In recent years, the field of radiotherapy has witnessed remarkable advancements with the integration of artificial intelligence (AI) technologies into clinical practice. Traditionally, radiotherapy treatment planning has been a labor-intensive process, requiring meticulous manual segmentation and optimization. With the advent of AI, particularly deep learning algorithms, the accuracy and efficiency of target delineation and organ-at-risk segmentation have significantly improved. AI-driven algorithms analyze voluminous medical imaging data, enabling rapid and precise contouring, thus expediting the planning phase and reducing inter-observer variability. Furthermore, AI's role extends to treatment plan optimization, where it intelligently explores vast parameter spaces to generate optimal plans tailored to individual patients. This not only saves dosimetrists' time but also enhances plan quality by accounting for complex anatomical variations and personalized clinical goals. In the realm of treatment delivery, AI-powered real-time image guidance enhances the accuracy of patient positioning, ensuring precise radiation targeting. Adaptive radiotherapy, enabled by AI, allows on-the-fly plan modifications in response to anatomical changes, significantly improving treatment accuracy in scenarios like tumor shrinkage or weight loss. Beyond planning and delivery, AI algorithms contribute to outcome prediction by analyzing historical patient data and treatment responses. This predictive capability aids clinicians in making informed decisions and refining treatment strategies for better prognoses. Despite the revolutionary potential, challenges remain in seamlessly integrating AI into clinical workflows. Ethical considerations, data privacy, and algorithm interpretability necessitate cautious implementation. Additionally, fostering interdisciplinary collaboration between AI experts and radiation oncologists is imperative to harness the technology's full potential. This paper explores the impact of AI in four key areas of radiotherapy: automated segmentation, dosimetric and machine quality assurance, adaptive radiation therapy, and clinical outcome prediction.

The exploration of heath data by clustering algorithms allows to better describe the populations of interest by seeking the sub-profiles that compose it. This therefore reinforces medical knowledge, whether it is about a disease or a targeted population in real life. Nevertheless, contrary to the so-called conventional biostatistical methods where numerous guidelines exist, the standardization of data science approaches in clinical research remains a little discussed subject. This results in a significant diversity in the execution of data science projects, whether in terms of algorithms used, reliability and credibility of the designed approach. Taking the path of parsimonious and judicious choice of both algorithms and implementations at each stage, this paper proposes Qluster, a practical workflow for performing clustering tasks. Indeed, this workflow makes a compromise between (1) genericity, as it is suitable regardless of the data volume (small/big) and regardless of the nature of the variables (continuous/qualitative/mixed), (2) ease of implementation, as it is based on few easy-to-use software packages, and (3) robustness, through the stability evaluation of the final clusters and through recognized algorithms and implementations. This workflow can be easily automated and/or routinely applied on a wide range of clustering projects. A synthesis of the literature on data clustering as well as the scientific rationale supporting the proposed workflow is also provided. Finally, a detailed application of the workflow on a concrete use case is provided, along with a practical discussion for data scientists. An implementation on the Dataiku platform is available upon request to the authors.

This paper aims to provide an overview of the complete process in the development of a Domain-Specific Language (DSL). It explains the construction steps such as preliminary research, language implementation, and evaluation. Moreover, it provides details for different key components which are commonly found in the DSLs such as the abstraction layer, DSL metamodel, and the applications. It also explains the general limitations related to the Domain-Specific Languages for Workflows.

The complexity of analysis pipelines in biomedical sciences poses a severe challenge for the transparency and reproducibility of results. Researchers are increasingly incorporating software development technologies and methods into their analyses, but this is a quickly evolving landscape and teams may lack the capabilities to set up their own complex IT infrastructure to aid reproducibility. Basing a reproducible research strategy on readily available solutions with zero or low set-up costs whilst maintaining technological flexibility to incorporate domain-specific software tools is therefore of key importance. We outline a practical approach for robust reproducibility of analysis results. In our examples, we rely exclusively on established open-source tools and free services. Special emphasis is put on the integration of these tools with best practices from software development and free online services for the biostatistics domain.

This study investigates the pivotal areas where Artificial Intelligence (AI) integration in healthcare warrants further exploration, leveraging insights from Boston Specialists, a forefront healthcare provider in AI adoption. Employing a qualitative case study approach, enriched by in-depth interviews and comprehensive literature reviews, we identify three main domains for potential AI expansion: scheduling efficiency, clinical documentation, and AI-driven medical research. Our results underscore the substantial enhancements AI brings to operational workflows and patient care, notably through improved scheduling systems, accuracy in medical documentation, and the facilitation of data-driven research methodologies. These findings suggest a critical need for healthcare institutions to further invest in AI technologies, focusing on these key areas to harness AI's full potential in personalizing care, optimizing efficiency, and advancing medical knowledge. The study concludes with a call for continued investigation into AI's integration within healthcare settings, emphasizing the importance of a supportive organizational infrastructure, ethical considerations, and data security in realizing AI's transformative impact on healthcare delivery and patient outcomes.

