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PubMed2026

Managing workflow executions with WESkit.

SUMMARY: In biomedical research, managing computational workflows across numerous projects-with varying parameters, tools, and environments-creates major challenges in scalability, reproducibility, and collaboration. Here, we present WESkit, an implementation of the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) interface, designed to streamline the execution, monitoring, and documentation of data processing workflows. It addresses the complexities involved in managing numerous executions with varying parameters across diverse research projects. Supporting both Snakemake and Nextflow, the system enables consistent automation and centralized monitoring, which benefits research groups aiming for long-term reproducibility and scalable collaboration. Its suitability for larger teams and service units is further enhanced by seamless integration into cloud environments, contributing to the GA4GH cloud framework. AVAILABILITY AND IMPLEMENTATION: The software WESkit is available under MIT license at the GitLab repository (https://gitlab.com/one-touch-pipeline/weskit). The WESkit main repository is archived at Software Heritage (https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://gitlab.com/one-touch-pipeline/weskit/api.git) and can be found using "one-touch-pipeline/weskit" term in the search section.

Workflow↗

PubMed2026

Tractor workflow: a scalable Nextflow framework for local ancestry-aware genome-wide association studies.

MOTIVATION: The routine exclusion of admixed individuals from traditional genome-wide association studies (GWAS) due to concerns about spurious associations has limited multi-ancestry genetic discovery. Tractor addresses this issue by incorporating local ancestry into association testing, enabling the identification of ancestry-enriched signals and generating ancestry-specific summary statistics. However, adoption has been constrained by the complexity of prerequisite steps, including phasing and local ancestry inference, which require substantial bioinformatics expertise and introduce key analytical decision points. RESULTS: We developed a scalable, automated Nextflow workflow that integrates phasing, local ancestry inference, and Tractor association testing into a reproducible end-to-end pipeline. To demonstrate its utility, we applied the workflow to 32 blood biomarkers in 6245 two-way African-European admixed individuals from the UK Biobank. This pipeline performed efficiently at scale, replicating known associations and uncovering key ancestry-specific loci. These associations were largely driven by variants present on African ancestral tracts but absent from European tracts, underscoring the value of local ancestry-aware methods in uncovering previously masked genetic signals. AVAILABILITY AND IMPLEMENTATION: The workflow is modular, customizable, and compatible with commonly used phasing and local ancestry tools, minimizing manual intervention while preserving analytical flexibility. By lowering technical barriers to implementation, this framework facilitates broader adoption of local ancestry-aware GWAS, paving the way for expanded genetic discovery.

Humans↗

PubMed2026

scGPA: an LLM-assisted workflow for directional virtual gene perturbation analysis from single-cell transcriptomes.

BACKGROUND: Existing virtual perturbation methods can often infer directional changes by comparing predicted post-perturbation expression profiles with control cells. However, workflows that directly return direction-specific downstream candidate genes together with confidence scores, evidence support and interpretable summaries remain limited. We developed scGPA, an LLM-assisted workflow system for directional single-cell virtual gene perturbation analysis. METHODS: scGPA starts from raw single-cell RNA sequencing data and performs quality control, normalization, dimensionality reduction, clustering and cell-group selection. It then constructs cell-group-specific wild-type regulatory networks using repeated subsampling, principal component regression (PCR)/Ridge-based network inference and CP tensor denoising. Based on these networks, scGPA simulates dose-aware virtual knockdown of the target gene and applies signed perturbation propagation to estimate the magnitude and direction of downstream transcriptional responses. LLM assistance is used for marker-based cell-type annotation, evidence-guided candidate prioritization and user-facing biological summarization. RESULTS: We benchmarked scGPA across five public Perturb-seq datasets and compared its performance with GEARS, scGPT and a random baseline. The overall correct prediction rate of scGPA was 23.0%, exceeding those of GEARS (20.7%), scGPT (15.1%) and the random baseline (13.6%). These results indicate that scGPA achieved a higher correct prediction rate than the two comparator models and the random baseline. We subsequently evaluated scGPA using a public osteosarcoma single-cell dataset and performed qRT-PCR validation in 143B osteosarcoma cells. Among genes with significant experimental changes, scGPA achieved a directional concordance of 76.9%. When all tested downstream genes were counted, 37.0% were directionally correct, 51.9% showed no significant change and 11.1% changed in the opposite direction. CONCLUSIONS: scGPA provides a practical workflow system for predicting and prioritizing direction-specific downstream transcriptional responses after target-gene perturbation. By integrating single-cell regulatory network inference, signed virtual perturbation and LLM-assisted interpretation, scGPA supports target-gene function inference and downstream mechanistic investigation from single-cell transcriptomic data.

