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Contributions to Open Science for Reproducible Research [article]

Sheeba Samuel
2020 Figshare  
Slides presented for the invited speaker talk on "Contributions to Open Science for Reproducible Research" in QPTDat OpenScience Workshop on 23rd January 2020 at FIZ Karlsruhe.  ...  Combining P-Plan and the REPRODUCE-ME ontology to achieve semantic enrichment of scientific experiments using interactive notebooks. The Semantic Web: ESWC 2018 Satellite Events (pp. 126-130).  ...  ] 34 CAESAR A Collaborative Environment for Scientific Analysis with Reproducibility CAESAR CollAborative Environment for Scientific Analysis with Reproducibility [Samuel et al. 2017, Samuel  ... 
doi:10.6084/m9.figshare.11728974.v1 fatcat:vuayc7y7xncwtgkgymbhnwyaiq

Document Automation Architectures and Technologies: A Survey [article]

Mohammad Ahmadi Achachlouei, Omkar Patil, Tarun Joshi, Vijayan N. Nair
2021 arXiv   pre-print
The objective of DA is to reduce the manual effort during the generation of documents by automatically integrating input from different sources and assembling documents conforming to defined templates.  ...  The current survey of DA reviews the academic literature and provides a clearer definition and characterization of DA and its features, identifies state-of-the-art DA architectures and technologies in  ...  Jupyter notebooks provide an interactive web application allowing users to create and share programmatic analysis in over 40 languages and provides features to add data commentary in the same environment  ... 
arXiv:2109.11603v1 fatcat:alqvdban5ndr7m3gjjtqqumk7y

Wrattler: Reproducible, live and polyglot notebooks

Tomas Petricek, James Geddes, Charles Sutton
2018 Workshop on the Theory and Practice of Provenance  
Alas, most notebook systems use an architecture that leads to a limited model of interaction and makes reproducibility and versioning difficult.  ...  Wrattler separates state management from script evaluation and controls the evaluation using a dependency graph maintained in the web browser.  ...  We thank to our colleagues Chris Williams, Zoubin Ghahramani and Ian Horrocks and attendees of a recent AIDA project workshop.  ... 
dblp:conf/tapp/0001GS18 fatcat:wszcfl724vckrhnarnwplw5yve

Notebook-as-a-VRE (NaaVRE): from private notebooks to a collaborative cloud virtual research environment [article]

Zhiming Zhao, Spiros Koulouzis, Riccardo Bianchi, Siamak Farshidi, Zeshun Shi, Ruyue Xin, Yuandou Wang, Na Li, Yifang Shi, Joris Timmermans, W. Daniel Kissling
2021 arXiv   pre-print
Notebook environments, such as Jupyter, allow researchers to rapidly prototype scientific code and share their experiments as online accessible notebooks.  ...  This enables users to scale out the processing of multi-terabyte LiDAR point clouds for ecological applications to more data sources in a distributed cloud environment.  ...  The semantic search engine provides a web interface to do a search from external catalogs (e.g., for data sets, services, or other assets), and also API for the application to invoke via Jupyter. C.  ... 
arXiv:2111.12785v1 fatcat:r5yku5fiibb7xmbmlh77nxlrry

Dataset Relationship Management

Zack Ives, Yi Zhang, Soonbo Han, Nan Zheng
2019 Conference on Innovative Data Systems Research  
We argue that the recent adoption of computational notebooks (particularly JupyterLab and Jupyter Notebook), as a unified interface over data tools, provides an ideal way of gathering detailed information  ...  Data scientists frequently point to a strong need for data management -with respect to their many datasets and data products.  ...  Data analysis is not simply being performed over an existing data warehouse. Instead, datasets are pulled from distributed filesystems and the open web, and possibly stored in a data lake.  ... 
dblp:conf/cidr/IvesZHZ19 fatcat:rpngzqwzfndchlpdpjpi2r5lbm

JOVIAL: Notebook-based astronomical data analysis in the cloud

M. Araya, M. Osorio, M. Díaz, C. Ponce, M. Villanueva, C. Valenzuela, M. Solar
2018 Astronomy and Computing  
In this paper we present the architecture and features of JOVIAL, a Cloud service where astronomers can safely use Jupyter notebooks over a personal space designed for high-performance processing under  ...  Using Jupyter Notebooks as a remote service is a recent trend in data analysis that aims to deal with this problem, but harnessing the infrastructure to serve the astronomer without increasing the complexity  ...  Jupyter Notebooks Jupyter is an open-source web application for authoring interactive notebooks that has gained an important popularity in recent years.  ... 
doi:10.1016/j.ascom.2018.09.001 fatcat:ddgcq55sbbf6bi42sgh5bvey7y

refnx: neutron and X-ray reflectometry analysis in Python

Andrew R. J. Nelson, Stuart W. Prescott
2019 Journal of Applied Crystallography  
The package is designed to facilitate reproducible research; its use in Jupyter notebooks, and subsequent distribution of those notebooks as supporting information, permits straightforward reproduction  ...  Its graphical user interface is browser based, through a Jupyter notebook.  ...  (ii) lipid.ipynb -the Jupyter notebook used for the lipid analysis example. (iii) rg5158sup2.pdf -a PDF view of the Jupyter notebook used for the lipid analysis example.  ... 
doi:10.1107/s1600576718017296 pmid:30800030 pmcid:PMC6362611 fatcat:eirv3fl26na6tm7nh7zescgyky

Jupyter notebooks as discovery mechanisms for open science: Citation practices in the astronomy community