Citizen Science has come up to perform analytics over the SARS-CoV-2 genome. Public GALAXY servers provide an automated platform for genomics analysis. Study includes design of GALAXY workflows for RNASEQ assembly and annotation as well as genomic variant discovery and perform analysis across four samples of SARS-CoV-2 infected humans obtained from the local population of Wuhan, China. It provides information about transcriptomics and genomic variants across the SARS-CoV-2 genome. Study can be extended to perform evolutionary and comparative study across each species of coronaviruses. Augmented and integrated study with cheminformatics and immunoinformatics will be a way forward for drug discovery and vaccine development.

Metabolites are at the end of the gene-transcript-protein-metabolism cascade. As such, metabo-lomics is the omic approach that offers the most direct correlation with phenotype. This allows that, where genomics, transcriptomics and proteomics fail to explain a trait, metabolomics might give an answer. Complex phenotypes, which are determined by the influence of multiple small effect alleles, are an example of these situations. Consequently, the interest in metabolomics has increased ex-ponentially in the last years. As a newer discipline, the metabolomics bioinformatics analysis pipe-lines are not as standardized as in the other omic approaches. In this review we synthesized the different steps that need to be carried out to obtain biological insight from the annotated metabolite abundance raw data. These steps were grouped in three different modules: preprocessing, statistical analyses and metabolic pathway enrichment. We included within each one of them the different state-of-the art procedures and tools that can be used depending on the characteristics of the study, providing details about the characteristics of each method has, as well as the issues the reader might encounter. Finally, we introduce genome scale metabolic modeling as a tool for obtaining pseu-do-metabolomic data in situations where its acquisition is difficult, being possible to analyze the resulting data with the modules of the described workflow.

With nearly 1,700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help in understanding the biological functions of these microorganisms, complete genome sequencing is used routinely. Nevertheless, the proper prediction of their gene catalogue is challenging due to taxon-specific evolutionary features. As innovative genome annotation strategies are needed to obtain a representative snapshot of the overall lifestyle of these parasites, the MicroAnnot tool, a dedicated workflow for microsporidian sequence annotation using data from curated databases of accurately annotated microsporidian genes, has been developed. Furthermore, specific modules have been implemented to perform small genes (< 300bp) and transposable element identification. Finally, functional annotation was performed using the signature-based InterProScan software. MicroAnnot’s accuracy has been verified by the re-annotation of four microsporidian genomes for which structural annotation had previously been validated. With its comparative approach and transcriptional signal identification method, MicroAnnot provides accurate prediction of translation initiation sites, efficient identification of transposable elements, as well as high specificity and sensitivity for microsporidian genes including those under 300 bp. Thanks to its web interface (https://microannot.org), MicroAnnot is available to the community to ensure high quality annotation of microsporidian genomes.

The unprecedented COVID-19 pandemic posed major challenges to local, regional, and global economies and health systems, and fast clinical diagnostic workflows were urgently needed to contain the spread of SARS-CoV-2. Here, we describe the platform and workflow established at the Cornell COVID-19 Testing Laboratory (CCTL) for high-throughput testing of clinical samples from the university and the surrounding community. This workflow enabled efficient and rapid detection, and successful control of SARS-CoV-2 infection on campus and its surrounding communities. Our cost-effective and fully automated workflow enabled testing of over 8,000 pooled samples per day and provided results for over 2 million samples. Automation of time- and effort-intensive sample processing steps such as accessioning and pooling increased laboratory efficiency. Customized software applications were developed to track and store samples, deconvolute positive pools, track and report results and for workflow integration from sample receipt to result reporting. Additionally, quality control dashboards and turn-around time tracking applications were built to monitor assay and laboratory performance. As infectious disease outbreaks pose a constant threat to both human and animal health, the highly effective workflow implemented at CCTL could be modeled to establish regional high-capacity testing hubs for infectious disease preparedness and emergency response.