Single-Cell Gene Expression Analysis↗

PubMed2006

A workflow spatial scan statistic.

We propose a modification of the spatial scan statistic that takes account of workflow, which is the movement of individuals between home and work. The objective is to detect clusters of disease in situations where exposure occurs in the workplace, but only home address is available for analysis. In these situations, application of the usual spatial scan statistic does not account for possible differences between home and work address, thereby reducing the power of detection. We describe an extension to the usual spatial scan statistic that uses workflow data to search for disease clusters resulting from workplace exposure. We also present results from simulations that demonstrate the increased power of the workflow scan statistic over the usual scan statistic for detecting clusters arising from exposures in the workplace.

Anthrax↗

PubMed2000

Radiology workflow and patient volume: effect of picture archiving and communication systems on technologists and radiologists.

This study was performed to evaluate the changes in workflow and efficiency in various clinical settings in the radiology department after the introduction of a picture archiving and communication system (PACS). Time and motion data were collected when conventional image management was used, and again after the introduction of a PACS. Changes in the elapsed time from examination request until the image dispatch to the radiologist, and from dispatch until report dictation, were evaluated. The relationship between patient volume and throughput was evaluated. The time from examination request until dispatch was significantly longer after the introduction of PACS for examinations taken on patients from the emergency department (ED) (pre-PACS, 20 minutes; post-PACS, 25 minutes; P < .0001), and for examinations taken on patients in the medical intensive care unit (MICU) (pre-PACS, 34 minutes; post-PACS, 42 minutes; P < .0001). The interval from image dispatch until report dictation shortened significantly after the introduction of PACS in the ED (pre-PACS, 38 minutes; post-PACS, 23 minutes; P < .0001) and in the outpatient department (OPD) (pre-PACS, 38 minutes; post-PACS, 20 minutes; P < .0001). Simple least squares regression showed a significant relationship between daily patient volume and the daily median time until report dictation (F = 43.42, P < .001). PACS slowed technologists by prolonging the quality-control procedure. Radiologist workflow was shortened or not affected. Efficiency is dependent on patient volume, and workflow improvements are due to a shift from batch to on-line reading that is enabled by the ability of PACS to route enough examinations to keep radiologists fully occupied.

Appointments and Schedules↗

PubMed1999

Implementation and evaluation of workflow based on hospital information system/radiology information system/picture archiving and communications system.

The purpose of this presentation is to review and evaluate computerized workflow of selected sites that have integrated systems of the hospital information system (HIS), radiology information system (RIS), and picture archiving and communications system (PACS). We then focus on some essential points of integration of those systems, such as avoiding multiple entries of patients demographic data, prefetching current and previous images to the correspondent workstations, and workflow management. To realize them by integrating multiple subsystems such as HIS/RIS/PACS integration, there must be exchange of the workflow control information, and consistency of the information between subsystems.

Computer Systems↗

PubMed2002

Clinical implementation of the IHE presentation of grouped procedures integration profile in a multivendor environment--workflow modification and barriers to implementation.

