Michael R. Crusoe

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Stian Soiland-ReyesSenior Lecturer, Department of Computer Science, The University of ManchesterVerified email at manchester.ac.uk
Björn GrüningUniversity of FreiburgVerified email at informatik.uni-freiburg.de
Hervé MénagerInstitut PasteurVerified email at pasteur.fr
Peter AmstutzCuriiVerified email at curii.com
Carole GobleProfessor of Computer Science, University of ManchesterVerified email at manchester.ac.uk
Marius van den BeekSci-ScaleVerified email at sci-scale.net
Andrey KartashovCo-Founder, Datirium LLCVerified email at datirium.com
Jeremy GoecksAssistant Center Director, Research Informatics at the Moffitt Cancer CenterVerified email at moffitt.org
Nicola SoranzoEarlham InstituteVerified email at earlham.ac.uk
Helena RascheOnderzoeker in Opleiding, Department Pathology, Erasmus Medical CenterVerified email at erasmusmc.nl
Daniel GarijoOntology Engineering Group, UPM and Information Sciences Institute, USCVerified email at upm.es
Farah Zaib KhanSchool of Computing and Information Systems, The University of MelbourneVerified email at unimelb.edu.au
Robert D. FinnMicrobiome Informatics Team Leader, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SDVerified email at ebi.ac.uk
C. Titus BrownProfessor, UC DavisVerified email at ucdavis.edu
Andrew LonieDirector, Australian Bioinformatics Commons, University of MelbourneVerified email at unimelb.edu.au
Sanne AbelnProfessor of AI Technology for Life, Utrecht UniversityVerified email at uu.nl
Alexandru IosupProfessor of Comp.Sci., VU University AmsterdamVerified email at vu.nl
Timo SachsenbergStaff Scientist, University of TübingenVerified email at uni-tuebingen.de
Peter van HeusdenSouth African National Bioinformatics Institute, University of the Western Cape, South AfricaVerified email at sanbi.ac.za
Dr. Faisal M. FadlelmolaCentre for Bioinformatics & Systems Biology, Faculty of Science, University of KhartoumVerified email at uofk.edu

Michael R. Crusoe

Other namesMichael Crusoe

Common Workflow Language project, and others

Verified email at commonwl.org - Homepage

workflows escience


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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update E Afgan, D Baker, B Batut, M Van Den Beek, D Bouvier, M Čech, J Chilton, ... Nucleic acids research 46 (W1), W537-W544, 2018	4447	2018
MGnify: the microbiome analysis resource in 2020 AL Mitchell, A Almeida, M Beracochea, M Boland, J Burgin, G Cochrane, ... Nucleic acids research 48 (D1), D570-D578, 2020	590	2020
The khmer software package: enabling efficient nucleotide sequence analysis MR Crusoe, HF Alameldin, S Awad, E Boucher, A Caldwell, R Cartwright, ... F1000Research 4, 2015	435*	2015
Common Workflow Language v1.0 P Amstutz, MR Crusoe, N Tijanić, B Chapman, J Chilton, M Heuer, ... FigShare, 2016	306*	2016
FAIR computational workflows C Goble, S Cohen-Boulakia, S Soiland-Reyes, D Garijo, Y Gil, MR Crusoe, ... Data Intelligence 2 (1-2), 108-121, 2020	179	2020
Methods included: Standardizing computational reuse and portability with the Common Workflow Language. MR Crusoe, S Abeln, A Iosup, P Amstutz, J Chilton, N Tijanić, H Ménager, ... Communications of the ACM 65 (6), 54-63, 2022	153	2022
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv FZ Khan, S Soiland-Reyes, RO Sinnott, A Lonie, C Goble, MR Crusoe GigaScience 8 (11), giz095, 2019	90	2019
Comparative genomics reveals accelerated evolution in conserved pathways during the diversification of anole lizards M Tollis, ED Hutchins, J Stapley, SM Rupp, WL Eckalbar, I Maayan, ... Genome Biology and Evolution 10 (2), 489-506, 2018	51	2018
Recommendations for the packaging and containerizing of bioinformatics software B Gruening, O Sallou, P Moreno, F da Veiga Leprevost, H Ménager, ... F1000Research 7, ISCB Comm J-742, 2019	50	2019
Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics S Baichoo, Y Souilmi, S Panji, G Botha, A Meintjes, S Hazelhurst, ... BMC bioinformatics 19, 1-13, 2018	41	2018
Enabling precision medicine via standard communication of HTS provenance, analysis, and results G Alterovitz, D Dean, C Goble, MR Crusoe, S Soiland-Reyes, A Bell, ... PLoS biology 16 (12), e3000099, 2018	40	2018
Workflows community summit 2022: A roadmap revolution RF da Silva, RM Badia, V Bala, D Bard, PT Bremer, I Buckley, ... arXiv preprint arXiv:2304.00019, 2023	39	2023
Scalable workflows and reproducible data analysis for genomics F Strozzi, R Janssen, R Wurmus, MR Crusoe, G Githinji, P Di Tommaso, ... Evolutionary Genomics: Statistical and Computational Methods, 723-745, 2019	36	2019
Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis S Möller, SW Prescott, L Wirzenius, P Reinholdtsen, B Chapman, P Prins, ... Data Science and Engineering, 1-13, 2017	29	2017
Workflows Community Summit: Bringing the Scientific Workflows Community Together R Ferreira da Silva, H Casanova, K Chard, D Laney, D Ahn, S Jha, ... arXiv e-prints, arXiv: 2103.09181, 2021	28*	2021
Workflows community summit: Advancing the state-of-the-art of scientific workflows management systems research and development RF da Silva, H Casanova, K Chard, T Coleman, D Laney, D Ahn, S Jha, ... arXiv preprint arXiv:2106.05177, 2021	20	2021
Existing workflow systems. P Amstutz (No Title), 2021	20	2021
Organizing and running bioinformatics hackathons within Africa: the H3ABioNet cloud computing experience AE Ahmed, PT Mpangase, S Panji, S Baichoo, Y Souilmi, FM Fadlelmola, ... AAS Open Research 1, 9, 2019	19	2019
Perspectives on automated composition of workflows in the life sciences AL Lamprecht, M Palmblad, J Ison, V Schwämmle, MS Al Manir, I Altintas, ... F1000Research 10, 2021	18	2021
Channeling Community Contributions to Scientific Software: A Sprint Experience CTB Michael R. Crusoe Journal of Open Research Software 4, 2016	13*	2016

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