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Using ReproZip for Reproducibility and Library Services

Vicky Steeves, Rémi Rampin, Fernando Chirigati
2017 IASSIST Quarterly  
, applications, software, and computational environments.  ...  The dependencies required to reproduce the computational environments in which research happens can be exceptionally hard to track – in many cases, these dependencies are hidden or nested too deeply to  ...  Juliana Freire, the Principal Investigator of the ReproZip project, for her support in continuing to build ReproZip. We'd also like to thank Dr.  ... 
doi:10.29173/iq18 fatcat:oj4o6wbelvg7tofm5rf6d2q6tu

Reproducibility, Preservation, and Access to Research with ReproZip and ReproServer

Rémi Rampin, Vicky Steeves, Fernando Chirigati
2019 Zenodo  
The truth is, reproducibility is technically difficult to achieve due to the complexities of computational environments.  ...  ReproServer is a cloud application that allows users to upload or provide a link to a ReproZip bundle, and then interact with/reproduce the contents from the comfort of their browser.  ...  Python, R) Computational Environment E (Linux) reprozip Executing Tracing Creating Configuration Configuration File Data Analysis Package (.rpz file) Configuring Packing Input files  ... 
doi:10.5281/zenodo.3612732 fatcat:7aoeimz7j5bi7otknmryzbppeq

Reproducibility, preservation, and access to research with ReproZip and ReproServer

Vicky Steeves, Rémi Rampin, Fernando Chirigati
2020 IASSIST Quarterly  
The truth is, reproducibility is technically difficult to achieve due to the complexities of computational environments.  ...  Everything is then bundled into an rpz file, which users can use to reproduce the work with ReproZip and a suitable unpacker (e.g.: using Vagrant or Docker).  ...  Juliana Freire, the Principal Investigator of the ReproZip project, for her support in continuing to build ReproZip and now ReproServer.  ... 
doi:10.29173/iq969 fatcat:bygje7b4s5gqpo4et7qix5ie2i

A Serverless Tool for Platform Agnostic Computational Experiment Management [article]

Gregory Kiar, Shawn T Brown, Tristan Glatard, Alan C Evans
2018 arXiv   pre-print
Neuroscience has been carried into the domain of big data and high performance computing (HPC) on the backs of initiatives in data collection and an increasingly compute-intensive tools.  ...  While managing HPC experiments requires considerable technical acumen, platforms and standards have been developed to ease this burden on scientists.  ...  Executions were tested locally using Docker (17.12.0-ce), and on Compute Canada's Cedar high performance cluster using Singularity (2.5.1-dist).  ... 
arXiv:1809.07693v1 fatcat:4v33y6ggqzaqdjtrungvm6hol4

Publishing computational research - a review of infrastructures for reproducible and transparent scholarly communication

Markus Konkol, Daniel Nüst, Laura Goulier
2020 Research Integrity and Peer Review  
The applications support authors to publish reproducible research predominantly with literate programming.  ...  The applications were found through a literature search and interactions with the reproducible research community.  ...  ReproZip ReproZip [31, 32] provides a set of CLI commands for encapsulating data, code, and the computational environment.  ... 
doi:10.1186/s41073-020-00095-y pmid:32685199 pmcid:PMC7359270 fatcat:clovjhifpnc2lpol7yr2mv4v5e

A Serverless Tool for Platform Agnostic Computational Experiment Management

Gregory Kiar, Shawn T. Brown, Tristan Glatard, Alan C. Evans
2019 Frontiers in Neuroinformatics  
Neuroscience has been carried into the domain of big data and high performance computing (HPC) on the backs of initiatives in data collection and an increasingly compute-intensive tools.  ...  While managing HPC experiments requires considerable technical acumen, platforms, and standards have been developed to ease this burden on scientists.  ...  Computational experiments must be re-executable as a critical condition for reproducibility, and this bare minimum requirement becomes increasingly challenging with larger datasets and more complex analyses  ... 
doi:10.3389/fninf.2019.00012 pmid:30890927 pmcid:PMC6411646 fatcat:7uwik54sbjddxd3w553xilt2ha

containerit: Generating Dockerfiles for reproducible research with R

Daniel Nüst, Matthias Hinz
2019 Journal of Open Source Software  
Acknowledgements This work is supported by the project Opening Reproducible Research (Offene Reproduzierbare Forschung) funded by the German Research Foundation (DFG) under project numbers PE 1 632/10-  ...  However, capturing a computational environment in containers can be complex, making container use difficult for domain scientists with limited programming experience. containerit opens up the advantages  ...  Nüst et al., (2019). containerit: Generating Dockerfiles for reproducible research with R. Journal of Open Source Software, 4(40), 1603. https://doi.org/10.21105/joss.01603  ... 
doi:10.21105/joss.01603 fatcat:fpgfd6rfsng4za6ty6zszndheu

An Analysis of Security Vulnerabilities in Container Images for Scientific Data Analysis [article]

Bhupinder Kaur, Mathieu Dugré, Aiman Hanna, Tristan Glatard
2021 arXiv   pre-print
Software containers greatly facilitate the deployment and reproducibility of scientific data analyses in various platforms.  ...  We conclude with recommendations on how to build container images with a reduced amount of vulnerabilities.  ...  Base images often come with packages that are useful in personal computers or servers, but not in containers dedicated to a specific data analysis.  ... 
arXiv:2010.13970v2 fatcat:4tshbs74szc2ldnxwhendrbmlq

