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Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language [article]

Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilovic, Carole Goble
2021 arXiv   pre-print
Here we present the Common Workflow Language (CWL) project which produces free and open standards for describing command-line tool based workflows.  ...  The CWL standards support polylingual workflows, enabling portability and reuse of such workflows, easing for example scholarly publication, fulfilling regulatory requirements, collaboration in/between  ...  Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language 29 "Ajax Command Definitions" as produced  ... 
arXiv:2105.07028v2 fatcat:7sbudwpfzzdy5ffniruiq65fc4

When computational pipelines go 'clank'

Vivien Marx
2020 Nature Methods  
Brown and his team, including postdoctoral fellow N.  ...  Tessa Pierce, are putting together a computational pipeline for decontaminating genome assemblies in metagenomics and are using the workflow manager Snakemake 1 to do so.  ...  Jude, open workflow standards like CWL and WDL appear to be the leading workflow languages.  ... 
doi:10.1038/s41592-020-0886-9 pmid:32601427 fatcat:2w5qi2spgnasdl6eczgiwfft3a

A Method for Reusing TOSCA-based Applications and Management Plans

Sebastian Wagner, Uwe Breitenbücher, Frank Leymann
2016 Proceedings of the 6th International Conference on Cloud Computing and Services Science  
To validate the approach, we apply the concept to the choreography language BPEL4CHOR and the Cloud standard TOSCA.  ...  In this paper, we present an approach that tackles these issues by enabling the usage of choreographies to systematically combine available management workflows of existing application building blocks.  ...  ACKNOWLEDGEMENTS This work was partially funded by the BMWi project NEMAR (03ET40188) and the DFG project SitOPT (610872).  ... 
doi:10.5220/0005808201810191 dblp:conf/closer/0001BL16 fatcat:rnk23ejfbnfu5ijdxpnkcgoqjq

Sharing and organizing research products as R packages

Matti Vuorre, Matthew J. C. Crump
2020 Behavior Research Methods  
The sharing method should be easy to adopt by already busy researchers. We suggest the R package standard as a solution for creating, curating, and communicating research assets.  ...  The R package standard, with extensions discussed herein, provides a format for assets and metadata that satisfies the above desiderata, facilitates reproducibility, open access, and sharing of materials  ...  The authors declare equal authorship. MV is funded by the Adolescent Well-Being in the Digital Age project funded by the Huo Family Foundation.  ... 
doi:10.3758/s13428-020-01436-x pmid:32875401 fatcat:hxfnwaj5ovetpehsosoctlnawa

A Learning Management System Including Laboratory Experiments on Measurement Instrumentation

S. Rapuano, F. Zoino
2006 IEEE Transactions on Instrumentation and Measurement  
Then, the remote laboratory system relying on virtual instruments (VIs) developed in LabVIEW and its integration with an off-the-shelf LMS are described in a project financed by the Italian Ministry of  ...  The proposed approach integrates a traditional Learning Management System (LMS) with the remote access to real instrumentation located in different laboratories, without requiring specific software components  ...  access to the system using their desktop computers based on common hardware and software technologies, with no need for powerful processors or high memory capacity, and connecting to the Internet through  ... 
doi:10.1109/tim.2006.880309 fatcat:prbflykprnekjjt53oz3bf4glm

Open standard, open source and peer-to-peer tools and methods for collaborative product development

Hayder Aziz, James Gao, Paul Maropoulos, Wai M. Cheung
2005 Computers in industry (Print)  
This is implementable at low cost, the scalability increases in line with user numbers. Ontologies, rules and workflows are reusable and extendable.  ...  To overcome these, an ontological knowledge management methodology utilising the semantic web initiative data formats was added to a PLM and an opensource alternative.  ...  Firstly the UK Engineering and Physical Science Research Council (EPSRC) for its financial support, in addition to the industrial collaborators ArvinMeritor, LSC Group, Mabey and Johnson and PTC Corporation  ... 
doi:10.1016/j.compind.2004.12.002 fatcat:r7gizqakbfbyjomenukhspnw7e

Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation

Ben Marwick
2016 Journal of Archaeological Method and Theory  
The use of computers and complex software is pervasive in archaeology, yet their role in the analytical pipeline is rarely exposed for other researchers to inspect or reuse.  ...  Abstract The use of computers and complex software is pervasive in archaeology, yet their role in the analytical pipeline is rarely exposed for other researchers to inspect or reuse.  ...  Lowe, and Jacqueline Matthews for their cooperation with the JHE paper.  ... 
doi:10.1007/s10816-015-9272-9 fatcat:qrncm7dfyzhshi2qdnpzphapnm

From Raw Data to FAIR Data: The FAIRification Workflow for Health Research

A. Anil Sinaci, Francisco J. Núñez-Benjumea, Mert Gencturk, Malte-Levin Jauer, Thomas Deserno, Catherine Chronaki, Giorgio Cangioli, Carlos Cavero-Barca, Juan M. Rodríguez-Pérez, Manuel M. Pérez-Pérez, Gokce B. Laleci Erturkmen, Tony Hernández-Pérez (+2 others)
2020 Methods of Information in Medicine  
Methods A common FAIRification workflow was developed by applying restrictions on existing steps and introducing new steps for specific requirements of health data.  ...  Background FAIR (findability, accessibility, interoperability, and reusability) guiding principles seek the reuse of data and other digital research input, output, and objects (algorithms, tools, and workflows  ...  Aguayo-Canela, with a file number GA82466 in Seville, September 25, 2018.  ... 
doi:10.1055/s-0040-1713684 pmid:32620019 fatcat:a7mpkludszd5zauhy2nivhhbou