Modern agent-based models (ABM) and other simulation models require evaluation and testing of many different parameters. Managing that testing for large scale parameter sweeps (grid searches) as well as storing simulation data requires multiple, potentially customizable steps that may vary across simulations. Furthermore, parameter testing, processing, and analysis are slowed if simulation and processing jobs cannot be shared across teammates or computational resources. While high-performance computing (HPC) has become increasingly available, models can often be tested faster through the use of multiple computers and HPC resources. To address these issues, we created the Distributed Automated Parameter Testing (DAPT) Python package. By hosting parameters in an online (and often free) "database", multiple individuals can run parameter sets simultaneously in a distributed fashion, enabling ad hoc crowdsourcing of computational power. Combining this with a flexible, scriptable tool set, teams can evaluate models and assess their underlying hypotheses quickly. Here we describe DAPT and provide an example demonstrating its use.

Since their introduction, process trees have been frequently used as a process modeling formalism in many process mining algorithms. A process tree is a (mathematical) tree-based model of a process, in which internal vertices represent behavioral control-flow relations and leaves represent process activities. Translation of a process tree into a sound Workflow net is trivial; however, the reverse is not the case. Simultaneously, an algorithm that translates a WF-net into a process tree is of great interest, e.g., the explicit knowledge of the control-flow hierarchy in a WF-net allows one to reason on its behavior more easily. Hence, in this paper, we present such an algorithm, i.e., it detects whether a WF-net corresponds to a process tree, and, if so, constructs it. We prove that, when the algorithm finds a process tree, the language of the process tree is equal to the language of the original WF-net. The experiments conducted show that the algorithm’s corresponding implementation has a quadratic time complexity in the size of the WF-net. Furthermore, the experiments show strong evidence of process tree re-discoverability.

Large-scale land cover plays a crucial role in global resource monitoring and management, as well as research on sustainable development. However, the complexity of the mapping process, coupled with significant computational and data storage requirements, often leads to delays between data processing and product publication, creating challenges for dynamic monitoring of large-scale land cover. Therefore, improving the efficiency of each stage in large-scale land cover mapping and automating the mapping process is currently an urgent and critical issue that needs to be addressed. We propose a high-performance automated large-scale land cover mapping framework(HALF) that introduces high-performance computing technology to the field of land cover production. HALF optimizes key processes, such as automated sample point extraction, sample-remote sensing image matching, and large-scale classification result mosaic and update. We selected several 10°×10° regions globally and the research makes several significant contributions:(1)We design HALF for land cover mapping based on docker and CWL-Airflow, which solves the heterogeneity of models between complex processes in land cover mapping and simplifies the model deployment process. By introducing workflow organization, this method achieves a high degree of decoupling between the production models of each stage and the overall process, enhancing the scalability of the framework. (2)HALF propose an automatic sample points method that generates a large number of samples by overlaying and analyzing multiple prior products, thus saving the cost of manual sample selection. Using high-performance computing technology improved the computational efficiency of sample-image matching and feature extraction phase, with 10 times faster than traditional matching methods.(3)HALF propose a high-performance classification result mosaic method based on the idea of grid division. By quickly establishing the spatial relationship between the image and the product and performing parallel computing, the efficiency of the mosaicking in large areas is significantly improved. The average processing time for a single image is around 6.5 seconds.

Background: Advancement of next-generation sequencing (NGS) technologies provides opportunities for large-scale Pharmacogenetic (PGx) studies and pre-emptive PGx testing to cover a wide range of genotypes present in diverse populations. However, NGS-based PGx testing is limited by the lack of comprehensive computational tools to support genetic data analysis and clinical decisions. Methods: Bioinformatics utilities specialized for human genomics and the latest cloud-based technologies are used for developing a bioinformatics pipeline for analyzing the genomic sequence data and reporting PGx genotypes. A database was created and integrated in the pipeline for filtering the actionable PGx variants and clinical interpretations. Strict quality verification procedures were conducted on variant calls with whole genome sequencing (WGS) dataset of the 1000 Genomes Project (G1K). The accuracy of PGx allele identification was validated using the whole genome sequencing dataset of the Pharmacogenetics Reference Materials from the Centers for Disease Control and Prevention (CDC). Results: The newly created bioinformatics pipeline, Pgxtools, can analyze genomic sequence data, identify actionable variants in 13 PGx relevant genes, and generate reports annotated with specific interpretations and recommendations based on clinical practice guidelines. Verified with two independent methods, we have found that Pgxtools consistently identifies variants more accurately than the results in the G1K dataset on GRCh37 and GRCh38. Conclusions: Pgxtools provides an integrated workflow for large-scale genomic data analysis and PGx clinical decision support. Implemented with cloud-native technologies, it is highly portable in a wide variety of environments from a single laptop to high performance computing clusters and cloud platforms for different production scales and requirements.