The implementation of presentation of grouped procedures (PGP) integration profile, as described in the Integrating the Healthcare Enterprise (IHE) Technical Framework, on computed tomography (CT) and magnetic resonance (MR) scanners as well as the picture archiving communication system (PACS) addresses the problem faced by many institutions in which there are multiple-requested procedures performed in one acquisition. It is a solution that, just like the initial implementation of PACS, requires substantial modification to workflow. Implementation of PGP not only speeds access to relevant images for the requested procedure, it reduces network traffic and is less demanding on workstation hardware because of the smaller data sets transmitted. These workflow issues show that PGP implementation is not complete when the vendors install the necessary hardware and software modifications. This report discusses the workflow modifications and the barriers to implementing the PGP solution.

Data Display↗

PubMed2002

Workflow assessment of digital versus computed radiography and screen-film in the outpatient environment.

An objective assessment and comparison of computed radiography (CR) versus digital radiography (DR) and screen-film in terms of workflow, productivity, speed-of-service, and potential cost justification for imaging ambulatory patients is presented. Perceived ease-of-use and workflow of each device is collected via a technologist opinion survey. Productivity is measured as the rate of patient throughput from normalized timing studies. The overall speed-of-service is calculated from the time of examination ordering as stamped in the radiology information system (RIS), to the time of image availability on the picture archiving and communication system (PACS), to the time of interpretation rendered (from the RIS). Comparative results of screen-film (analog) versus a CR reader and a DR dedicated chest unit show a higher patient throughput for the digital systems. A mean of 10.7 patients were moved through the DR chest room per hour, and 9.2 patients per hour using CR, versus 8.2 patients per hour for the analog device. Measured time to image availability for interpretation is much faster for both DR and CR versus screen-film, with the mean minutes to image availability calculated as 5.7 +/- 2.5 minutes for DR, 6.7 +/- 1.5 minutes for CR, and 29.2 +/- 14.3 minutes for screen film. DR and CR can improve workflow and productivity over analog screen-film in a PACS for delivery of projection radiography services in an outpatient environment, but DR requires high volume to be cost effective over CR.

Efficiency, Organizational↗

PubMed2006

Analog to digital workflow improvement: a quantitative study.

This study tracked a radiology department's conversion from utilization of a Kodak Amber analog system to a Kodak DirectView DR 5100 digital system. Through the use of ProModel Optimization Suite, a workflow simulation software package, significant quantitative information was derived from workflow process data measured before and after the change to a digital system. Once the digital room was fully operational and the radiology staff comfortable with the new system, average patient examination time was reduced from 9.24 to 5.28 min, indicating that a higher patient throughput could be achieved. Compared to the analog system, chest examination time for modality specific activities was reduced by 43%. The percentage of repeat examinations experienced with the digital system also decreased to 8% vs. the level of 9.5% experienced with the analog system. The study indicated that it is possible to quantitatively study clinical workflow and productivity by using commercially available software.

Efficiency, Organizational↗

PubMed2005

Comparing 0.2 tesla with 1.5 tesla intraoperative magnetic resonance imaging analysis of setup, workflow, and efficiency.

