{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2283458f5c817451555fdcc740d8d2b2f/hermann", "tags" : [ "forschungsdatenmanagement","oa","software","workflowTracking","workflowmananagement" ], "intraHash" : "283458f5c817451555fdcc740d8d2b2f", "interHash" : "b4b7657aba419223edad670740f31a61", "label" : "Open is not enough", "user" : "hermann", "description" : "", "date" : "2019-06-13 16:14:26", "changeDate" : "2019-10-01 07:53:43", "count" : 1, "pub-type": "article", "journal": "Nature Physics", "year": "2019", "url": "https://doi.org/10.1038/s41567-018-0342-2", "author": [ "Xiaoli Chen","Sünje Dallmeier-Tiessen","Robin Dasler","Sebastian Feger","Pamfilos Fokianos","Jose Benito Gonzalez","Harri Hirvonsalo","Dinos Kousidis","Artemis Lavasa","Salvatore Mele","Diego Rodriguez Rodriguez","Tibor Šimko","Tim Smith","Ana Trisovic","Anna Trzcinska","Ioannis Tsanaktsidis","Markus Zimmermann","Kyle Cranmer","Lukas Heinrich","Gordon Watts","Michael Hildreth","Lara Lloret Iglesias","Kati Lassila-Perini","Sebastian Neubert" ], "authors": [ {"first" : "Xiaoli", "last" : "Chen"}, {"first" : "Sünje", "last" : "Dallmeier-Tiessen"}, {"first" : "Robin", "last" : "Dasler"}, {"first" : "Sebastian", "last" : "Feger"}, {"first" : "Pamfilos", "last" : "Fokianos"}, {"first" : "Jose Benito", "last" : "Gonzalez"}, {"first" : "Harri", "last" : "Hirvonsalo"}, {"first" : "Dinos", "last" : "Kousidis"}, {"first" : "Artemis", "last" : "Lavasa"}, {"first" : "Salvatore", "last" : "Mele"}, {"first" : "Diego Rodriguez", "last" : "Rodriguez"}, {"first" : "Tibor", "last" : "Šimko"}, {"first" : "Tim", "last" : "Smith"}, {"first" : "Ana", "last" : "Trisovic"}, {"first" : "Anna", "last" : "Trzcinska"}, {"first" : "Ioannis", "last" : "Tsanaktsidis"}, {"first" : "Markus", "last" : "Zimmermann"}, {"first" : "Kyle", "last" : "Cranmer"}, {"first" : "Lukas", "last" : "Heinrich"}, {"first" : "Gordon", "last" : "Watts"}, {"first" : "Michael", "last" : "Hildreth"}, {"first" : "Lara", "last" : "Lloret Iglesias"}, {"first" : "Kati", "last" : "Lassila-Perini"}, {"first" : "Sebastian", "last" : "Neubert"} ], "volume": "15","number": "2","pages": "113--119","abstract": "The solutions adopted by the high-energy physics community to foster reproducible research are examples of best practices that could be embraced more widely. This first experience suggests that reproducibility requires going beyond openness.", "issn" : "17452481", "refid" : "Chen2019", "doi" : "10.1038/s41567-018-0342-2", "bibtexKey": "chen2019enough" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2393a65462bfbebf8b996919972117e9d/hermann", "tags" : [ "obib","vfu","workflowTracking" ], "intraHash" : "393a65462bfbebf8b996919972117e9d", "interHash" : "5bb81f4b5050237c099041cdec25c5a7", "label" : "Data provenance tracking as the basis for a biomedical virtual research environment", "user" : "hermann", "description" : "Data provenance tracking as the basis for a biomedical virtual research environment - Research Repository", "date" : "2018-02-21 10:43:08", "changeDate" : "2018-02-21 09:43:08", "count" : 2, "pub-type": "article", "journal": "Proceedings of Science","booktitle": "International Symposium on Grids and Clouds 2017 (ISGC 2017)","address":"Trieste, Italy", "year": "2018", "url": "http://eprints.uwe.ac.uk/33527/", "author": [ "R. McClatchey" ], "authors": [ {"first" : "R.", "last" : "McClatchey"} ], "volume": "293","abstract": "In complex data analyses it is increasingly important to capture information about the usage of data sets in addition to their preservation over time to ensure reproducibility of results, to verify the work of others and to ensure appropriate conditions data have been used for specific analyses. Scientific workflow based studies are beginning to realize the benefit of capturing this provenance of data and the activities used to process, transform and carry out studies on those data. This is especially true in biomedicine where the collection of data through experiment is costly and/or difficult to reproduce and where that data needs to be preserved over time. One way to support the development of workflows and their use in (collaborative) biomedical analyses is through the use of a Virtual Research Environment. The dynamic and distributed nature of Grid/Cloud computing, however, makes the capture and processing of provenance information a major research challenge. Furthermore most workflow provenance management services are designed only for data-flow oriented workflows and researchers are now realising that tracking data or workflows alone or separately is insufficient to support the scientific process. What is required for collaborative research is traceable and reproducible provenance support in a full orchestrated Virtual Research Environment (VRE) that enables researchers to define their studies in terms of the datasets and processes used, to monitor and visualize the outcome of their analyses and to log their results so that others users can call upon