Literature DB >> 29756001

Experiences with Deriva: An Asset Management Platform for Accelerating eScience.

Alejandro Bugacov1, Karl Czajkowski1, Carl Kesselman1, Anoop Kumar1, Robert E Schuler1, Hongsuda Tangmunarunkit1.   

Abstract

The pace of discovery in eScience is increasingly dependent on a scientist's ability to acquire, curate, integrate, analyze, and share large and diverse collections of data. It is all too common for investigators to spend inordinate amounts of time developing ad hoc procedures to manage their data. In previous work, we presented Deriva, a Scientific Asset Management System, designed to accelerate data driven discovery. In this paper, we report on the use of Deriva in a number of substantial and diverse eScience applications. We describe the lessons we have learned, both from the perspective of the Deriva technology, as well as the ability and willingness of scientists to incorporate Scientific Asset Management into their daily workflows.

Entities:  

Year:  2017        PMID: 29756001      PMCID: PMC5939963          DOI: 10.1109/eScience.2017.20

Source DB:  PubMed          Journal:  Proc IEEE Int Conf Escience        ISSN: 2325-372X


  6 in total

1.  GPCRDB information system for G protein-coupled receptors.

Authors:  Florence Horn; Emmanuel Bettler; Laerte Oliveira; Fabien Campagne; Fred E Cohen; Gerrit Vriend
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

2.  Enterprise Data Analysis and Visualization: An Interview Study.

Authors:  S Kandel; A Paepcke; J M Hellerstein; J Heer
Journal:  IEEE Trans Vis Comput Graph       Date:  2012-12       Impact factor: 4.579

3.  Six red flags for suspect work.

Authors:  C Glenn Begley
Journal:  Nature       Date:  2013-05-23       Impact factor: 49.962

4.  A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

Authors:  Christopher J Mungall; David B Emmert
Journal:  Bioinformatics       Date:  2007-07-01       Impact factor: 6.937

5.  Toward interoperable bioscience data.

Authors:  Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; Eamonn Maguire; Chris Taylor; Oliver Hofmann; Hong Fang; Steffen Neumann; Weida Tong; Linda Amaral-Zettler; Kimberly Begley; Tim Booth; Lydie Bougueleret; Gully Burns; Brad Chapman; Tim Clark; Lee-Ann Coleman; Jay Copeland; Sudeshna Das; Antoine de Daruvar; Paula de Matos; Ian Dix; Scott Edmunds; Chris T Evelo; Mark J Forster; Pascale Gaudet; Jack Gilbert; Carole Goble; Julian L Griffin; Daniel Jacob; Jos Kleinjans; Lee Harland; Kenneth Haug; Henning Hermjakob; Shannan J Ho Sui; Alain Laederach; Shaoguang Liang; Stephen Marshall; Annette McGrath; Emily Merrill; Dorothy Reilly; Magali Roux; Caroline E Shamu; Catherine A Shang; Christoph Steinbeck; Anne Trefethen; Bryn Williams-Jones; Katherine Wolstencroft; Ioannis Xenarios; Winston Hide
Journal:  Nat Genet       Date:  2012-01-27       Impact factor: 38.330

6.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand 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 't 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
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

  6 in total
  6 in total

Review 1.  FaceBase: A Community-Driven Hub for Data-Intensive Research.

Authors:  R E Schuler; A Bugacov; J G Hacia; T V Ho; J Iwata; L Pearlman; B D Samuels; C Williams; Z Zhao; C Kesselman; Y Chai
Journal:  J Dent Res       Date:  2022-07-31       Impact factor: 8.924

2.  CUF-Links: Continuous and Ubiquitous FAIRness Linkages for reproducible research.

Authors:  Ian Foster; Carl Kesselman
Journal:  Computer (Long Beach Calif)       Date:  2022-08-02       Impact factor: 2.256

3.  Sharing Begins at Home: How Continuous and Ubiquitous FAIRness Can Enhance Research Productivity and Data Reuse.

Authors:  William Dempsey; Ian Foster; Scott Fraser; Carl Kesselman
Journal:  Harv Data Sci Rev       Date:  2022-07-28

4.  MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses.

Authors:  Jay Devine; Marta Vidal-García; Wei Liu; Amanda Neves; Lucas D Lo Vercio; Rebecca M Green; Heather A Richbourg; Marta Marchini; Colton M Unger; Audrey C Nickle; Bethany Radford; Nathan M Young; Paula N Gonzalez; Robert E Schuler; Alejandro Bugacov; Campbell Rolian; Christopher J Percival; Trevor Williams; Lee Niswander; Anne L Calof; Arthur D Lander; Axel Visel; Frank R Jirik; James M Cheverud; Ophir D Klein; Ramon Y Birnbaum; Amy E Merrill; Rebecca R Ackermann; Daniel Graf; Myriam Hemberger; Wendy Dean; Nils D Forkert; Stephen A Murray; Henrik Westerberg; Ralph S Marcucio; Benedikt Hallgrímsson
Journal:  Sci Data       Date:  2022-05-25       Impact factor: 8.501

5.  SigCom LINCS: data and metadata search engine for a million gene expression signatures.

Authors:  John Erol Evangelista; Daniel J B Clarke; Zhuorui Xie; Alexander Lachmann; Minji Jeon; Kerwin Chen; Kathleen M Jagodnik; Sherry L Jenkins; Maxim V Kuleshov; Megan L Wojciechowicz; Stephan C Schürer; Mario Medvedovic; Avi Ma'ayan
Journal:  Nucleic Acids Res       Date:  2022-05-07       Impact factor: 19.160

6.  Regional synapse gain and loss accompany memory formation in larval zebrafish.

Authors:  William P Dempsey; Zhuowei Du; Anna Nadtochiy; Colton D Smith; Karl Czajkowski; Andrey Andreev; Drew N Robson; Jennifer M Li; Serina Applebaum; Thai V Truong; Carl Kesselman; Scott E Fraser; Don B Arnold
Journal:  Proc Natl Acad Sci U S A       Date:  2022-01-18       Impact factor: 11.205

  6 in total

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