RATIONALE AND OBJECTIVES: To compare low-field with high-field intraoperative magnetic resonance imaging (MRI) in respect to setup, workflow, and efficiency. MATERIALS AND METHODS: A total of 750 patients were investigated either with a 0.2 T (March 1996-July 2001) or a 1.5 T (April 2002-August 2004) MRI system adapted for intraoperative use. RESULTS: With the low-field setup, 330 patients were examined in 65 months; with the high-field setup, 420 patients were examined in 29 months, which is a 2.8-fold increase in cases per month (14.5 versus 5.1) reflecting improved ease of use. Concerning intraoperative workflow, the time for preparation to start intraoperative imaging decreased fivefold (2 minutes instead of 10 minutes); navigation was applied more often with 57% versus 51% (240/420 versus 167/330), whereas functional data were integrated in 35% versus 39% (84/240 versus 65/167). Application of navigation updates was doubled (22% versus 11%; 53/240 versus 18/167). Image acquisition time was reduced by a factor of two, allowing a more detailed imaging protocol, whereas the image quality is clearly improved in the high-field setup, where there was no difference between the standard preoperative image quality compared with the intraoperative quality. This contributed to an increased detection of tumor remnants and extended resections in pituitary (36% versus 29%; 47/129 versus 17/59) and glioma surgery (41% versus 26%; 38/93 versus 28/106). CONCLUSION: Compared with the low-field setup, the high-field setup results not only in clearly superior image quality and increased imaging armamentarium, contributing to increased rates of detected tumor remnants, but also in a distinct improvement of intraoperative workflow. Furthermore, intraoperative high-field MRI offers various modalities beyond standard anatomic imaging, such as magnetic resonance spectroscopy, diffusion tensor imaging, and functional MRI.

Brain Diseases↗

PubMed2005

Evaluation of analytical methods and workflow performance of the Architect ci8200 integrated serum/plasma analyzer system.

BACKGROUND: The Architect ci8200 is an integrated serum analyzer for photometric, electrochemical and immunological assays. Several assays of each category and the workflow performance of the system were compared with established laboratory procedures in two laboratories. METHODS: Measurements were compared with the ELECSYS 2010 (Roche Diagnostics) for CEA, PSA, FPSA, AFP, folate, vitamin B12, with the CENTAUR (Bayer) for TSH, T4, FT4, FSH and Estradiol, with the LIAISON (DiaSorin) for TSH, FT4 and FT3, with the Behring Nephelometer BN II (Dade-Behring) for ferritin, and with the INTEGRA 800 (Roche Diagnostics), and the AU640 (Olympus) for clinical chemistry assays. Workflow studies were performed to compare times of analysis required for defined analytical workloads. RESULTS: The coefficients of variation (CVs) for within-run imprecision were between 3% and 6% for CEA, PSA, FPSA, AFP and ferritin, and between 3% and 11% for TSH, FT4, FT3, folate and vitamin B12. The CVs for day-to-day imprecision for immunoassays were between 3% and 10%, except for vitamin B12 (CVs 11-13%) and FT4 (CV 10% -13%). For clinical chemistry tests corresponding CVs for within-run imprecision were < 1%, except for HDL, triglyceride, creatinine, ALT, LD and lipase (CVs<2%) and bicarbonate (CV 3%-6%) and magnesium (CV < 3%). The CVs for day-to-day imprecision for clinical chemistry tests were < 1%, except for sodium, CO(2), magnesium, phosphorus, glucose, uric acid, HDL, triglyceride, ALT, AST CK, lipase with CVs < 6% and for CO(2)<11%. Dilutional linearity testing of seven immunoassays and five clinical chemistry analytes resulted in recovery rates of 90-110%. Correlation studies with 15 immunoassays and 25 clinical chemistry tests showed acceptable agreements with established methods. Work flow analyses demonstrated a net gain in time of analysis up to 109 min depending on the size of the sample batch analyzed with the Architect ci8200 as the main analyzer as compared to the currently installed routine laboratory equipment. Median turn-around times were 7 and 30 min for chemistry assays and immunoassays, respectively, when ordered as STAT analyses, and 18 min when chemistry assays were ordered as routine determinations. CONCLUSIONS: Assays on the Architect ci8200 performed well, fulfilling quality control requirements as defined for instance by German quality control guidelines (RiliBAK). Method comparisons showed acceptable agreements with established assays. Workflow studies using the Architect ci8200 documented shorter times of analyses as compared with the conventionally established laboratory routine demonstrating the potential of integrated chemistry/immunoassay analyzers to provide faster and more efficient performance.

Bicarbonates↗

PubMed2026

A Robust, Self-Digestion-Resistant LysN with Superior Activity and Cleavage Fidelity for Advanced Proteomic Workflows.

