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Towards computational reproducibility: researcher perspectives on the use and sharing of software

Yasmin AlNoamany, John A. Borghi
2018 PeerJ Computer Science  
Based on the responses of 215 participants, representing a range of research disciplines, we found that researchers create, use, and share software in a wide variety of forms for a wide variety of purposes  ...  Research software, which includes both source code and executables used as part of the research process, presents a significant challenge for efforts aimed at ensuring reproducibility.  ...  Efforts aimed at fostering 74 computational reproducibility are often focused on the sharing of source code but may also include the 75 establishment of best practice guidelines related to how software  ... 
doi:10.7717/peerj-cs.163 pmid:33816816 pmcid:PMC7924683 fatcat:qizld7nblfcxdn2rdwsohkys6u

Towards reproducible computational drug discovery

Nalini Schaduangrat, Samuel Lampa, Saw Simeon, Matthew Paul Gleeson, Ola Spjuth, Chanin Nantasenamat
2020 Journal of Cheminformatics  
It is therefore inevitable that the field of computational drug design would adopt an open approach towards the collection, curation and sharing of data/code.  ...  This article provides an in-depth coverage on the reproducibility of computational drug discovery.  ...  Sirarat Sarntivijai from the European Bioinformatics Institute and Dr. Likit Preeyanon from the Department of Community Medical Technology for fruitful discussions.  ... 
doi:10.1186/s13321-020-0408-x pmid:33430992 fatcat:bvdcvjhi4jhlnifpc25t6cjthq

Towards Long-term and Archivable Reproducibility

Mohammad Akhlaghi, Raul Infante-Sainz, Boudewijn Roukema, Mohammadreza Khellat, David Valls-Gabaud, Roberto Baena Galle
2021 Computing in science & engineering (Print)  
As a proof of concept, we introduce "Maneage" (managing data lineage), enabling cheap archiving, provenance extraction, and peer verification that has been tested in several research publications.  ...  primarily in plain text); modular design; minimal complexity; scalability; verifiable inputs and outputs; version control; linking analysis with narrative; and free and open-source software.  ...  The latest merged Maneage branch commit was 6e4ec9a (17 Apr 2021). This project was built on an x86 64 machine with Little Endian byteorder and address sizes 39 bits physical, 48 bits virtual.  ... 
doi:10.1109/mcse.2021.3072860 fatcat:ngzmxo2mxvak3o55jwjpmdgcxq

Toward Reproducibility in Online Social Network Research

Luke Hutton, Tristan Henderson
2018 IEEE Transactions on Emerging Topics in Computing  
We characterise reproducible OSN research using three main themes: reporting of methods, availability of code, and sharing of research data.  ...  The challenge of conducting reproducible computational research is acknowledged across myriad disciplines from biology to computer science.  ...  Reproducing OSN experimental workflows Our analysis of the state of the art in reproducibility in OSN research shows mixed progress towards the three pillars of data sharing, code re-use, and methodology  ... 
doi:10.1109/tetc.2015.2458574 fatcat:gqbcrfvpvnampejppwfntvdwoq

Towards Reproducible Descriptions of Neuronal Network Models

Eilen Nordlie, Marc-Oliver Gewaltig, Hans Ekkehard Plesser, Karl J. Friston
2009 PLoS Computational Biology  
We further observe great variation in the graphical representation of networks and the notation used in equations.  ...  We analyze here 14 research papers proposing neuronal network models of different complexity and find widely varying approaches to model descriptions, with regard to both the means of description and the  ...  Acknowledgments We would like to thank Markus Diesmann and Sven Schrader as well as three anonymous reviewers for stimulating feedback on earlier versions of the manuscript and Kittel Austvoll for help  ... 
doi:10.1371/journal.pcbi.1000456 pmid:19662159 pmcid:PMC2713426 fatcat:i3273wrl5vd3zhqal5ocvwub4i

The Road Towards Reproducibility in Science: The Case of Data Citation [chapter]

Nicola Ferro, Gianmaria Silvello
2017 Communications in Computer and Information Science  
In this paper, we present the state of the art of data citation and we discuss open issues and research directions with a specific focus on reproducibility.  ...  Data citation has a profound impact on the reproducibility of science, a hot topic in many disciplines such as as astronomy, biology, physics, computer science and more.  ...  Even if you use the same datasets and even if you rely on shared open source software, there are often many hidden parameters and tunings which hamper the reproducibility of algorithms and techniques.  ... 
doi:10.1007/978-3-319-68130-6_2 fatcat:v3b3e3qo4jfyzomypmwmfkgb5m

Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals

Victoria Stodden, Peixuan Guo, Zhaokun Ma, Dmitri Zaykin
2013 PLoS ONE  
Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science.  ...  This reflects a striking one year increase of 16% in the number of data policies, a 30% increase in code policies, and a 7% increase in the number of supplemental materials policies.  ...  The NIH expects and supports the timely release and sharing of final research data from NIH-supported studies for use by other researchers.''  ... 
doi:10.1371/journal.pone.0067111 pmid:23805293 pmcid:PMC3689732 fatcat:qkvwxvuxyzbttgdeqyagq5ud2a

Computation of adherence to medication and visualization of medication histories in R with AdhereR: Towards transparent and reproducible use of electronic healthcare data