that acquired knowledge to support subsequent studies. We have extended the work carried out in the neuGRID and N4U projects in providing a so-called Virtual Laboratory to provide the foundation for a generic VRE in which sets of biomedical data (images, laboratory test results, patient records, epidemiological analyses etc.) and the workflows (pipelines) used to process those data, together with their provenance data and results sets are captured in the CRISTAL software. This paper outlines the functionality provided for a VRE by the Open Source CRISTAL software and examines how that can provide the foundations for a practice-based knowledge base for biomedicine and, potentially, for a wider research community.", "bibtexKey": "mcclatchey2018provenance" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/29939f820260707d20a20959c24755a90/hermann", "tags" : [ "forschungsdaten","software","wms","workflowTracking" ], "intraHash" : "9939f820260707d20a20959c24755a90", "interHash" : "7599d411773725595145ddf60115622b", "label" : "Scientific workflows: Past, present and future", "user" : "hermann", "description" : "Scientific workflows: Past, present and future - ScienceDirect", "date" : "2018-02-14 21:56:01", "changeDate" : "2018-02-14 20:56:01", "count" : 1, "pub-type": "article", "journal": "Future Generation Computer Systems", "year": "2017", "url": "http://www.sciencedirect.com/science/article/pii/S0167739X17311202", "author": [ "Malcolm Atkinson","Sandra Gesing","Johan Montagnat","Ian Taylor" ], "authors": [ {"first" : "Malcolm", "last" : "Atkinson"}, {"first" : "Sandra", "last" : "Gesing"}, {"first" : "Johan", "last" : "Montagnat"}, {"first" : "Ian", "last" : "Taylor"} ], "volume": "75","pages": "216 - 227","abstract": "This special issue and our editorial celebrate 10 years of progress with data-intensive or scientific workflows. There have been very substantial advances in the representation of workflows and in the engineering of workflow management systems (WMS). The creation and refinement stages are now well supported, with a significant improvement in usability. Improved abstraction supports cross-fertilisation between different workflow communities and consistent interpretation as WMS evolve. Through such re-engineering the WMS deliver much improved performance, significantly increased scale and sophisticated reliability mechanisms. Further improvement is anticipated from substantial advances in optimisation. We invited papers from those who have delivered these advances and selected 14 to represent today\u2019s achievements and representative plans for future progress. This editorial introduces those contributions with an overview and categorisation of the papers. Furthermore, it elucidates responses from a survey of major workflow systems, which provides evidence of substantial progress and a structured index of related papers. We conclude with suggestions on areas where further research and development is needed and offer a vision of future research directions.", "issn" : "0167-739X", "doi" : "https://doi.org/10.1016/j.future.2017.05.041", "bibtexKey": "ATKINSON2017216" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2cee6beee13cb8926a81fd68609095f76/hermann", "tags" : [ "Workflow","forschungsdaten","management","processing","software","systems","workflowTracking" ], "intraHash" : "cee6beee13cb8926a81fd68609095f76", "interHash" : "d2e5fb161c8874dfbde96a79d3a6e0e7", "label" : "A characterization of workflow management systems for extreme-scale applications", "user" : "hermann", "description" : "", "date" : "2018-02-14 21:53:58", "changeDate" : "2018-02-14 20:53:58", "count" : 2, "pub-type": "article", "journal": "Future Generation Computer Systems", "year": "2017", "url": "http://www.sciencedirect.com/science/article/pii/S0167739X17302510", "author": [ "Rafael Ferreira da Silva","Rosa Filgueira","Ilia Pietri","Ming Jiang","Rizos Sakellariou","Ewa Deelman" ], "authors": [ {"first" : "Rafael Ferreira", "last" : "da Silva"}, {"first" : "Rosa", "last" : "Filgueira"}, {"first" : "Ilia", "last" : "Pietri"}, {"first" : "Ming", "last" : "Jiang"}, {"first" : "Rizos", "last" : "Sakellariou"}, {"first" : "Ewa", "last" : "Deelman"} ], "volume": "75","pages": "228 - 238", "issn" : "0167-739X", "doi" : "https://doi.org/10.1016/j.future.2017.02.026", "bibtexKey": "dasilva2017characterization" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2cbac7bbce0d416a00b588a3600379814/hermann", "tags" : [ "forschungsdaten","obib","software","workflowTracking" ], "intraHash" : "cbac7bbce0d416a00b588a3600379814", "interHash" : "02206f7260c61903fbf980d0d2460b2d", "label" : "Workflows and e-Science: An overview of workflow system features and capabilities", "user" : "hermann", "description" : "Workflows and e-Science: An overview of workflow system features and capabilities - ScienceDirect", "date" : "2018-02-14 21:50:11", "changeDate" : "2018-02-26 16:25:02", "count" : 2, "pub-type": "article", "journal": "Future Generation