Literature DB >> 29375158

Workflows and Provenance: Toward Information Science Solutions for the Natural Sciences.

Michael R Gryk1,2, Bertram Ludäscher2.   

Abstract

The era of big data and ubiquitous computation has brought with it concerns about ensuring reproducibility in this new research environment. It is easy to assume computational methods self-document by their very nature of being exact, deterministic processes. However, similar to laboratory experiments, ensuring reproducibility in the computational realm requires the documentation of both the protocols used (workflows) as well as a detailed description of the computational environment: algorithms, implementations, software environments as well as the data ingested and execution logs of the computation. These two aspects of computational reproducibility (workflows and execution details) are discussed in the context of biomolecular Nuclear Magnetic Resonance spectroscopy (bioNMR) as well as the PRIMAD model for computational reproducibility.

Entities:  

Year:  2017        PMID: 29375158      PMCID: PMC5779102          DOI: 10.1353/lib.2017.0018

Source DB:  PubMed          Journal:  Libr Trends        ISSN: 0024-2594


  5 in total

1.  NMRbox: A Resource for Biomolecular NMR Computation.

Authors:  Mark W Maciejewski; Adam D Schuyler; Michael R Gryk; Ion I Moraru; Pedro R Romero; Eldon L Ulrich; Hamid R Eghbalnia; Miron Livny; Frank Delaglio; Jeffrey C Hoch
Journal:  Biophys J       Date:  2017-04-25       Impact factor: 4.033

2.  CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

Authors:  Matthew Fenwick; Gerard Weatherby; Jay Vyas; Colbert Sesanker; Timothy O Martyn; Heidi J C Ellis; Michael R Gryk
Journal:  J Biomol NMR       Date:  2015-06-12       Impact factor: 2.835

3.  Enhancing reproducibility for computational methods.

Authors:  Victoria Stodden; Marcia McNutt; David H Bailey; Ewa Deelman; Yolanda Gil; Brooks Hanson; Michael A Heroux; John P A Ioannidis; Michela Taufer
Journal:  Science       Date:  2016-12-09       Impact factor: 47.728

4.  CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMR-protein spectral assignment.

Authors:  Matthew Fenwick; Jeffrey C Hoch; Eldon Ulrich; Michael R Gryk
Journal:  J Biomol NMR       Date:  2015-08-08       Impact factor: 2.835

5.  BioMagResBank.

Authors:  Eldon L Ulrich; Hideo Akutsu; Jurgen F Doreleijers; Yoko Harano; Yannis E Ioannidis; Jundong Lin; Miron Livny; Steve Mading; Dimitri Maziuk; Zachary Miller; Eiichi Nakatani; Christopher F Schulte; David E Tolmie; R Kent Wenger; Hongyang Yao; John L Markley
Journal:  Nucleic Acids Res       Date:  2007-11-04       Impact factor: 16.971

  5 in total

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