Firalink: A bioinformatics pipeline for long non-coding RNA data analysis by Louis Chauviere, Lucien Hoffbeck, Muhammad Shoaib, Florent Tessier, Huseyin Firat, Venkata Satagopam, Yvan Devaux

“…The pipeline is implemented with the Nextflow workflow manager using Python and R scripts. It will remain available for at least two years following publication and will be regularly updated and upgraded. …”
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Semi-automatic staging area for high-quality structured data extraction from scientific literature by Luca Foppiano, Tomoya Mato, Kensei Terashima, Pedro Ortiz Suarez, Taku Tou, Chikako Sakai, Wei-Sheng Wang, Toshiyuki Amagasa, Yoshihiko Takano, Masashi Ishii

“…Here we report our curation interface (SuperCon2 Interface) and a workflow managing the state transitions of each examined record, to validate the dataset of superconductors from PDF documents collected using Grobid-superconductors in a previous work. …”
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ReporType: A Flexible Bioinformatics Tool for Targeted Loci Screening and Typing of Infectious Agents by Helena Cruz, Miguel Pinheiro, Vítor Borges

“…Developed using the snakemake workflow manager, ReporType integrates multiple software for read quality control and de novo assembly, and then applies ABRicate for locus screening, culminating in the production of easily interpretable reports for the identification of pathogen genotypes and/or screening of specific genomic loci. …”
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Automatic Information Exchange in the Early Rescue Chain Using the International Standard Accident Number (ISAN) by Mostafa Haghi, Ramon Barakat, Nicolai Spicher, Christian Heinrich, Justin Jageniak, Gamze Söylev Öktem, Maike Krips, Ju Wang, Siegfried Hackel, Thomas M. Deserno

“…The suggested platform is composed of an alerting, responding, and curing system manager, a workflow manager, and a communication manager. First, the ICT systems of all parties in the early rescue chain register with their according system manager, which tracks the keep-alive. …”
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HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes by Thomas M. Adams, Moray Smith, Yuhan Wang, Lynn H. Brown, Micha M. Bayer, Ingo Hein

“…These workflows are implemented via Snakemake, a python-based workflow manager. Software dependencies are either shipped with the release or handled with conda. …”
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Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service by Marco Antonio Tangaro, Pietro Mandreoli, Matteo Chiara, Giacinto Donvito, Marica Antonacci, Antonio Parisi, Angelica Bianco, Angelo Romano, Daniela Manila Bianchi, Davide Cangelosi, Paolo Uva, Ivan Molineris, Vladimir Nosi, Raffaele A. Calogero, Luca Alessandri, Elena Pedrini, Marina Mordenti, Emanuele Bonetti, Luca Sangiorgi, Graziano Pesole, Federico Zambelli

“…One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of “on-demand” Galaxy instances over the cloud. …”
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Spatial non-linearity of methane release dynamics in underground boreholes for sustainable mining by Ada K. Dzhioeva, Vladimir S. Brigida

“…Identification of patterns in the influence of situational geomechanical conditions of coal mining on the initiation of metastable gas-coal solution transformation and genesis of wave processes in the coal-rock mass allows to improve reliability of predicting methane release dynamics, as well as workflow manageability of mining operations. Presented results demonstrate that development of high-methane Donbass seams is associated with insufficient reliability of gas drainage system operation at distances over 40 m behind the longwall face. …”
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Data assimilation for the Model for Prediction Across Scales – Atmosphere with the Joint Effort for Data assimilation Integration (JEDI-MPAS 2.0.0-beta): ensemble of 3D ensemble-va... by J. J. Guerrette, J. J. Guerrette, Z. Liu, C. Snyder, B.-J. Jung, C. S. Schwartz, J. Ban, S. Vahl, S. Vahl, Y. Wu, Y. Wu, I. H. Baños, Y. G. Yu, Y. G. Yu, S. Ha, Y. Trémolet, T. Auligné, C. Gas, B. Ménétrier, A. Shlyaeva, M. Miesch, M. Miesch, S. Herbener, E. Liu, E. Liu, D. Holdaway, D. Holdaway, B. T. Johnson

“…Basic software building blocks are reused from previously presented deterministic 3DEnVar functionality and combined with a formal experimental workflow manager in MPAS-Workflow. En-3DEnVar is used to produce an 80-member ensemble of analyses, which are cycled with ensemble forecasts in a 1-month experiment. …”
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Exploiting Machine Learning for Improving In-Memory Execution of Data-Intensive Workflows on Parallel Machines by Riccardo Cantini, Fabrizio Marozzo, Alessio Orsino, Domenico Talia, Paolo Trunfio

“…This paper proposed a novel solution, called the Intelligent In-memory Workflow Manager (IIWM), for optimizing the in-memory execution of data-intensive workflows on parallel machines. …”
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