Computer Systems", "year": "2009", "url": "http://www.sciencedirect.com/science/article/pii/S0167739X08000861", "author": [ "Ewa Deelman","Dennis Gannon","Matthew Shields","Ian Taylor" ], "authors": [ {"first" : "Ewa", "last" : "Deelman"}, {"first" : "Dennis", "last" : "Gannon"}, {"first" : "Matthew", "last" : "Shields"}, {"first" : "Ian", "last" : "Taylor"} ], "volume": "25","number": "5","pages": "528 - 540","abstract": "Scientific workflow systems have become a necessary tool for many applications, enabling the composition and execution of complex analysis on distributed resources. Today there are many workflow systems, often with overlapping functionality. A key issue for potential users of workflow systems is the need to be able to compare the capabilities of the various available tools. There can be confusion about system functionality and the tools are often selected without a proper functional analysis. In this paper we extract a taxonomy of features from the way scientists make use of existing workflow systems and we illustrate this feature set by providing some examples taken from existing workflow systems. The taxonomy provides end users with a mechanism by which they can assess the suitability of workflow in general and how they might use these features to make an informed choice about which workflow system would be a good choice for their particular application.", "issn" : "0167-739X", "doi" : "https://doi.org/10.1016/j.future.2008.06.012", "bibtexKey": "deelman2009workflows" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2e8be1c01e172e42cefde3367c43d86e1/hermann", "tags" : [ "forschungsdaten","software","workflowTracking" ], "intraHash" : "e8be1c01e172e42cefde3367c43d86e1", "interHash" : "b711d076272dcb270f155e652dd14782", "label" : "YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering\r\n Workflow Information from Scripts", "user" : "hermann", "description" : "[1502.02403] YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts", "date" : "2018-02-14 21:49:16", "changeDate" : "2018-02-14 20:49:16", "count" : 1, "pub-type": "article", "year": "2015", "url": "http://arxiv.org/abs/1502.02403", "author": [ "Timothy McPhillips","Tianhong Song","Tyler Kolisnik","Steve Aulenbach","Khalid Belhajjame","Kyle Bocinsky","Yang Cao","Fernando Chirigati","Saumen Dey","Juliana Freire","Deborah Huntzinger","Christopher Jones","David Koop","Paolo Missier","Mark Schildhauer","Christopher Schwalm","Yaxing Wei","James Cheney","Mark Bieda","Bertram Ludaescher" ], "authors": [ {"first" : "Timothy", "last" : "McPhillips"}, {"first" : "Tianhong", "last" : "Song"}, {"first" : "Tyler", "last" : "Kolisnik"}, {"first" : "Steve", "last" : "Aulenbach"}, {"first" : "Khalid", "last" : "Belhajjame"}, {"first" : "Kyle", "last" : "Bocinsky"}, {"first" : "Yang", "last" : "Cao"}, {"first" : "Fernando", "last" : "Chirigati"}, {"first" : "Saumen", "last" : "Dey"}, {"first" : "Juliana", "last" : "Freire"}, {"first" : "Deborah", "last" : "Huntzinger"}, {"first" : "Christopher", "last" : "Jones"}, {"first" : "David", "last" : "Koop"}, {"first" : "Paolo", "last" : "Missier"}, {"first" : "Mark", "last" : "Schildhauer"}, {"first" : "Christopher", "last" : "Schwalm"}, {"first" : "Yaxing", "last" : "Wei"}, {"first" : "James", "last" : "Cheney"}, {"first" : "Mark", "last" : "Bieda"}, {"first" : "Bertram", "last" : "Ludaescher"} ], "note": "cite arxiv:1502.02403","abstract": "Scientific workflow management systems offer features for composing complex\r\ncomputational pipelines from modular building blocks, for executing the\r\nresulting automated workflows, and for recording the provenance of data\r\nproducts resulting from workflow runs. Despite the advantages such features\r\nprovide, many automated workflows continue to be implemented and executed\r\noutside of scientific workflow systems due to the convenience and familiarity\r\nof scripting languages (such as Perl, Python, R, and MATLAB), and to the high\r\nproductivity many scientists experience when using these languages. YesWorkflow\r\nis a set of software tools that aim to provide such users of scripting\r\nlanguages with many of the benefits of scientific workflow systems. YesWorkflow\r\nrequires neither the use of a workflow engine nor the overhead of adapting code\r\nto run effectively in such a system. Instead, YesWorkflow enables scientists to\r\nannotate existing scripts with special comments that reveal the computational\r\nmodules and dataflows otherwise implicit in these scripts. YesWorkflow tools\r\nextract and analyze these comments, represent the scripts in terms of entities\r\nbased on the typical scientific workflow model, and provide graphical\r\nrenderings of this workflow-like view of the scripts. Future versions of\r\nYesWorkflow also will allow the prospective provenance of the data products of\r\nthese scripts to be queried in ways similar to those available to users of\r\nscientific workflow systems.", "bibtexKey": "mcphillips2015yesworkflow" } ] }