Barcode medication administration (BCMA) is advocated as a technology that reduces medication errors relating to incorrect patient identity, drug or dose. Little is known, however, about the impact it has on nursing workflow. Our aim was to investigate the impact of BCMA on nursing activity and workflow. A comparative study was conducted on two similar surgical wards within an acute UK hospital. We observed nurses during drug rounds on a non-BCMA ward and a BCMA ward. Data were collected on drug round duration, timeliness of medication administration, patient identification, medication verification and general workflow patterns. BCMA appears not to alter drug round duration, although it may reduce the administration time per dose. Workflow was streamlined, with a reduction in use of the medicines room. The rate of patient identification increased from 74% (of 47) patients to 100% (of 43), with 95% of 255 scannable medication doses verified using the system. This study suggests that BCMA does not affect drug round duration; further research is required to determine the impact it has on timeliness of medication administration. There was reduced variability in the medication administration workflow of nurses, along with an increased patient identification rate and high medication scan rate, representing potential benefits to patient safety.

Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer-review and increases the impact of datasets by enhancing their visibility, accessibility, and re-usability. We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivise researchers to publish high-quality data sets, we created a workflow for streamlined import of omics metadata directly into a data paper manuscript. An omics data paper template was designed by defining key article sections which encourage the description of omics datasets and methodologies. The workflow was based on REpresentational State Transfer services and Xpath to extract information from the European Nucleotide Archive, ArrayExpress and BioSamples databases, which follow community-agreed standards. The workflow for automatic import of standard-compliant metadata into an omics data paper manuscript facilitates the authoring process. It demonstrates the importance and potential of creating machine-readable and standard-compliant metadata. The omics data paper structure and workflow to import omics metadata improves the data publishing landscape by providing a novel mechanism for creating high-quality, enhanced metadata records, peer reviewing and publishing of these. It constitutes a powerful addition for distribution, visibility, reproducibility and re-usability of scientific data. We hope that streamlined metadata re-use for scholarly publishing encourages authors to improve the quality of their metadata to achieve a truly FAIR data world.

Taiwan’s Chi Mei Medical Center has a vision of becoming a sustainable organization. They found they violated the sustainable development goal (SDG) 13 (“Climate Action”) since its workflows consume excessive tangible resources and waste much operation time. To fulfill the vision, the Chi Mei Medical Center first introduced electronic invoicing. Implementing this electronic invoicing included adopting cloud E-invoice data and creating a software robot for auditing them. This study presents this software robot and its contributions. The software robot replaces an internal auditor to log into Taiwan’s E-invoice platform, download cloud E-invoice data, and detect the inconsistency between these cloud and on-premise data. Internal auditors of the Chi Mei Medical Center only needed to confirm the detection results. They welcome this software robot since it significantly reduces their work burdens. They approved more software robots for assisting other workflows. Besides, the Chi Mei Medical Center earned profits after eliminating paper invoices. This elimination helped release less carbon. This study concludes that chasing a sustainable organization is unnecessarily equivalent to the requirement of more costs. A software robot represents the last puzzle for constructing a paperless workflow since it can resolve the resistance of existing workers to a new workflow.

The Last Planner System (LPS) aims to enhance planning reliability by reducing variability in construction processes. While LPS applications have been explored in construction and detailed design, its application in architectural design remains underrepresented due to its abstract nature. This study addresses this gap by proposing an LPS framework tailored for architectural design, utilizing LPS metrics to assess planning reliability. Key issues hindering formal planning methods' implementation are identified, and relevant LPS principles are aligned with these challenges, culminating in a conceptual LPS model designed for architectural projects. Building upon the conceptual model, an implementation model is then developed and put into practice within an architectural design company in the United States, resulting in measured improvements in planning reliability and responsiveness. Additionally, it unveils hidden challenges associated with emerging tasks, guiding future design process enhancements. This study demonstrates how tracking design planning performance with LPS metrics can promote LPS adoption in architectural design, offering a benchmark for necessary interventions to achieve desired performance in architectural design.

Environmental policy involving citizen science (CS) is of growing interest. In support of this open data stream, validation or quality assessment of the CS data and their appropriate usage for evidence-based policy making, needs a flexible and easily adaptable data curation process ensuring transparency. Addressing these needs, this paper describes an approach for automatic quality assurance as proposed by the Citizen OBservatory WEB (COBWEB) FP7 project. This approach is based upon a workflow composition that combines different quality controls, each belonging to seven categories or ‘pillars’. Each pillar focuses on a specific dimension in the types of reasoning algorithms for CS data qualification. These pillars attribute values to a range of quality elements belonging to three complementary quality models. Additional data from various sources, such as Earth Observation (EO) data, are often included as part of the inputs of quality controls within the pillars. However, qualified CS data can also contribute to the validation of EO data. Therefore, the question of validation can be considered as ‘two sides of the same coin’. Based on an invasive species CS study, concerning Fallopia japonica (Japanese knotweed), the paper discusses the flexibility and usefulness of qualifying CS data, either when using an EO data for the validation within the quality assurance process, or validating an EO data product that describes the risk of occurrence of the plant. Both validation paths are found to be improved by quality assurance of the CS data. Addressing the reliability of CS open data, issues and limitations of the role of quality assurance for validation, due to the quality of secondary data used within the automatic workflow, are described, e.g. error propagation, paving the route to improvements in the approach.