The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web [article]

Khalid Belhajjame and Jun Zhao and Daniel Garijo and Kristina Hettne and Raul Palma and Óscar Corcho and José-Manuel Gómez-Pérez and Sean Bechhofer and Graham Klyne and Carole Goble
2014 arXiv   pre-print
Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results.  ...  In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions.  ...  traces of their executions, which are very common in any computational experiment.  ... 
arXiv:1401.4307v2 fatcat:rdch6zkgqjfpzcimlsfi75owbq

AIBench: A rapid application development framework for translational research in biomedicine

D. Glez-Peña, M. Reboiro-Jato, P. Maia, M. Rocha, F. Díaz, F. Fdez-Riverola
2010 Computer Methods and Programs in Biomedicine  
repeatability and user interface workflow management, among others.  ...  In this context this paper presents AIBench, an open-source Java desktop application framework for scientific software development with the goal of providing support to both fundamental and applied research  ...  of Minho) and Spain (University of Vigo), the project  ... 
doi:10.1016/j.cmpb.2009.12.003 pmid:20047774 fatcat:ktx3i7xqsvflrgb3lzsb3zdvau

Making Canonical Workflow Building Blocks interoperable across workflow languages

Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital
2021 Zenodo  
We argue such practice is a necessary requirement for FAIR Computational Workflows [Goble 2020] to improve widespread adoption and reuse of a computational method across workflow language barriers.  ...  multiple workflow languages and execution platforms.  ...  Acknowledgements This work has been done as part of the BioExcel CoE (, a project funded by the European Union contract H2020-INFRAEDI-02-2018  ... 
doi:10.5281/zenodo.4602854 fatcat:idc7qtlwi5c27ci33iduue7zvu

Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics

Hirotaka Suetake, Tomoya Tanjo, Manabu Ishii, Bruno P. Kinoshita, Takeshi Fujino, Tsuyoshi Hachiya, Yuichi Kodama, Takatomo Fujisawa, Osamu Ogasawara, Atsushi Shimizu, Masanori Arita, Tsukasa Fukusato (+2 others)
2022 F1000Research  
The current implementation supports the execution of workflows in four languages: Common Workflow Language, Workflow Description Language, Snakemake, and Nextflow.  ...  The API follows the Workflow Execution Service API standard proposed by the Global Alliance for Genomics and Health.  ...  the project: the Pitagora Meetup, Workflow Meetup Japan, NBDC/DBCLS BioHackathon Series, Elixir's BioHackathon Europe Series, GA4GH Cloud WorkStream, Common Workflow Language Community, Nextflow Community  ... 
doi:10.12688/f1000research.122924.1 fatcat:yss5w5lwfbgmzp3wzxv44b3kby

Methods for enhancing the reproducibility of biomedical research findings using electronic health records

Spiros Denaxas, Kenan Direk, Arturo Gonzalez-Izquierdo, Maria Pikoula, Aylin Cakiroglu, Jason Moore, Harry Hemingway, Liam Smeeth
2017 BioData Mining  
standardization and re-use of common data management and analytical approaches.  ...  Conclusion: The adoption of such approaches will enable scientists to systematically document and share EHR analytical workflows and increase the reproducibility of biomedical research using such complex  ...  Acknowledgements We would like to thank Václav Papež for his help in preparing the figures included in this manuscript.  ... 
doi:10.1186/s13040-017-0151-7 pmid:28912836 pmcid:PMC5594436 fatcat:uk4ldgnrs5gelptssf3j7kuhtq

A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows

Pei-Chi Yang, Shweta Purawat, Pek U. Ieong, Mao-Tsuen Jeng, Kevin R. DeMarco, Igor Vorobyov, Andrew D. McCulloch, Ilkay Altinas, Rommie E. Amaro, Colleen E. Clancy, Herbert Sauro
2019 PLoS Computational Biology  
It invariably involves specific and detailed sequences of data analysis and simulation, often with multiple tools and datasets, and the community recognizes improved modularity, reuse, reproducibility,  ...  In this article, we develop, describe and test a computational workflow that serves as a proof of concept of a platform for the robust integration and implementation of a reusable and reproducible multi-scale  ...  The approach brings us closer to the increasingly shared goal of computational scientists to enable model modularity, reuse, reproducibility, portability and scalability.  ... 
doi:10.1371/journal.pcbi.1006856 pmid:30849072 pmcid:PMC6426265 fatcat:3gucgod6mfbsrf644otegioozm

FAIR Computational Workflows

Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober
2019 Zenodo  
Computational workflows describe the complex multi-step methods that are used for data collection, data preparation, analytics, predictive modelling, and simulation that lead to new data products.  ...  They can inherently contribute to the FAIR data principles: by processing data according to established metadata; by creating metadata themselves during the processing of data; and by tracking and recording  ...  Kristian Peters is funded by the German Network for Bioinformatics Infrastructure (de.NBI) and acknowledges BMBF funding under grant number 031L0107.  ... 
doi:10.5281/zenodo.3528076 fatcat:lfirfhlbpreg7ac3kcb5vwirza
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