LysN is a valuable protease in proteomics because it cleaves peptide bonds N-terminal to lysine, generating peptides with physicochemical properties complementary to those produced by LysC and trypsin. However, the broader adoption of LysN in proteomic workflows has been limited by the lack of commercially available enzymes that combine high activity, low missed-cleavage rates, and sufficient stability under practical sample-processing conditions. Here, we report the recombinant production and proteomic characterization of a self-digestion-resistant and highly active LysN from Shewanella loihica (SL-LysN). Using terminomics, we mapped the mature N- and C-termini of the enzyme and established the primary structure of the active protease. We further developed a high-density fermentation, refolding, and purification workflow to obtain highly purified recombinant SL-LysN. Biochemical and proteomic benchmarking showed that SL-LysN displayed 3.3-fold higher specific activity than commercial LysN and reduced missed cleavages by approximately 80%. Notably, SL-LysN retained high activity in the presence of 8 M urea or 1% SDS and showed strong resistance to autolysis, indicating exceptional robustness for proteomic sample preparation. In complex mammalian proteome digests, SL-LysN achieved >95% cleavage specificity and a missed-cleavage rate of only 5.9%. These features address a long-standing bottleneck in N-terminal proteolysis and establish SL-LysN as a high-performance enzymatic tool for advanced proteomic workflows, including deep protein sequencing, quantitative proteomics, terminomics, de novo sequencing and analyses requiring efficient digestion under denaturing conditions.

Shewanella↗

PubMed2026

2-Mercaptoethanol/DMSO Workflow Enables Highly Reproducible Quantitative Proteomics.

Proteomics provides a systematic and high-throughput approach to comprehensively characterize protein networks, enabling insights into cellular functions and disease mechanisms. Carbamidomethylation using iodoacetamide (IAA), a common method for cysteine alkylation, is known to cause nonspecific modifications that increase spectral complexity in mass spectrometry and reduce quantitative accuracy. Here, we established a reproducibility-focused 2-mercaptoethanol (2-ME)/dimethyl sulfoxide (DMSO) workflow and systematically evaluated its quantitative performance at the proteome-wide level. Mouse liver proteomes were processed using either 2-ME/DMSO or conventional IAA treatment, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The optimized 2-ME treatment increased the number of cysteine-modified peptides by 1.6- to 1.9-fold. Although total protein identifications were comparable, 77% of proteins exhibited improved sequence coverage with the optimized 2-ME treatment. Quantitative reproducibility was also enhanced, with the peptide quantified CV ≤ 20% increasing from 61.4% with IAA treatment to 86.1% with 2-ME treatment, and protein quantified CV ≤ 20% increasing from 80.6% with IAA treatment to 93.5% with 2-ME treatment. Application of this new workflow to ovarian clear cell carcinoma reliably detected cisplatin-induced alterations. The 2-ME/DMSO workflow offers a simple and highly reproducible proteomics strategy for accurate quantitative proteomics.

Animals↗

PubMed2006

Web-accessible scientific workflow system for performance monitoring.

We describe the design and implementation of a web-accessible scientific workflow system for environmental performance monitoring. This workflow environment integrates distributed automated data acquisition with server side data management and information visualization through flexible browser-based data access tools. Component technologies include a rich browser-based client, a back-end server for methodical data processing, user management, and result delivery, and third party applications which are invoked by the back-end using web services. This environment allows for reproducible, transparent result generation by a diverse user base, and provides a seamless integration between data selection, analysis applications, and result delivery. This workflow system has been implemented for several sites and monitoring systems with different degrees of complexity.

Databases, Factual↗

PubMed2003

Specifying workflow process requirements for an emergency medical service.

