Evaluating An Automated Compounding Workflow Software for Safety and Efficiency: Implementation Study by Ülle Helena Meren, James Waterson

“…A solution that offers entire workflow management for oncology is desirable because (in terms of cytotoxic delivery of a regimen to a patient) the chain that starts with prescription and the assay of the patient’s laboratory results and ends with administration has multiple potential safety gaps and choke points. …”
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Comprehensive Analysis of Large-Scale Transcriptomes from Multiple Cancer Types by Baoting Nong, Mengbiao Guo, Weiwen Wang, Zhou Songyang, Yuanyan Xiong

“…It was developed based on Nextflow, a reproducible workflow management system. PipeOne is composed of three modules, data processing and feature matrices construction, disease feature prioritization, and disease subtyping. …”
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Pharmacy practice in hospital settings in GCC countries: Dispensing and administration by Ahmed Y. Mayet, Fowad Khurshid, Hussain A. Al-Omar, Sarah S Alghanem, Mohammed S. Alsultan, Ahmed H. Al-jedai

“…Compounding sterile preparations in the pharmacy, barcode verification technology, workflow management technology, and robotic technology were used by 17.2%, 15.6%, and 4.7% of hospitals, respectively. …”
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SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes [version 2; peer review: 2 approved] by Vincent Hervé, Nachida Tadrent, Franck Dedeine

“…Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. …”
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2469 by Ram Gouripeddi, Mollie Cummins, Randy Madsen, Bernie LaSalle, Andrew Middleton Redd, Angela Paige Presson, Xiangyang Ye, Julio C. Facelli, Tom Green, Steve Harper

“…Data-intensive process will use process-workflow management platforms such as Activiti, Pegasus, and Taverna. …”
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COSAP: Comparative Sequencing Analysis Platform by Mehmet Arif Ergun, Omer Cinal, Berkant Bakışlı, Abdullah Asım Emül, Mehmet Baysan

“…COSAP is developed as a workflow management system and designed to enhance cooperation among scientists with different backgrounds. …”
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Semantic Knowledge Management : An Ontology-Based Framework / by Zilli, Antonio, editor 502264, Damiani, Ernesto, editor 263007, Ceravolo, Paolo, editor 651885, Corallo, Angelo, editor 651886, Elia, Gianluca, editor 651887, Gale Group (Online service) 651863

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ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses by Natasha Pavlovikj, Joao Carlos Gomes-Neto, Jitender S. Deogun, Andrew K. Benson

“…ProkEvo was specifically developed to achieve the following goals: (1) Automation and scaling of complex combinations of computational analyses for many thousands of bacterial genomes from inputs of raw Illumina paired-end sequence reads; (2) Use of workflow management systems (WMS) such as Pegasus WMS to ensure reproducibility, scalability, modularity, fault-tolerance, and robust file management throughout the process; (3) Use of high-performance and high-throughput computational platforms; (4) Generation of hierarchical-based population structure analysis based on combinations of multi-locus and Bayesian statistical approaches for classification for ecological and epidemiological inquiries; (5) Association of antimicrobial resistance (AMR) genes, putative virulence factors, and plasmids from curated databases with the hierarchically-related genotypic classifications; and (6) Production of pan-genome annotations and data compilation that can be utilized for downstream analysis such as identification of population-specific genomic signatures. …”
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Using ontologies to provide different levels of abstraction in scientific workflows by de Oliveira, D, Ogasawara, E, Baião, F, Mattoso, M

“…Scientific experiments are usually modeled as scientific workflows, and may be enacted using Scientific Workflow Management Systems (SWfMS). There is a huge variety of SWfMS available, such as Taverna and VisTrails, which enables the specification and execution of a chain of activities usually represented by programs or services. …”

Cost Analysis of Orthoptist-Led Neurofibromatosis Type 1 Screening Clinics by Navdeep Kaur, Catherine Lewis, Sandra Staffieri, Jonathan Ruddle, Ilias Goranitis, Jay Stiles, Gabriel Dabscheck

“…Methods: Patients with NF1 examined in the orthoptist-led NF1 screening clinic and/or consultant-led clinics during the study period were identified. The workflow management software Q-Flow 6® provided data documenting patient’s time spent with the orthoptist, nurse, and ophthalmologist. …”
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Cluster-randomized implementation trial of two facilitation strategies to implement a novel information and communications technology at the Veterans Health Administration by Chelsea Leonard, Evan Carey, Ariel Holstein, P. Michael Ho, Jeffrey T. Heckman

“…Methods FLOW3 is a computerized workflow management system comprised of three applications that facilitate the three steps for prosthesis authorization. …”
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A deep learning approach for projection and body-side classification in musculoskeletal radiographs by Anna Fink, Hien Tran, Marco Reisert, Alexander Rau, Jörg Bayer, Elmar Kotter, Fabian Bamberg, Maximilian F. Russe

