Literature DB >> 28327935

Science in the cloud (SIC): A use case in MRI connectomics.

Gregory Kiar1,2, Krzysztof J Gorgolewski3, Dean Kleissas4, William Gray Roncal4,5, Brian Litt6,7, Brian Wandell3,8, Russel A Poldrack3, Martin Wiener9, R Jacob Vogelstein, Randal Burns5, Joshua T Vogelstein1,2.   

Abstract

Modern technologies are enabling scientists to collect extraordinary amounts of complex and sophisticated data across a huge range of scales like never before. With this onslaught of data, we can allow the focal point to shift from data collection to data analysis. Unfortunately, lack of standardized sharing mechanisms and practices often make reproducing or extending scientific results very difficult. With the creation of data organization structures and tools that drastically improve code portability, we now have the opportunity to design such a framework for communicating extensible scientific discoveries. Our proposed solution leverages these existing technologies and standards, and provides an accessible and extensible model for reproducible research, called 'science in the cloud' (SIC). Exploiting scientific containers, cloud computing, and cloud data services, we show the capability to compute in the cloud and run a web service that enables intimate interaction with the tools and data presented. We hope this model will inspire the community to produce reproducible and, importantly, extensible results that will enable us to collectively accelerate the rate at which scientific breakthroughs are discovered, replicated, and extended.
© The Author 2017. Published by Oxford University Press.

Entities:  

Keywords:  Cloud Computing; Connectomics; MRI; Reproducibility

Mesh:

Year:  2017        PMID: 28327935      PMCID: PMC5467033          DOI: 10.1093/gigascience/gix013

Source DB:  PubMed          Journal:  Gigascience        ISSN: 2047-217X            Impact factor:   6.524


  24 in total

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Authors:  Mark Jenkinson; Peter Bannister; Michael Brady; Stephen Smith
Journal:  Neuroimage       Date:  2002-10       Impact factor: 6.556

2.  Reproducible research in computational science.

Authors:  Roger D Peng
Journal:  Science       Date:  2011-12-02       Impact factor: 47.728

3.  Neurodata Without Borders: Creating a Common Data Format for Neurophysiology.

Authors:  Jeffery L Teeters; Keith Godfrey; Rob Young; Chinh Dang; Claudia Friedsam; Barry Wark; Hiroki Asari; Simon Peron; Nuo Li; Adrien Peyrache; Gennady Denisov; Joshua H Siegle; Shawn R Olsen; Christopher Martin; Miyoung Chun; Shreejoy Tripathy; Timothy J Blanche; Kenneth Harris; György Buzsáki; Christof Koch; Markus Meister; Karel Svoboda; Friedrich T Sommer
Journal:  Neuron       Date:  2015-11-18       Impact factor: 17.173

4.  Multi-parametric neuroimaging reproducibility: a 3-T resource study.

Authors:  Bennett A Landman; Alan J Huang; Aliya Gifford; Deepti S Vikram; Issel Anne L Lim; Jonathan A D Farrell; John A Bogovic; Jun Hua; Min Chen; Samson Jarso; Seth A Smith; Suresh Joel; Susumu Mori; James J Pekar; Peter B Barker; Jerry L Prince; Peter C M van Zijl
Journal:  Neuroimage       Date:  2010-11-20       Impact factor: 6.556

5.  Is it time to re-prioritize neuroimaging databases and digital repositories?

Authors:  John Darrell Van Horn; Arthur W Toga
Journal:  Neuroimage       Date:  2009-04-14       Impact factor: 6.556

6.  Bringing your tools to CyVerse Discovery Environment using Docker.

Authors:  Upendra Kumar Devisetty; Kathleen Kennedy; Paul Sarando; Nirav Merchant; Eric Lyons
Journal:  F1000Res       Date:  2016-06-21

7.  Dipy, a library for the analysis of diffusion MRI data.

Authors:  Eleftherios Garyfallidis; Matthew Brett; Bagrat Amirbekian; Ariel Rokem; Stefan van der Walt; Maxime Descoteaux; Ian Nimmo-Smith
Journal:  Front Neuroinform       Date:  2014-02-21       Impact factor: 4.081

8.  CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research.

Authors:  Tarek Sherif; Pierre Rioux; Marc-Etienne Rousseau; Nicolas Kassis; Natacha Beck; Reza Adalat; Samir Das; Tristan Glatard; Alan C Evans
Journal:  Front Neuroinform       Date:  2014-05-21       Impact factor: 4.081

9.  Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant.