Recent trends in healthcare delivery have led to a gradual shift in the conceptualisation of healthcare information systems towards supporting healthcare processes in a more direct way. The move towards integrated and managed care, which requires designing healthcare processes around patient needs and incorporating efficiency considerations has led to an increased interest in process-oriented healthcare information systems based on workflow technology. This means to actively deliver the tasks to be performed to the right persons at the right time with the necessary information and the application functions needed. Moreover, workflow technology promotes a component-oriented development whereby the process logic is separated from application logic. This paper presents an approach to capturing process logic requirements for healthcare workflow systems with a view to design a system that is easily adjustable to process changes and to evolving organizational structures at a reasonable cost.

Efficiency, Organizational↗

PubMed2025

Tractor Workflow Pipeline: A Scalable Nextflow Framework for Local Ancestry-Aware Genome-Wide Association Studies.

The routine exclusion of admixed individuals from traditional Genome-Wide Association Studies (GWAS) due to concerns about spurious associations has hindered genetic analyses involving multiple ancestries. Tractor GWAS addresses this issue by incorporating local ancestry into its analysis, empowering identification of ancestry-enriched hits and generating ancestry-specific summary statistics. However, Tractor requires accurate genomic phasing and local ancestry inference as prerequisite steps, which requires additional bioinformatics expertise and decision points regarding reference panel setup. To streamline, harmonize, and automate this process, we present a scalable Nextflow workflow that integrates all necessary steps, minimizing the need for manual intervention while remaining modular and customizable. The workflow supports multiple commonly used tools and offers flexibility in how Tractor is implemented. To demonstrate its utility, we applied this pipeline to analyze 32 blood biomarkers in 6,245 two-way AFR-EUR admixed individuals from the UK Biobank. This pipeline ran efficiently at scale, replicated known associations, and identified novel ancestry-specific loci. These novel associations were largely driven by variants present on African ancestral tracts but absent from European tracts, underscoring the value of local ancestry-aware methods in uncovering previously missed genetic signals. By enabling the efficient analysis of admixed individuals, our workflow facilitates Tractor use, paving the way for more broader genetic discovery.

Journal Article↗

PubMed2003

Workflow-enabled distributed component-based information architecture for digital medical imaging enterprises.

Few information systems today offer a flexible means to define and manage the automated part of radiology processes, which provide clinical imaging services for the entire healthcare organization. Even fewer of them provide a coherent architecture that can easily cope with heterogeneity and inevitable local adaptation of applications and can integrate clinical and administrative information to aid better clinical, operational, and business decisions. We describe an innovative enterprise architecture of image information management systems to fill the needs. Such a system is based on the interplay of production workflow management, distributed object computing, Java and Web techniques, and in-depth domain knowledge in radiology operations. Our design adapts the approach of "4+1" architectural view. In this new architecture, PACS and RIS become one while the user interaction can be automated by customized workflow process. Clinical service applications are implemented as active components. They can be reasonably substituted by applications of local adaptations and can be multiplied for fault tolerance and load balancing. Furthermore, the workflow-enabled digital radiology system would provide powerful query and statistical functions for managing resources and improving productivity. This paper will potentially lead to a new direction of image information management. We illustrate the innovative design with examples taken from an implemented system.

Computer Communication Networks↗

PubMed2006

Predicting changes in workflow resulting from healthcare information systems: ensuring the safety of healthcare.

This paper describes an approach to studying medical error and workflow that can be applied to help ensure the safety of new healthcare information systems. The approach focuses on identification of usability problems resulting from implementation of new information technology, as well as identification of problems related to changes in workflow. The paper illustrates how the approach can be applied in the simulation-based analyses of emerging healthcare information systems. The paper includes discussion of the application of an approach to identifying inadvertent changes in healthcare workflow that may result from design issues in a range of information technologies including medication order entry systems. General implications for the design, development and evaluation of safer healthcare information systems are discussed. It is argued that there is a need for thorough simulation-based testing of systems under a variety of conditions before they are released in order to ensure the safety of healthcare.

Efficiency, Organizational↗