“…Abstract Background The growing prevalence of musculoskeletal diseases increases radiologic workload, highlighting the need for optimized workflow management and automated metadata classification systems. …”
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Simplified and effective resource provisioning for scientific workflows in IaaS clouds by Zhou, Chi

“…We integrate our systems into a popular workflow management system named Pegasus. Experimental results with real-world scientific workflow applications on Amazon EC2 and a cloud simulator demonstrate that (1) the cloud dynamics greatly affect the monetary cost and performance optimization results of scientific workflows; (2) our declarative language is expressive to describe a wide class of optimization problems for scientific workflows; (3) our systems are able to optimize the monetary cost and performance goals while satisfying probabilistic QoS constraints.…”
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VGEA: an RNA viral assembly toolkit by Paul E. Oluniyi, Fehintola Ajogbasile, Judith Oguzie, Jessica Uwanibe, Adeyemi Kayode, Anise Happi, Alphonsus Ugwu, Testimony Olumade, Olusola Ogunsanya, Philomena Ehiaghe Eromon, Onikepe Folarin, Simon D.W. Frost, Jonathan Heeney, Christian T. Happi

“…VGEA was built on the Snakemake workflow management system and utilizes existing tools for each step: fastp (Chen et al., 2018) for read trimming and read-level quality control, BWA (Li & Durbin, 2009) for mapping sequencing reads to the human reference genome, SAMtools (Li et al., 2009) for extracting unmapped reads and also for splitting bam files into fastq files, IVA (Hunt et al., 2015) for de novo assembly to generate contigs, shiver (Wymant et al., 2018) to pre-process reads for quality and contamination, then map to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences, SeqKit (Shen et al., 2016) for cleaning shiver assembly for QUAST, QUAST (Gurevich et al., 2013) to evaluate/assess the quality of genome assemblies and MultiQC (Ewels et al., 2016) for aggregation of the results from fastp, BWA and QUAST. …”
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Recognition and Prioritization of Inhibitory Factors of E- Service Deployment by Abdolali Keshtegar, Mohammad Ghasemi, Mohammad Rezaie Zohan

“…The existence of an electronic court, as part of an e-government project, is, from the point of view of some experts, the starting point and the background of the existence of a successful e-government, a very important and an essential element of e-government; the electronic court is a court in which even one paper It is not used and it has a workflow management system that automatically refers to the employee after the work is done. …”
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Challenges for Implementing FAIR Digital Objects with High Performance Workflows by Line Pouchard, Tanzima Islam, Bogdan Nicolae

“…These workflows can be orchestrated by workflow management systems (WMS) and built upon composable blocks that facilitate task placement and resource allocation for parallel executions on high performance systems [Lee et al. 2021, Merzky et al. 2021].The scientific computing communities running these kinds of workflows have been slow to adopt Findable, Accessible, Interpretable, and Re-usable (FAIR) principles, in part due to the complexity of workflow life cycles, the numerous WMS, and the specificity of HPC systems with rapidly evolving architectures and software stacks, and execution modes that require resource managers and batch schedulers [Plale et al. 2021]. …”
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Advancing caching and automation with FDO by Amirpasha Mozaffari, Niklas Selke, Martin Schultz

“…In the following months, we will focus on creating a demonstrator for the caching system, adopting an FDO typing that could fit the best with the planned tasks, and creating a workflow management system that could support such a dynamic system with interfaces to API-enabled web-services, cloud computing resources and conventional HPC resources.…”
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Data workflows and visualization in support of surveillance practice by Wiktor Gustafsson, Fernanda C. Dórea, Stefan Widgren, Jenny Frössling, Gema Vidal, Hyeyoung Kim, Wonhee Cha, Arianna Comin, Ivana Rodriguez Ewerlöf, Thomas Rosendal

“…The computational resources include both local and cloud-based systems, with automatic workflows managed in the cloud. The workflows are designed to be flexible and adaptable to changing data sources and stakeholder demands, with the ultimate goal to create a robust infrastructure for the delivery of actionable epidemiological information.…”
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MetaPhage: an Automated Pipeline for Analyzing, Annotating, and Classifying Bacteriophages in Metagenomics Sequencing Data by Mattia Pandolfo, Andrea Telatin, Gioele Lazzari, Evelien M. Adriaenssens, Nicola Vitulo

“…The pipeline is implemented in Nextflow, a widely adopted workflow manager that enables an optimized parallelization of tasks. …”
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Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools by Jose Espinosa-Carrasco, Ionas Erb, Toni Hermoso Pulido, Julia Ponomarenko, Mara Dierssen, Cedric Notredame

“…They are also easy to reproduce thanks to their integration within Nextflow, a workflow manager using containerized software. : Biological Sciences; Genetics; Behavioral Neuroscience; Bioinformatics Subject Areas: Biological Sciences, Genetics, Behavioral Neuroscience, Bioinformatics…”
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