Alexandra Lelia Dima, Dan Dediu, Christophe Leroyer
2017 PLoS ONE  
OPEN ACCESS Citation: Dima AL, Dediu D (2017) Computation of adherence to medication and visualization of medication histories in R with AdhereR: Towards transparent and reproducible use of electronic  ...  We introduce AdhereR, a package for the widely used opensource statistical environment R, designed to support researchers in computing EHD-based adherence estimates and in visualizing individual medication  ...  Depending on the complexity of the computation and the hardware, this might be more or less instantaneous (see software performance benchmarks in the following section).  ... 
doi:10.1371/journal.pone.0174426 pmid:28445530 pmcid:PMC5405929 fatcat:556num7ylzhnvgxrhzwrcitfeu

Toward a standard benchmark for computer security research

Tudor Dumitras, Darren Shou
2011 Proceedings of the First Workshop on Building Analysis Datasets and Gathering Experience Returns for Security - BADGERS '11  
WINE includes representative field data, collected worldwide from 240,000 sensors, for new empirical studies, and it will enable the validation of research on all the phases in the lifecycle of security  ...  In this paper, we review the unique characteristics of the WINE data, we discuss why rigorous benchmarking will provide fresh insights on the security arms race and we propose a research agenda for this  ...  Acknowledgments We thank Roy Maxion, Dave Brumley, Jon McCune, Ahren Studer, Jim Newsome and Marc Dacier for their early feedback on the ideas presented in this paper.  ... 
doi:10.1145/1978672.1978683 dblp:conf/badgers/DumitrasS11 fatcat:jwikl2e6bnhr7mmwwvarngynjq

Towards Replication in Computational Cognitive Modeling: a Machine Learning Perspective

Chris Emmery, Ákos Kádár, Travis J. Wiltshire, Andrew T. Hendrickson
2019 Computational Brain & Behavior  
change towards open science, the scalability and interpretability of required practices, and the downstream effects of having robust practices that are fully transparent.  ...  The suggestions proposed by Lee et al. to improve cognitive modeling practices have significant parallels to the current best practices for improving reproducibility in the field of Machine Learning.  ...  tasks and benchmarks, the ability to share complete research code, and a tendency towards open-access publication (Munafò et al. 2017) .  ... 
doi:10.1007/s42113-019-00055-w fatcat:2nsqefuq7vbkrnjlozexjqsaoq

Reproducibility: A Researcher-Centered Definition

Sebastian Stefan Feger, Paweł W. Woźniak
2022 Multimodal Technologies and Interaction  
Based on a narrative literature review of work that defines characteristics of open science, reproducibility, replicability, and repeatability, as well as a review of recent work on researcher-centered  ...  The scientific community, publishers, funding agencies, and the public expect research to adhere to principles of openness, reproducibility, replicability, and repeatability.  ...  Human-Computer Interaction Perspective The findings and contributions of this paper stem largely from a human-computer interaction perspective.  ... 
doi:10.3390/mti6020017 doaj:2e368cfecd2c4487bbb01fe6c4c1ccc6 fatcat:3nhq4niidrfjtdobmt2zbj3f4m

Reproducing Statistical Results

Victoria Stodden
2015 Annual Review of Statistics and Its Application  
The reproducibility of statistical findings has become a concern not only for statisticians, but for all researchers engaged in empirical discovery.  ...  stability of statistical findings; providing access to digital research objects, in particular data and software; and ensuring these objects are legally reusable.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Pakwesi Taylor provided outstanding research assistance.  ... 
doi:10.1146/annurev-statistics-010814-020127 fatcat:w4jqdd3e5bbchc5sj6nq5jdva4

Exploration of reproducibility issues in scientometric research Part 1: Direct reproducibility [article]

Ludo Waltman, Sybille Hinze, Andrea Scharnhorst, Jesper Wiborg Schneider, Theresa Velden
2018 arXiv   pre-print
The first part of the study focuses on direct reproducibility - that is the ability to reproduce the specific evidence produced by an original study using the same data, methods, and procedures.  ...  The second part (Velden et al. 2018) is dedicated to conceptual reproducibility - that is the robustness of knowledge claims towards verification by an alternative approach using different data, methods  ...  Software tools We suggest that from the perspective of direct reproducibility it is useful to distinguish four levels of accessibility of software tools.  ... 
arXiv:1804.05024v1 fatcat:5n3uujqj7vbnlbeoyx54tgpuiq

Computational Forensics: Towards Hybrid-Intelligent Crime Investigation

Katrin Franke, Sargur N. Srihari
2007 Third International Symposium on Information Assurance and Security  
The state of the art is described, some practical examples are given and a viewpoint is expressed that the methods can be extended to functions that currently rely only on expert knowledge.  ...  This paper gives a brief overview of the potential of computational methods in forensics.  ...  For the synthesis of data samples not only software methods, but also robots are used [6] .  ... 
doi:10.1109/isias.2007.4299803 fatcat:vuf4vlggd5gevdubez3iezplwm

Computational Forensics: Towards Hybrid-Intelligent Crime Investigation

Katrin Franke, Sargur N. Srihari
2007 Third International Symposium on Information Assurance and Security  
The state of the art is described, some practical examples are given and a viewpoint is expressed that the methods can be extended to functions that currently rely only on expert knowledge.  ...  This paper gives a brief overview of the potential of computational methods in forensics.  ...  For the synthesis of data samples not only software methods, but also robots are used [6] .  ... 
doi:10.1109/ias.2007.84 dblp:conf/IEEEias/FrankeS07 fatcat:yakxwpoukngbjkudgljvqv53nu
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