Reproducibility and Transparency by Design
Abstract
Public trust of scientific research is often affected by the clarity of published conclusions and also the perceived transparency of the method. Even among scientists, there is often a skeptical reception to new research because of difficulty and sometimes inability to recreate or reproduce the result. The silent crisis of irreproducibility has many potential contributing factors, including: pressure to publish groundbreaking results, the difficulty of a single peer expert to fully review multi-disciplinary team science endeavors, and perceived lack of scientific credit for replicating or disproving a previous result. Although irreproducibility is not exclusive to biology, strong public interest in environmental and biomedical discoveries seems to have focused the spotlight here following a number of high profile studies that failed to be reproduced.
- Authors:
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1766607
- Alternate Identifier(s):
- OSTI ID: 1572490
- Report Number(s):
- PNNL-SA-111442
Journal ID: ISSN 1535-9476; S1535947620327729; PII: S1535947620327729
- Grant/Contract Number:
- Early Career Research Program; AC05-76RL01830
- Resource Type:
- Published Article
- Journal Name:
- Molecular and Cellular Proteomics
- Additional Journal Information:
- Journal Name: Molecular and Cellular Proteomics Journal Volume: 18 Journal Issue: 8 S1; Journal ID: ISSN 1535-9476
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Petyuk, Vladislav A., Gatto, Laurent, and Payne, Samuel H. Reproducibility and Transparency by Design. United States: N. p., 2019.
Web. doi:10.1074/mcp.IP119.001567.
Petyuk, Vladislav A., Gatto, Laurent, & Payne, Samuel H. Reproducibility and Transparency by Design. United States. https://doi.org/10.1074/mcp.IP119.001567
Petyuk, Vladislav A., Gatto, Laurent, and Payne, Samuel H. Thu .
"Reproducibility and Transparency by Design". United States. https://doi.org/10.1074/mcp.IP119.001567.
@article{osti_1766607,
title = {Reproducibility and Transparency by Design},
author = {Petyuk, Vladislav A. and Gatto, Laurent and Payne, Samuel H.},
abstractNote = {Public trust of scientific research is often affected by the clarity of published conclusions and also the perceived transparency of the method. Even among scientists, there is often a skeptical reception to new research because of difficulty and sometimes inability to recreate or reproduce the result. The silent crisis of irreproducibility has many potential contributing factors, including: pressure to publish groundbreaking results, the difficulty of a single peer expert to fully review multi-disciplinary team science endeavors, and perceived lack of scientific credit for replicating or disproving a previous result. Although irreproducibility is not exclusive to biology, strong public interest in environmental and biomedical discoveries seems to have focused the spotlight here following a number of high profile studies that failed to be reproduced.},
doi = {10.1074/mcp.IP119.001567},
journal = {Molecular and Cellular Proteomics},
number = 8 S1,
volume = 18,
place = {United States},
year = {Thu Aug 01 00:00:00 EDT 2019},
month = {Thu Aug 01 00:00:00 EDT 2019}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1074/mcp.IP119.001567
https://doi.org/10.1074/mcp.IP119.001567
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 3 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
How open science helps researchers succeed
journal, July 2016
- McKiernan, Erin C.; Bourne, Philip E.; Brown, C. Titus
- eLife, Vol. 5
R Markdown: Integrating A Reproducible Analysis Tool into Introductory Statistics
journal, January 2014
- Baumer, Ben; Cetinkaya-Rundel, Mine; Bray, Andrew
- Technology Innovations in Statistics Education, Vol. 8, Issue 1
Five selfish reasons to work reproducibly
journal, December 2015
- Markowetz, Florian
- Genome Biology, Vol. 16, Issue 1
Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)
journal, December 2011
- Kinsinger, Christopher R.; Apffel, James; Baker, Mark
- Molecular & Cellular Proteomics, Vol. 10, Issue 12
Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages
journal, December 2013
- Ohnishi, Yusuke; Huber, Wolfgang; Tsumura, Akiko
- Nature Cell Biology, Vol. 16, Issue 1
Use of proteomic patterns in serum to identify ovarian cancer
journal, February 2002
- Petricoin, Emanuel F.; Ardekani, Ali M.; Hitt, Ben A.
- The Lancet, Vol. 359, Issue 9306
Orchestrating high-throughput genomic analysis with Bioconductor
journal, January 2015
- Huber, Wolfgang; Carey, Vincent J.; Gentleman, Robert
- Nature Methods, Vol. 12, Issue 2
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
journal, August 2016
- Wang, Mingxun; Carver, Jeremy J.; Phelan, Vanessa V.
- Nature Biotechnology, Vol. 34, Issue 8
Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis
journal, January 2019
- Chalkley, Robert J.; MacCoss, Michael J.; Jaffe, Jacob D.
- Molecular & Cellular Proteomics, Vol. 18, Issue 1
Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells
journal, July 2012
- Reaves, M. L.; Sinha, S.; Rabinowitz, J. D.
- Science, Vol. 337, Issue 6093
Toward a Shared Vision for Cancer Genomic Data
journal, September 2016
- Grossman, Robert L.; Heath, Allison P.; Ferretti, Vincent
- New England Journal of Medicine, Vol. 375, Issue 12
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
journal, October 2016
- Deutsch, Eric W.; Csordas, Attila; Sun, Zhi
- Nucleic Acids Research, Vol. 45, Issue D1
Widespread RNA and DNA Sequence Differences in the Human Transcriptome
journal, May 2011
- Li, M.; Wang, I. X.; Li, Y.
- Science, Vol. 333, Issue 6038
Cancer Biomarkers: Can We Turn Recent Failures into Success?
journal, August 2010
- Diamandis, E. P.
- JNCI Journal of the National Cancer Institute, Vol. 102, Issue 19
BioContainers: an open-source and community-driven framework for software standardization
journal, March 2017
- da Veiga Leprevost, Felipe; Grüning, Björn A.; Alves Aflitos, Saulo
- Bioinformatics, Vol. 33, Issue 16
Ten Simple Rules for Taking Advantage of Git and GitHub
journal, July 2016
- Perez-Riverol, Yasset; Gatto, Laurent; Wang, Rui
- PLOS Computational Biology, Vol. 12, Issue 7
A data repository and analysis framework for spontaneous neural activity recordings in developing retina
journal, March 2014
- Eglen, Stephen John; Weeks, Michael; Jessop, Mark
- GigaScience, Vol. 3, Issue 1
Blazing Signature Filter: a library for fast pairwise similarity comparisons
journal, June 2018
- Lee, Joon-Yong; Fujimoto, Grant M.; Wilson, Ryan
- BMC Bioinformatics, Vol. 19, Issue 1
Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry
journal, April 2007
- Asara, J. M.; Schweitzer, M. H.; Freimark, L. M.
- Science, Vol. 316, Issue 5822
Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping
journal, April 2013
- Laufer, Christina; Fischer, Bernd; Billmann, Maximilian
- Nature Methods, Vol. 10, Issue 5