Morgan Wofford, Bernadette Marie Boscoe, Christine Borgman, Irene Pasquetto, Milena Golshan
2019 Computing in science & engineering (Print)  
We report on a study of references to Jupyter notebooks in astronomy over a 5-year period (2014-2018).  ...  Jupyter notebooks appear better suited to supporting the research process than to providing access to research objects.  ...  We also gratefully acknowledge use of NASA's Astrophysics Data System Bibliographic Services.  ... 
doi:10.1109/mcse.2019.2932067 fatcat:q2vemqobhfgajnqqfu7hdsar4u

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research

Ziv Yaniv, Bradley C. Lowekamp, Hans J. Johnson, Richard Beare
2017 Journal of digital imaging  
The Jupyter notebook web application is the basis of an environment that enables flexible, welldocumented, and reproducible workflows via literate programming.  ...  Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation  ...  SimpleITK Jupyter Notebooks Originally introduced in 2011 as IPython notebooks, Jupyter notebooks ( are an open-source interactive web-based application facilitating literate programing  ... 
doi:10.1007/s10278-017-0037-8 pmid:29181613 fatcat:wnywc5vj3ffixeljqvz6gxbpiu

Teachers' perception of Jupyter and R Shiny as digital tools for open education and science [article]

Jozef Hanč, Peter Štrauch, Eva Paňková, Martina Hančová
2020 arXiv   pre-print
Despite the fact that open-source Jupyter notebooks are natural and easy as email or web, the results suggest that in-service teachers are not prepared for Jupyter technology and open analysis, but positively  ...  All results support the ongoing worldwide effort to implement Jupyter in traditional education as a promising free open-source interactive learning tool to foster learning process, especially for the upcoming  ...  Acknowledgments The authors would like to thank Andrej Gajdoš for his advice in using R in advanced multivariate statistical analysis.  ... 
arXiv:2007.11262v2 fatcat:uhifrwehvrdpbl2qq4isvt5qfq

Distributed workflows with Jupyter

Iacopo Colonnelli, Marco Aldinucci, Barbara Cantalupo, Luca Padovani, Sergio Rabellino, Concetto Spampinato, Roberto Morelli, Rosario Di Carlo, Nicolò Magini, Carlo Cavazzoni
2021 Future generations computer systems  
We advocate the Jupyter Notebooks' potential to express complex distributed workflows, identifying the general requirements for a Jupyter-based Workflow Management System (WMS) and introducing a proof-of-concept  ...  Jupyter Notebooks, with their capability to describe both imperative and declarative code in a unique format, allow taking the best of the two approaches, maintaining a clear separation between application  ...  Acknowledgments This article describes work undertaken in the context of the DeepHealth project, 12 ''Deep-Learning and HPC to Boost Biomedical Applications for Health'' which has received funding from  ... 
doi:10.1016/j.future.2021.10.007 fatcat:2al5dpxqmrgeboqxgkgxbefxga

Dynamic Reusable Workflows for Ocean Science

Richard Signell, Filipe Fernandes, Kyle Wilcox
2016 Journal of Marine Science and Engineering  
A series of Jupyter Notebooks are used to capture and document the end-to-end workflow using a collection of Python tools that facilitate working with standardized catalog and data services.  ...  that automate-end-to-end-data search, analysis, and visualization of data from multiple distributed sources.  ...  Filipe Fernandes developed most of the notebook code and played a major role in making the software environment reproducible.  ... 
doi:10.3390/jmse4040068 fatcat:4km4vsvvcbfhzkqm667huhbybe

The Story of an Experiment: A Provenance-based Semantic Approach towards Research Reproducibility

Sheeba Samuel, Kathrin Groeneveld, Frank Taubert, Daniel Walther, Tom Kache, Teresa Langenstück, Birgitta König-Ries, H. Martin Bücker, Christoph Biskup
2018 Figshare  
In this paper, we present a provenance-based semantic approach to explain the story of a scientific experiment with the primary goal of reproducibility.  ...  End-to-end reproducibility of scientific experiments is a keyto the foundation of science.  ...  RDF are available here https://github. com/Sheeba-Samuel/REPRODUCE-ME/  ... 
doi:10.6084/m9.figshare.7345865.v2 fatcat:kmmk2sub5vd67n5mmalrepmtpi

Curating Scientific Information in Knowledge Infrastructures

Markus Stocker, Pauli Paasonen, Markus Fiebig, Martha A Zaidan, Alex Hardisty
2018 Data Science Journal  
For a use case in aerosol science, we elucidate these problems and present a Jupyter based prototype infrastructure that exploits a machine learning approach to interpretation and could support a research  ...  community in interpreting observational data and, more importantly, in curating and further using resulting information about a studied natural phenomenon.  ...  Yin Chen and EGI Federated Cloud providers for the use of resources.  ... 
doi:10.5334/dsj-2018-021 fatcat:r6imb3vwj5c3honaibdwfho4re

PhenoMeNal: processing and analysis of metabolomics data in the cloud

Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M D Ebbels, Carles Foguet, Robert Glen, Alejandra Gonzalez-Beltran, Ulrich L Günther, Evangelos Handakas (+44 others)
2018 GigaScience  
However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution.  ...  Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism.  ...  Also, computational notebooks can, to some extent, be used as a way to document code executions and to make executions more reproducible [64] .  ... 
doi:10.1093/gigascience/giy149 pmid:30535405 pmcid:PMC6377398 fatcat:srtrsdrzd5bitjztymyqy4nypy
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