Using a suite of ontologies for preserving workflow-centric research objects
Khalid Belhajjame,Jun Zhao,Daniel Garijo,Matthew Gamble,Kristina Hettne,Raul Palma,Eleni Mina,Oscar Corcho,Jose Manuel Gomez-Perez,Sean Bechhofer,Graham Klyne,Carole Goble +11 more
TLDR
A novel approach to the preservation of scientific workflows through the application of research objects-aggregations of data and metadata that enrich the workflow specifications that support the creation of workflow-centric research objects.About:
This article is published in Journal of Web Semantics.The article was published on 2015-05-01 and is currently open access. It has received 133 citations till now. The article focuses on the topics: Workflow engine & Workflow technology.read more
Citations
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뀀Ƞ WINGS:뀀ȠIntelligent뀀ȠWorkflow-Based뀀ȠDesign뀀Ƞ뀀Ƞ of뀀ȠComputational뀀ȠExperiments뀀Ƞ
Yolanda Gil,Varun Ratnakar,Jihie Kim,Pedro A. González-Calero,Paul Groth,Joshua Moody,Ewa Deelman +6 more
TL;DR: The Wings intelligent workflow system as mentioned in this paper assists scientists with designing computational experiments by automatically tracking constraints and ruling out invalid designs, letting scientists focus on their experiments and goals, allowing them to focus on the goals of their experiments.
Journal ArticleDOI
Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities
Sarah Cohen-Boulakia,Khalid Belhajjame,Olivier Collin,Jérôme Chopard,Christine Froidevaux,Alban Gaignard,Konrad Hinsen,Pierre Larmande,Yvan Le Bras,Frédéric Lemoine,Fabien Mareuil,Hervé Ménager,Christophe Pradal,Christophe Blanchet +13 more
TL;DR: This study characterize and define the criteria that need to be catered for by reproducibility-friendly scientific workflow systems, and use such criteria to place several representative and widely used workflow systems and companion tools within such a framework.
Journal ArticleDOI
Tximeta: Reference sequence checksums for provenance identification in RNA-seq.
Michael I. Love,Charlotte Soneson,Charlotte Soneson,Peter Hickey,Peter Hickey,Lisa K. Johnson,N. T. Pierce,Lori Shepherd,Martin Morgan,Rob Patro +9 more
TL;DR: This work provides a solution in the form of an R/Bioconductor package tximeta that performs numerous annotation and metadata gathering tasks automatically on behalf of users during the import of transcript quantification files.
Journal ArticleDOI
Big data hurdles in precision medicine and precision public health
TL;DR: Data science for precision medicine and public health warrants an informatics-oriented formalization of the study design and interoperability throughout all levels of the knowledge inference process, from the research semantics, to model development, and ultimately to implementation.
Journal ArticleDOI
A characterization of workflow management systems for extreme-scale applications
Rafael Ferreira da Silva,Rosa Filgueira,Rosa Filgueira,Ilia Pietri,Ming Jiang,Rizos Sakellariou,Ewa Deelman +6 more
TL;DR: A novel characterization of workflow management systems using features commonly associated with extreme-scale computing applications is presented and 15 popular workflow management Systems are classified in terms of workflow execution models, heterogeneous computing environments, and data access methods.
References
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A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes
Marcy E. MacDonald,Christine Ambrose,Mabel P. Duyao,Richard H. Myers,Carol Lin,Lakshmi Srinidhi,Glenn Barnes,Sherryl A.M. Taylor,Marianne James,Nicolet Groot,Heather MacFarlane,Barbara Jenkins,Mary Anne Anderson,Nancy S. Wexler,James F. Gusella,Gillian P. Bates,Sarah Baxendale,Holger Hummerich,Susan F. Kirby,Mike North,S. Youngman,Richard Mott,Günther Zehetner,Zdenek Sedlacek,Annemarie Poustka,Anna-Maria Frischauf,Hans Lehrach,Alan Buckler,Deanna M. Church,Lynn Doucette-Stamm,Michael Conlon O'Donovan,Laura Riba-Ramirez,Manish A. Shah,Vincent P. Stanton,Scott A. Strobel,Karen M. Draths,Jennifer L. Wales,Peter B. Dervan,David E. Housman,Michael R. Altherr,Rita Shiang,Leslie M. Thompson,Thomas J. Fielder,John J. Wasmuth,Danilo A. Tagle,John Valdes,Lawrence W. Elmer,Marc W. Allard,Lucio H. Castilla,Manju Swaroop,Kris Blanchard,Francis S. Collins,Russell G. Snell,Tracey Holloway,Kathleen Gillespie,Nicole A. Datson,Duncan Shaw,Peter S. Harper +57 more
TL;DR: In this article, the authors used haplotype analysis of linkage disequilibrium to spotlight a small segment of 4p16.3 as the likely location of the defect, which is expanded and unstable on HD chromosomes.
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A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group.
Manish A. Shah,Nicole A. Datson,Lakshmi Srinidhi,Vincent P. Stanton,Marcy E. MacDonald,Marc W. Allard,S. Youngman,Anna-Maria Frischauf,Richard Mott,KM Draths,Günther Zehetner,C. O’Donovan,Thomas J. Fielder,Bruce G. Jenkins,Manju Swaroop,Sherryl A.M. Taylor,Lynn Doucette-Stamm,Heather MacFarlane,Scott A. Strobel,H. E. McFarlane,Alan Buckler,Nicolet Groot,Holger Hummerich,Deanna M. Church,M. A. Anderson,Marianne James,Glenn Barnes,M. Christine,Francis S. Collins,Mabel P. Duyao,Peter B. Dervan,Gillian P. Bates,T Holloway,Peter S. Harper,TW Mcdonald,M North,K Blanchard,John J. Wasmuth,D. Shaw,Hans Lehrach,Danilo A. Tagle,Annemarie Poustka,David E. Housman,T. Huntington,Zdenek Sedlacek,Laura Riba,Susan F. Kirby,Carol Lin,Richard H. Myers,Leslie M. Thompson,Russell G. Snell,Michael Conlon O'Donovan,K Gillespie,Rita Shiang,Nancy S. Wexler,Christine Ambrose,J. F. Gusella,Sarah Baxendale,N. Groat,John Valdes +59 more
TL;DR: The Huntington's disease mutation involves an unstable DNA segment, similar to those described in fragile X syndrome, spino-bulbar muscular atrophy, and myotonic dystrophy, acting in the context of a novel 4p16.3 gene to produce a dominant phenotype.
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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
TL;DR: Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis and provide support for capturing the context and intent of computational methods.
Journal ArticleDOI
IPython: A System for Interactive Scientific Computing
Fernando Perez,Brian E. Granger +1 more
TL;DR: The IPython project as mentioned in this paper provides an enhanced interactive environment that includes, among other features, support for data visualization and facilities for distributed and parallel computation for interactive work and a comprehensive library on top of which more sophisticated systems can be built.
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