Authors:  Andreas Bremges; Irena Maus; Peter Belmann; Felix Eikmeyer; Anika Winkler; Andreas Albersmeier; Alfred Pühler; Andreas Schlüter; Alexander Sczyrba
Journal:  Gigascience       Date:  2015-07-30       Impact factor: 6.524

10.  Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.

Authors:  Mikel Egaña Aranguren; Mark D Wilkinson
Journal:  Gigascience       Date:  2015-12-03       Impact factor: 6.524

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  7 in total

1.  Connectome Smoothing via Low-Rank Approximations.

Authors:  Runze Tange; Michael Ketcha; Alexandra Badea; Evan D Calabrese; Daniel S Margulies; Joshua T Vogelstein; Carey E Priebe; Daniel L Sussman
Journal:  IEEE Trans Med Imaging       Date:  2018-12-10       Impact factor: 10.048

2.  The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services.

Authors:  Paolo Avesani; Brent McPherson; Soichi Hayashi; Cesar F Caiafa; Robert Henschel; Eleftherios Garyfallidis; Lindsey Kitchell; Daniel Bullock; Andrew Patterson; Emanuele Olivetti; Olaf Sporns; Andrew J Saykin; Lei Wang; Ivo Dinov; David Hancock; Bradley Caron; Yiming Qian; Franco Pestilli
Journal:  Sci Data       Date:  2019-05-23       Impact factor: 6.444

3.  BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.

Authors:  Krzysztof J Gorgolewski; Fidel Alfaro-Almagro; Tibor Auer; Pierre Bellec; Mihai Capotă; M Mallar Chakravarty; Nathan W Churchill; Alexander Li Cohen; R Cameron Craddock; Gabriel A Devenyi; Anders Eklund; Oscar Esteban; Guillaume Flandin; Satrajit S Ghosh; J Swaroop Guntupalli; Mark Jenkinson; Anisha Keshavan; Gregory Kiar; Franziskus Liem; Pradeep Reddy Raamana; David Raffelt; Christopher J Steele; Pierre-Olivier Quirion; Robert E Smith; Stephen C Strother; Gaël Varoquaux; Yida Wang; Tal Yarkoni; Russell A Poldrack
Journal:  PLoS Comput Biol       Date:  2017-03-09       Impact factor: 4.475

4.  Transcriptome annotation in the cloud: complexity, best practices, and cost.

Authors:  Roberto Vera Alvarez; Leonardo Mariño-Ramírez; David Landsman
Journal:  Gigascience       Date:  2021-01-29       Impact factor: 6.524

5.  A Dictionary Learning Approach for Signal Sampling in Task-Based fMRI for Reduction of Big Data.

Authors:  Bao Ge; Xiang Li; Xi Jiang; Yifei Sun; Tianming Liu
Journal:  Front Neuroinform       Date:  2018-04-12       Impact factor: 4.081

6.  Management and Quality Control of Large Neuroimaging Datasets: Developments From the Barcelonaβeta Brain Research Center.

Authors:  Jordi Huguet; Carles Falcon; David Fusté; Sergi Girona; David Vicente; José Luis Molinuevo; Juan Domingo Gispert; Grégory Operto
Journal:  Front Neurosci       Date:  2021-04-15       Impact factor: 4.677

7.  Toward a scalable framework for reproducible processing of volumetric, nanoscale neuroimaging datasets.

Authors:  Erik C Johnson; Miller Wilt; Luis M Rodriguez; Raphael Norman-Tenazas; Corban Rivera; Nathan Drenkow; Dean Kleissas; Theodore J LaGrow; Hannah P Cowley; Joseph Downs; Jordan K Matelsky; Marisa J Hughes; Elizabeth P Reilly; Brock A Wester; Eva L Dyer; Konrad P Kording; William R Gray-Roncal
Journal:  Gigascience       Date:  2020-12-21       Impact factor: 6.524

  7 in total

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