Topic · Information Systems and Management · Decision Sciences
OpenAlex topic; a paper is listed when OpenAlex scores it at least 0.5 for this topic.
311 papers
Marco Enrico Piras, Luca Pireddu, Gianluigi Zanetti
wft4galaxy provides automated testing for Galaxy workflows to enable continuous integration and defect detection.
Bioinformatics · Jul 21, 2017Peer-reviewedBioinformatics
Claire Rioualen, Lucie Khamvongsa-Charbonnier, Jacques van Helden
SnakeChunks provides modular Snakemake rules for reproducible NGS analyses, demonstrated on RNA-seq and ChIP-seq data.
bioRxiv · Jul 19, 2017 · PreprintBioinformatics
Baekdoo Kim, Thahmina A. Ali, Carlos Lijeron, Enis Afgan, Konstantinos Krampis
The paper introduces Bio-Docklets, Docker containers that simplify NGS pipeline execution by abstracting complex workflows into single-step tools.
GigaScience · Jun 27, 2017Peer-reviewedBioinformatics
Stephen J. Eglen, Ben Marwick, Yaroslav O. Halchenko, Michael Hanke, Shoaib Sufi, Padraig Gleeson, Robin Angus Silver, Andrew P. Davison, Linda Lanyon, Mathew Birdsall Abrams, Thomas Wächtler, David J Willshaw, Christophe Pouzat, Jean‐Baptiste Poline
The paper discusses the importance of sharing computational code in neuroscience and highlights challenges in current practices.
Nature Neuroscience · May 25, 2017Peer-reviewedNeuroscience
Adrienne M. Stilp, Stephanie M. Gogarten, Cathy C. Laurie, Tamar Sofer
The paper describes an integrated computing and tracking system for high-throughput genetic analysis, demonstrating its utility in reproducible research with large, restricted data.
bioRxiv · May 13, 2017 · PreprintBioinformatics
Krzysztof J. Gorgolewski, Fidel Alfaro‐Almagro, Tibor Auer, Pierre Bellec, Mihai Capotă, M. Mallar Chakravarty, Nathan W. Churchill, Alexander Li Cohen, Richard Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Estéban, Guillaume Flandin, Satrajit Ghosh, J. Swaroop Guntupalli, , Russell Alan Poldrack
This paper introduces BIDS Apps, a framework for creating portable neuroimaging analysis tools compatible with BIDS data, improving reproducibility and ease of use.
PLoS Computational Biology · Mar 9, 2017Peer-reviewedNeuroscience
Trevor Meiss, Ling‐Hong Hung, Yuguang Xiong, Eric A. Sobie, Ka Yee Yeung
This paper demonstrates that RNA-seq analysis can depend on the computing environment and shows that software containers improve reproducibility.
bioRxiv · Jan 6, 2017 · PreprintBioinformatics
Vishal Gupta, Jesús Irimia, Iván Pau, Alfonso Rodríguez‐Patón
BioBlocks provides a visual programming environment for automating biological experiments without requiring programming expertise.
ACS Synthetic Biology · Jan 4, 2017Peer-reviewedSynthetic Biology
Gaurav N. Kaushik, Sinisa Ivkovic, Janko Simonovic, Nebojša Tijanić, Brandi N. Davis‐Dusenbery, Deniz Kural
The paper introduces Rabix Executor, an open-source workflow engine that enhances reproducibility through reusability and interoperability of workflow descriptions.
Pacific Symposium on Biocomputing (PSB) · Nov 22, 2016Peer-reviewedBioinformatics
Ahmed Halioui, Petko Valtchev, Abdoulaye Baniré Diallo
The paper proposes an ontology-based framework to extract and mine bioinformatics workflows from scientific articles, focusing on phylogenetic analyses, to identify best practices and support workflow reuse.
bioRxiv · Oct 24, 2016 · PreprintBioinformatics