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Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, Alban Gaignard, Konrad Hinsen, Pierre Larmande, Yvan Le Bras, Frédéric Lemoine, Fabien Mareuil, Hervé Ménager (+2 others)
2017 Future generations computer systems  
We acknowledge funding by the call "Infrastructures in Biology and Health" in the framework of the French "Investments for the Future" (ANR-11-INBS-0012 and ANR-11-INBS-0013).  ...  This work was conducted in part at the IBC (Institute of Computational Biology) in Montpellier, France.  ...  We go on to discuss the challenges posed by reproducible scientific workflows in the life sciences and describe the remaining opportunities of research in several areas of computer science which may address  ... 
doi:10.1016/j.future.2017.01.012 fatcat:ssr36upvdrgr3nkwhdgc6nkh6q

Digitalization of Battery Manufacturing: Current Status, Challenges, and Opportunities

Elixabete Ayerbe, Maitane Berecibar, Simon Clark, Alejandro A. Franco, Janna Ruhland
2021 Advanced Energy Materials  
This review provides a detailed discussion of the current and nearterm developments for the digitalization of the battery cell manufacturing chain and presents future perspectives in this field.  ...  As the world races to respond to the diverse and expanding demands for electrochemical energy storage solutions, lithium-ion batteries (LIBs) remain the most advanced technology in the battery ecosystem  ...  Then, we summarize the challenges and opportunities of the implementation of these new technologies.  ... 
doi:10.1002/aenm.202102696 fatcat:wvuyyiyzp5aazibyizly52z54i

Gamification in Science

Sebastian S. Feger, Sünje Dallmeier-Tiessen, Pawel W. Wozniak, Albrecht Schmidt
2019 Proceedings of the 2019 CHI Conference on Human Factors in Computing Systems - CHI '19  
The need for data preservation and reproducible research is widely recognized in the scientific community.  ...  The evaluation of the prototypes showed that gamification needs to address core scientific challenges, in particular the fair reflection of quality and individual contribution.  ...  In the following discussion, we see how prevalent challenges in scientific work need to be reflected in design requirements for gamification in science.  ... 
doi:10.1145/3290605.3300690 dblp:conf/chi/FegerDW019 fatcat:elimcpycxvfjtara4bkzbkpyba

Interactive Tools for Reproducible Science – Understanding, Supporting, and Motivating Reproducible Science Practices [article]

Sebastian Stefan Feger
2020 arXiv   pre-print
On the one hand, this transition towards computational and data-intensive science poses new challenges for research reproducibility and reuse.  ...  On the other hand, increased availability and advances in computation and web technologies offer new opportunities to address the reproducibility crisis.  ...  Designing for Scientific Communities and Reproducible Science Today's general availability of computation and internet connectivity provides unprecedented opportunities for the systematic preservation  ... 
arXiv:2012.02570v1 fatcat:ejqwev3kybajtnwozt6zfewway

Digital Science Workshop Report

Caitlin Trasande
2014 Figshare  
The Digital Science Workshop series represents a unique opportunity to partner with academic, private and public institutes as well as fellow commercial enterprises to achieve the greater common good of  ...  For we know well that improved efficiencies in research extend beyond the researcher's office or laboratory.  ...  The panel also echoed Victoria Stodden's keynote speech in advocating for improved reproducibility in computational science.  ... 
doi:10.6084/m9.figshare.1124216 fatcat:r2y7dpyl4vfkjfnbdn3rcnzy3i

Data science: a game changer for science and innovation

Valerio Grossi, Fosca Giannotti, Dino Pedreschi, Paolo Manghi, Pasquale Pagano, Massimiliano Assante
2021 International Journal of Data Science and Analytics  
We present how data science impacts science and society at large in the coming years, including ethical problems in managing human behavior data and considering the quantitative expectations of data science  ...  AbstractThis paper shows data science's potential for disruptive innovation in science, industry, policy, and people's lives.  ...  as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.  ... 
doi:10.1007/s41060-020-00240-2 fatcat:x24cifqkofd33nbos5iwxkzciy

Knowledge formalization for Earth Science informed decision-making: The GEOEssential Knowledge Base

Paolo Mazzetti, Stefano Nativi, Mattia Santoro, Gregory Giuliani, Denisa Rodila, Antonietta Folino, Susie Caruso, Giovanna Aracri, Anthony Lehmann
2022 Environmental Science and Policy  
Environmental Science and Policy 131 (2022) 93-104  ...  and innovation programme under grant agreement N. 689443 (ERA-PLANET) and from the Ministry of University and Research of Italy (Decreto MIUR n. 1969.  ...  Acknowledgements The research leading to these results has received funding through the GEOEssential and SMURBS Transnational Projects from the European Commission Horizon 2020 -European Union (EU) research  ... 
doi:10.1016/j.envsci.2021.12.023 fatcat:xglmoat5dzfp7h5ijhcsdzzh4e

Perspectives on automated composition of workflows in the life sciences

Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil (+20 others)
2021 F1000Research  
Scientific data analyses often combine several computational tools in automated pipelines, or workflows.  ...  However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration  ...  In this article we report on the state of the art of automated workflow development in the life sciences, discuss current and future challenges and develop perspectives for the coming years.  ... 
doi:10.12688/f1000research.54159.1 pmid:34804501 pmcid:PMC8573700 fatcat:ht57fgnzwbbmdmkazs7wi7r5s4

