "article", "journal": "Journal of Big Data", "year": "2014", "url": "https://doi.org/10.1186/s40537-014-0009-5", "author": [ "Anand Kumar","Vladimir Grupcev","Meryem Berrada","Joseph C. Fogarty","Yi-Cheng Tu","Xingquan Zhu","Sagar A. Pandit","Yuni Xia" ], "authors": [ {"first" : "Anand", "last" : "Kumar"}, {"first" : "Vladimir", "last" : "Grupcev"}, {"first" : "Meryem", "last" : "Berrada"}, {"first" : "Joseph C.", "last" : "Fogarty"}, {"first" : "Yi-Cheng", "last" : "Tu"}, {"first" : "Xingquan", "last" : "Zhu"}, {"first" : "Sagar A.", "last" : "Pandit"}, {"first" : "Yuni", "last" : "Xia"} ], "volume": "2","number": "1","pages": "9","abstract": "Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface (i.e., SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression.", "issn" : "2196-1115", "doi" : "10.1186/s40537-014-0009-5", "bibtexKey": "Kumar2014" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/21952e97243dd71271aed552ba7113ff5/diglezakis", "tags" : [ "forschungsdaten","obib","engineering" ], "intraHash" : "1952e97243dd71271aed552ba7113ff5", "interHash" : "979907d0036696b1e6a60248e7eb0563", "label" : "The MoSGrid Science Gateway \u2013 A Complete Solution for Molecular Simulations", "user" : "diglezakis", "description" : "The MoSGrid Science Gateway \u2013 A Complete Solution for Molecular Simulations - Journal of Chemical Theory and Computation (ACS Publications)", "date" : "2017-08-21 13:09:34", "changeDate" : "2018-02-16 08:32:35", "count" : 1, "pub-type": "article", "journal": "Journal of Chemical Theory and Computation", "year": "2014", "url": "http://dx.doi.org/10.1021/ct500159h", "author": [ "Jens Krüger","Richard Grunzke","Sandra Gesing","Sebastian Breuers","André Brinkmann","Luis de la Garza","Oliver Kohlbacher","Martin Kruse","Wolfgang E. Nagel","Lars Packschies","Ralph Müller-Pfefferkorn","Patrick Schäfer","Charlotta Schärfe","Thomas Steinke","Tobias Schlemmer","Klaus Dieter Warzecha","Andreas Zink","Sonja Herres-Pawlis" ], "authors": [ {"first" : "Jens", "last" : "Krüger"}, {"first" : "Richard", "last" : "Grunzke"}, {"first" : "Sandra", "last" : "Gesing"}, {"first" : "Sebastian", "last" : "Breuers"}, {"first" : "André", "last" : "Brinkmann"}, {"first" : "Luis", "last" : "de la Garza"}, {"first" : "Oliver", "last" : "Kohlbacher"}, {"first" : "Martin", "last" : "Kruse"}, {"first" : "Wolfgang E.", "last" : "Nagel"}, {"first" : "Lars", "last" : "Packschies"}, {"first" : "Ralph", "last" : "Müller-Pfefferkorn"}, {"first" : "Patrick", "last" : "Schäfer"}, {"first" : "Charlotta", "last" : "Schärfe"}, {"first" : "Thomas", "last" : "Steinke"}, {"first" : "Tobias", "last" : "Schlemmer"}, {"first" : "Klaus Dieter", "last" : "Warzecha"}, {"first" : "Andreas", "last" : "Zink"}, {"first" : "Sonja", "last" : "Herres-Pawlis"} ], "volume": "10","number": "6","pages": "2232-2245","note": "PMID: 26580747","abstract": "The MoSGrid portal offers an approach to carry out high-quality molecular simulations on distributed compute infrastructures to scientists with all kinds of background and experience levels. A user-friendly Web interface guarantees the ease-of-use of modern chemical simulation applications well established in the field. The usage of well-defined workflows annotated with metadata largely improves the reproducibility of simulations in the sense of good lab practice. The MoSGrid science gateway supports applications in the domains quantum chemistry (QC), molecular dynamics (MD), and docking. This paper presents the open-source MoSGrid architecture as well as lessons learned from its design.", "doi" : "10.1021/ct500159h", "eprint" : "http://dx.doi.org/10.1021/ct500159h", "bibtexKey": "doi:10.1021/ct500159h" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2712508bc41923c2891a6eade1bac2398/diglezakis", "tags" : [ "forschungsdaten","motivation","obib","befragung" ], "intraHash" : "712508bc41923c2891a6eade1bac2398", "interHash" : "6194282839dda6ebe379ec4cc1c6c399", "label" : "Öffentlicher Abschlussbericht von\r\nbwFDM-Communities", "user" : "diglezakis", "description" : "", "date" : "2017-08-15 16:56:32", "changeDate" : "2018-02-16 08:40:12", "count" : 1, "pub-type": "techreport", "year": "2015", "url": "", "author": [ "Frank Tristram","Achim Streit" ], "authors": [ {"first" : "Frank", "last" : "Tristram"}, {"first" : "Achim", "last" : "Streit"} ], "bibtexKey": "tristram2015ffentlicher" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/28e03b4aeb58ea1b36ed9a9a6c72d54d1/diglezakis", "tags" : [ "bigdata","forschungsdaten","obib","engineering","iag" ], "intraHash" : "8e03b4aeb58ea1b36ed9a9a6c72d54d1", "interHash" : "bfc959092e0f6966f300d2ac25215c25", "label" : "Turbulence in the Era of Big Data: Recent Experiences with Sharing Large Datasets", "user" : "diglezakis", "description" : "", "date" : "2017-07-18 09:41:03", "changeDate" : "2018-02-16 08:37:20", "count" : 1, "pub-type": "inbook", "booktitle": "Whither turbulence and big data in the 21st century?","publisher":"Springer","address":"Switzerland", "year": "2017", "url": "", "author": [ "Charles Meneveau","Ivan Marusic" ], "authors": [ {"first" : "Charles", "last" : "Meneveau"}, {"first" : "Ivan", "last" : "Marusic"} ], "editor": [ "Andrew Pollard","Luciano Castillo","Luminita Danaila","Mark Glauser" ], "editors": [ {"first" : "Andrew", "last" : "Pollard"}, {"first" : "Luciano", "last" : "Castillo"}, {"first" : "Luminita", "last" : "Danaila"}, {"first" : "Mark", "last" : "Glauser"} ], "pages": "497-507","abstract": "In the context of the contemporary push for \u201Cbig data\u201D in many fields, we review recent experiences building large databases for turbulence research. We consider data from direct numerical simulations (DNS) of various canonical flows and from experimental studies and related numerical simulations of wall-bounded turbulence, where the data storage needs are particularly challenging due to the very large range of length and time scales that exists in these flows at high Reynolds numbers. The focus is on a move from the traditional approach of data-handling and analysis where datasets are moved to individual computers, to one where much of the analysis is moved to the hosting system that stores these data. In this context we give a summary of a unique open numerical laboratory that archives over 200\u2009Terabytes of DNS data, including full spatio-temporal flow fields of various canonical flows. Particular attention is given to the unique access requirements for large datasets to become open to the research community and the success the system has had in democratizing access to large datasets.", "isbn" : "978-3-319-41217-7", "doi" : "http://dx.doi.org/10.1007/978-3-319-41217-7", "bibtexKey": "meneveau2017turbulence" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/299e8a3d8e32d794bbb8872e3e32bf103/diglezakis", "tags" : [ "bigdata","forschungsdaten","reuse","dissemination","simulation","obib","engineering","iag" ], "intraHash" : "99e8a3d8e32d794bbb8872e3e32bf103", "interHash" : "dc6a0df4ec49e56c562c7b9c86c63cc7", "label" : "Public Dissemination of Raw Turbulence Data", "user" : "diglezakis", "description" : "PUMA", "date" : "2017-07-18 09:33:00", "changeDate" : "2018-02-16 08:39:42", "count" : 1, "pub-type": "inbook", "booktitle": "Whither turbulence and big data in the 21st century?","publisher":"Springer","address":"Switzerland", "year": "2017", "url": "", "author": [ "Juan A. Sillero","Javier Jiminéz" ], "authors": [ {"first" : "Juan A.", "last" : "Sillero"}, {"first" : "Javier", "last" : "Jiminéz"} ], "editor": [ "Andrew Pollard","Luciano Castillo","Luminita Danaila","Mark Glauser" ], "editors": [ {"first" : "Andrew", "last" : "Pollard"}, {"first" : "Luciano", "last" : "Castillo"}, {"first" : "Luminita", "last" : "Danaila"}, {"first" : "Mark", "last" : "Glauser"} ], "pages": "509-515","abstract": "It is argued that there is a certain urgency to the discussion of whether raw data should be made publicly available within the turbulence community, and about the best ways, technology and rules for possible dissemination. Besides expressing the personal opinion that such sharing would be advantageous for the field, the urgency mostly arises from the danger that funding agencies or other institutions would otherwise set standards without proper community input. This paper is in part a plea for community action in that direction. As an example, the experience of the Madrid school of Aeronautics with the dissemination of numerical simulation results is briefly reviewed, including the present technological solutions and usage statistics.", "isbn" : "978-3-319-41215-3", "doi" : "10.1007/978-3-3 19-41217-7_28", "bibtexKey": "noauthororeditor" } ] }