Different approaches for digital workflows have already been presented for their use in palatal plates for newborns and infants. However, there is no evidence on the accuracy of CAD/CAM manufactured orthodontic appliances for this kind of application. This study evaluates trueness and precision provided by different CAM technologies and materials for these appliances. Samples of a standard palatal stimulation plate were manufactured using stereolithography (SLA), direct light processing (DLP) and subtractive manufacturing (SM). The effect of material (for SM) and layer thickness (for DLP) were also investigated. Specimens were digitized with a laboratory scanner (D2000, 3Shape) and analyzed with a 3D inspection software (Geomagic Control X, 3D systems). For quantitative analysis, differences between 3D datasets were measured using root mean square (RMS) error values for trueness and precision. For qualitative analysis, color maps were generated to detect locations of deviations within each sample. SM showed higher trueness and precision than AM technologies. Reducing layer thickness in DLP did not significantly increase accuracy, but prolonged manufacturing time. All materials and technologies met the clinically acceptable range and are appropriate for their use. DLP with 100µm layer thickness showed the highest efficiency, obtaining high trueness and precision within the lowest manufacturing time.

The sensitivity of macroscopic mechanical and thermal properties of grey cast iron is computationally investigated for a variety of graphite microstructures over a wide temperature range. In order to represent common graphite microstructures according to DIN EN ISO 945-1, a synthetic approach is used to algorithmically generate simulation domains. The developed mechanical and thermal model is applied in a large simulation study. The study includes statistical volume elements of the graphite microstructures classes GG-15 and IA2 to IA5, with 10 v.-%, 11 v.-% and 12 v.-% graphite, respectively, for a temperature range from 20 °C to 750 °C. Homogenized macroscopic quantities such as the Young's moduli, Poisson's ratios, yield strengths and thermal conductivities are predicted for the different microstructure classes by applying simulation and data analysis tools of the research data infrastructure Kadi4Mat.

Attempts to use computers to aid in the detection of breast malignancies date back more than 20 years. Despite significant interest and investment, this has historically led to minimal or no significant improvement in performance and outcomes with traditional computer aided detection. However, recent advances in artificial intelligence and machine learning are now starting to deliver on the promise of improved performance. There are at present more than 20 FDA approved AI applications for breast imaging, but adoption and utilization are widely variable and overall low. Breast imaging is unique and has aspects that create both opportunities and challenges for AI development and implementation. Breast cancer screening programs worldwide rely on screening mammography to reduce the morbidity and mortality of breast cancer and many of the most exciting research and available AI applications focus on cancer detection for mammography. There are however multiple additional potential applications for AI in breast imaging including decision support, risk assessment, breast density quantitation, workflow and triage, quality evaluation, response to neoadjuvant chemotherapy assessment, and image enhancement. In this review the current status, availability, and future directions of investigation of these applications are discussed, as well as the opportunities and barriers to more widespread utilization.

This paper offers a comprehensive examination of the process involved in developing and automating supervised end-to-end machine learning workflows for forecasting and classification purposes. It offers a complete overview of the components (i.e. feature engineering, model selection, etc), principles (i.e. bias-variance decomposition, model complexity, overfitting, model sensitivity to feature assumptions and scaling, output interpretability, etc), models (i.e. neural networks, regression models, etc), methods (i.e. Cross-Validation, data augmentation, etc), metrics (i.e. Mean Squared Error, F1-score, etc) and tools that rule most supervised learning applications with numerical and categorical data, as well as their integration, automation, and deployment. The end goal and contribution of this paper is the education and guidance of the non-AI expert academic community over complete and rigorous machine learning pipelines and data science practices, from problem scoping to design and state-of-the-art automation tools, including basic principles and reasoning in the choice of methods. The paper delves into the critical stages of supervised machine learning workflow development, many of which are often omitted by researchers due to brevity, and covers foundational concepts essential for understanding and optimizing a functional machine learning workflow, thereby offering a holistic view of task-specific application development for applied researchers who are not AI experts.