Reproducibility of Data-Oriented Experiments in e-Science (Dagstuhl Seminar 16041)

Juliana Freire, Norbert Fuhr, Andreas Rauber, Marc Herbstritt
2016 Dagstuhl Reports  
This seminar brought together experts from various sub-fields of computer science to create a joint understanding of the problems of reproducibility of experiments, discussing existing solutions and impediments  ...  In many subfields of computer science, experiments play an important role.  ...  As a result, the minimum requirements for the reproducibility of applied Computer Systems research (that code used in experiments is available and that it builds) are generally not met.  ... 
doi:10.4230/dagrep.6.1.108 dblp:journals/dagstuhl-reports/FreireFR16 fatcat:tjrh57ezlngyfhtr35dwenzhyu

Minimal sufficient information about the scientific workflows to create reproducible experiment

Anna Banati, Peter Kacsuk, Miklos Kozlovszky
2015 2015 IEEE 19th International Conference on Intelligent Engineering Systems (INES)  
The reproducibility of an in-silico experiment is a great challenge because of the parallel and distributed environment and the complexity of the scientific workflows.  ...  The ultimate goal of our work is to propose a minimal dataset for recording and reporting scientific workflow based experiment, which will facilitate the reproducibility of such experiments, the public  ...  In our previous paper [2] we showed, that the rate of reproducibility of a scientific workflow can be computed with the help of which the reproducible parts of workflow can be determined.  ... 
doi:10.1109/ines.2015.7329705 fatcat:jaftruu5frcencteqlldi3hjqq

Sharing and Preserving Computational Analyses for Posterity with encapsulator

Thomas Pasquier, Matthew K. Lau, Xueyuan Han, Elizabeth Fong, Barbara S. Lerner, Emery R. Boose, Merce Crosas, Aaron M. Ellison, Margo Seltzer
2018 Computing in science & engineering (Print)  
Requiring minimal end-user expertise, encapsulator creates a "time capsule" with reproducible code in a self-contained computational environment. encapsulator provides end-users with a fully-featured desktop  ...  environment for reproducible research.  ...  To facilitate ease of adoption, we make sure that the time capsule contains all the tools scientists need to usefully interact with the computational process.  ... 
doi:10.1109/mcse.2018.042781334 fatcat:6ovslmcqwre6pnod26aybbn6pu

Sharing and Preserving Computational Analyses for Posterity with encapsulator [article]

Thomas Pasquier and Matthew K. Lau and Xueyuan Han and Elizabeth Fong and Barbara S. Lerner and Emery Boose and Merce Crosas and Aaron M. Ellison and Margo Seltzer
2018 arXiv   pre-print
Requiring minimal end-user expertise, encapsulator creates a "time capsule" with reproducible code in a self-contained computational environment. encapsulator provides end-users with a fully-featured desktop  ...  environment for reproducible research.  ...  To facilitate ease of adoption, we make sure that the time capsule contains all the tools scientists need to usefully interact with the computational process.  ... 
arXiv:1803.05808v2 fatcat:fcbsnojcdvgcdpl7yymorkhl3u

Reproducibility Analysis of Scientific Workflows

2017 Acta Polytechnica Hungarica  
Scientific workflows are efficient tools for specifying and automating compute and data intensive in-silico experiments. An important challenge related to their usage is their reproducibility.  ...  Our investigation deals with the critical dependencies of execution.  ...  The SCI-BUS project aims to ease the life of the e-Scientists by creating a new science gateway customization methodology based on the generic-purpose gUSE/WS-PGRADE portal family.  ... 
doi:10.12700/aph.14.2.2017.2.11 fatcat:r5ffdhjcnrbk3m7dwyccxdyh2i

An analysis of security vulnerabilities in container images for scientific data analysis

Bhupinder Kaur, Mathieu Dugré, Aiman Hanna, Tristan Glatard
2021 GigaScience  
Software containers greatly facilitate the deployment and reproducibility of scientific data analyses in various platforms.  ...  We provide recommendations on how to build container images with fewer vulnerabilities.  ...  Scientific data analyses typically involve a range of computational infrastructures, including personal workstations, laboratory servers, high-performance computing clusters, and cloud computing platforms  ... 
doi:10.1093/gigascience/giab025 pmid:34080631 pmcid:PMC8173661 fatcat:bwo5vdoblfhunagsxztse2toji

Information Integration for Machine Actionable Data Management Plans

Tomasz Miksa, Andreas Rauber, Roman Ganguly, Paolo Budroni
2017 International Journal of Digital Curation  
The complexity of data-driven experiments requires precise descriptions of tools and datasets used in computations to enable their reproducibility and reuse.  ...  In this paper, we propose machine-actionable data management plans that cover the same themes as standard data management plans, but particular sections are filled with information obtained from existing  ...  The complexity of data-driven experiments requires precise descriptions of tools and datasets used in computations to enable their reproducibility and reuse.  ... 
doi:10.2218/ijdc.v12i1.529 fatcat:z3ih6ivbwrgmhd6cgu5oq2ycnu
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