Development of a cloud-based platform for reproducible science: A case study of an IUCN Red List of Ecosystems Assessment

Siddeswara Guru, Ivan C. Hanigan, Hoang Anh Nguyen, Emma Burns, John Stein, Wade Blanchard, David Lindenmayer, Tim Clancy
2016 Ecological Informatics  
Acknowledgements The Authors thank Kim Olsson, Shilo Banihit and Matthew Mulholland for their contribution to the project. Special thanks to Victorian Government,  ...  Here, we demonstrate the use of a Kepler scientific workflow for reproducible science that is sharable, reusable, and re-executable.  ...  However, some of the challenges of reproducible science can be addressed using appropriate computational tools and cloud computing to provide an execution environment.  ... 
doi:10.1016/j.ecoinf.2016.08.003 fatcat:6ops3hrzszgm5ckuwvfe5kujmm

GESIS Open Science Strategy

2020 EUROLAB annual report  
Open Access Status Quo Open Access in the Social Sciences Open Access is a catalyst to Open Science.  ...  in a reproducible fashion) at the scientific journals, starting with the inhouse publications.  ... 
doi:10.21241/ssoar.68697 fatcat:ve7hka7mmnasjbxtjymyt3ntky

Data Science in Undergraduate Life Science Education: A Need for Instructor Skills Training

Nathan C Emery, Erika Crispo, Sarah R Supp, Kaitlin J Farrell, Andrew J Kerkhoff, Ellen K Bledsoe, Kelly L O'Donnell, Andrew C McCall, Matthew E Aiello-Lammens
2021 BioScience  
There is a clear demand for quantitative literacy in the life sciences, necessitating competent instructors in higher education.  ...  Coding, modeling, and reproducibility were less valued by the instructors, although this differed according to institution type and career stage.  ...  This article was possible thanks to the many survey participants who volunteered their perspectives on data science skills in the life sciences.  ... 
doi:10.1093/biosci/biab107 pmid:34867087 pmcid:PMC8634500 fatcat:fn34lunzc5gdxigb2rbpu22lui

A SOA-Based Environment Supporting Collaborative Experiments in E-Science

Andrea Bosin, Nicoletta Dessì, Bairappan Madusudhanan, Barbara Pes
2011 International Journal of Web Portals  
The proposed approach provides a simple-to-use and standardized way for the deployment of scientific workflows in a distributed scientific environment, including the Grid.  ...  This paper proposes to support scientists with an e-Science environment providing functionality in a simplified way, especially for communities whose IT skills are not so smart not only to consider the  ...  ACKNOWLEDGEMENTS The authors acknowledge Cybersar Project and the Italian Grid Infrastructure (IGI) for the use of their computing facilities.  ... 
doi:10.4018/jwp.2011070102 fatcat:i4hpbqfxrbevtowg6tp5p5yjz4

ELIXIR: Providing a Sustainable Infrastructure for Life Science Data at European Scale

Jennifer Harrow, Rachel Drysdale, Andrew Smith, Susanna Repo, Jerry Lanfear, Niklas Blomberg, Jonathan Wren
2021 Bioinformatics  
Acknowledgements: We are grateful to the numerous people who contributed to the discussions around this paper and in particular we would like to thank Premysl Velek and Xenia Perez Sitja for help preparing  ...  We also thank Janet Thornton and Francis Ouellette for critical reading of the manuscript draft and valuable insight on how to improve it for the general readership.  ...  space for life science in the EOSC.  ... 
doi:10.1093/bioinformatics/btab481 pmid:34175941 fatcat:iawlht3iajg43fbqyprsguaq4m

LSST DESC Science Roadmap [article]

The LSST Dark Energy Science Collaboration
2019 Zenodo  
The LSST DESC Science Roadmap (SRM) is primarily focused on providing a detailed framework (basic research priorities, along with infrastructure work in the form of software and dataset deliverables) that  ...  we will need to undertake for the collaboration to be ready to analyze the LSST Year 1 data, including the beginnings of a plan for LSST commissioning and SV.  ...  Approach: We will generate instance catalogs based on the extragalactic catalog produced in Deliverable "Extragalactic Catalogs for the DC2 Simulation".  ... 
doi:10.5281/zenodo.3547567 fatcat:52yfpyi5qrdxdmnwuisb4lll44

Cybercosm: New Foundations for a Converged Science Data Ecosystem [article]

Mark Asch, François Bodin, Micah Beck, Terry Moore, Michela Taufer, Martin Swany, Jean-Pierre Vilotte
2021 arXiv   pre-print
The Cybercosm vision presented in this white paper describes a radically different approach to the architecture of distributed systems for data-intensive science and its application workflows.  ...  as a spanning layer for its data plane that virtualizes and converges the local resources of the system's nodes in a fully interoperable manner.  ...  In it we will be adding and updating relevant explanations and material.  ... 
arXiv:2105.10680v3 fatcat:m2vytmdkdvdvzc2deal5odte4u
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