Literature DB >> 27803802

Bringing your tools to CyVerse Discovery Environment using Docker.

Upendra Kumar Devisetty1, Kathleen Kennedy1, Paul Sarando1, Nirav Merchant1, Eric Lyons1.   

Abstract

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. CyVerse's Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse's production environment for public use. This paper will help users bring their tools into CyVerse Discovery Environment (DE) which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but will also help users to share their apps with collaborators and release them for public use.

Entities:  

Keywords:  CyVerse; Discovery Environment; virtualization platform

Year:  2016        PMID: 27803802      PMCID: PMC5070597          DOI: 10.12688/f1000research.8935.1

Source DB:  PubMed          Journal:  F1000Res        ISSN: 2046-1402


  2 in total

1.  The iPlant Collaborative: Cyberinfrastructure for Plant Biology.

Authors:  Stephen A Goff; Matthew Vaughn; Sheldon McKay; Eric Lyons; Ann E Stapleton; Damian Gessler; Naim Matasci; Liya Wang; Matthew Hanlon; Andrew Lenards; Andy Muir; Nirav Merchant; Sonya Lowry; Stephen Mock; Matthew Helmke; Adam Kubach; Martha Narro; Nicole Hopkins; David Micklos; Uwe Hilgert; Michael Gonzales; Chris Jordan; Edwin Skidmore; Rion Dooley; John Cazes; Robert McLay; Zhenyuan Lu; Shiran Pasternak; Lars Koesterke; William H Piel; Ruth Grene; Christos Noutsos; Karla Gendler; Xin Feng; Chunlao Tang; Monica Lent; Seung-Jin Kim; Kristian Kvilekval; B S Manjunath; Val Tannen; Alexandros Stamatakis; Michael Sanderson; Stephen M Welch; Karen A Cranston; Pamela Soltis; Doug Soltis; Brian O'Meara; Cecile Ane; Tom Brutnell; Daniel J Kleibenstein; Jeffery W White; James Leebens-Mack; Michael J Donoghue; Edgar P Spalding; Todd J Vision; Christopher R Myers; David Lowenthal; Brian J Enquist; Brad Boyle; Ali Akoglu; Greg Andrews; Sudha Ram; Doreen Ware; Lincoln Stein; Dan Stanzione
Journal:  Front Plant Sci       Date:  2011-07-25       Impact factor: 5.753

2.  Fast and accurate short read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937

  2 in total
  10 in total

1.  Cenote-Taker 2 democratizes virus discovery and sequence annotation.

Authors:  Michael J Tisza; Anna K Belford; Guillermo Domínguez-Huerta; Benjamin Bolduc; Christopher B Buck
Journal:  Virus Evol       Date:  2020-12-30

2.  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

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

Authors:  Gregory Kiar; Krzysztof J Gorgolewski; Dean Kleissas; William Gray Roncal; Brian Litt; Brian Wandell; Russel A Poldrack; Martin Wiener; R Jacob Vogelstein; Randal Burns; Joshua T Vogelstein
Journal:  Gigascience       Date:  2017-05-01       Impact factor: 6.524

4.  Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons.

Authors:  Illyoung Choi; Alise J Ponsero; Matthew Bomhoff; Ken Youens-Clark; John H Hartman; Bonnie L Hurwitz
Journal:  Gigascience       Date:  2019-02-01       Impact factor: 6.524

5.  Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.

Authors:  Mikayla A Borton; David W Hoyt; Simon Roux; Rebecca A Daly; Susan A Welch; Carrie D Nicora; Samuel Purvine; Elizabeth K Eder; Andrea J Hanson; Julie M Sheets; David M Morgan; Richard A Wolfe; Shikha Sharma; Timothy R Carr; David R Cole; Paula J Mouser; Mary S Lipton; Michael J Wilkins; Kelly C Wrighton
Journal:  Proc Natl Acad Sci U S A       Date:  2018-06-25       Impact factor: 11.205

6.  Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.

Authors:  Markus List
Journal:  J Integr Bioinform       Date:  2017-06-10

7.  Plant Reactome: a knowledgebase and resource for comparative pathway analysis.

Authors:  Sushma Naithani; Parul Gupta; Justin Preece; Peter D'Eustachio; Justin L Elser; Priyanka Garg; Daemon A Dikeman; Jason Kiff; Justin Cook; Andrew Olson; Sharon Wei; Marcela K Tello-Ruiz; Antonio Fabregat Mundo; Alfonso Munoz-Pomer; Suhaib Mohammed; Tiejun Cheng; Evan Bolton; Irene Papatheodorou; Lincoln Stein; Doreen Ware; Pankaj Jaiswal
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

8.  Genome-Resolved Metagenomics Extends the Environmental Distribution of the Verrucomicrobia Phylum to the Deep Terrestrial Subsurface.

Authors:  Sophie L Nixon; Rebecca A Daly; Mikayla A Borton; Lindsey M Solden; Susan A Welch; David R Cole; Paula J Mouser; Michael J Wilkins; Kelly C Wrighton
Journal:  mSphere       Date:  2019-12-18       Impact factor: 4.389

9.  Transcriptome Analysis of Maternal Gene Transcripts in Unfertilized Eggs of Misgurnus anguillicaudatus and Identification of Immune-Related Maternal Genes.

Authors:  Chan-Hee Kim; Eun Jeong Kim; Chaehwa Seo; Yoon Kwon Nam
Journal:  Int J Mol Sci       Date:  2020-05-29       Impact factor: 5.923

10.  A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases.

Authors:  Michael J Tisza; Christopher B Buck
Journal:  Proc Natl Acad Sci U S A       Date:  2021-06-03       Impact factor: 11.205

  10 in total

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