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PubMed2026

Parallel Analysis of Repeat Expansions: An Updated Clinical Nanopore Cas9-Targeted Sequencing Workflow for Nanopore R10 Flow Cells.

Hereditary ataxias, caused by expansions of short tandem repeats, are difficult to diagnose using traditional PCR and Southern blot methods, which struggle to detect complex repeat expansions and cannot assess repeat interruptions or methylation. An updated Clinical Nanopore Cas9-Targeted Sequencing workflow is presented for analyzing repeat expansions, now compatible with the Oxford Nanopore Technologies R10 flow cell. The workflow incorporates the Oxford Nanopore Technologies wf-human-variation Epi2Me workflow, including the Straglr tool to analyze base-called reads, ensuring compatibility with past, current, and future sequencing chemistries. It expands the number of genes analyzed from 10 to 27 and introduces new gene panels for ataxia, myopathy, neurodegeneration, and amyotrophic lateral sclerosis/motor neuron disease. Validated with Coriell reference and clinical samples, this method improves the analysis of pathogenic repeat expansions, providing deeper insights into repeat structures while addressing the limitations of traditional approaches. In this work, the use of multiplexing, Flongle flow cells, and single-gene targeting were explored as alternatives to panel-based approaches in the Clinical Nanopore Cas9-Targeted Sequencing workflow, finding that only single-gene targeting provides compatibility and reliable performance.

Journal Article↗

PubMed1998

A study of medical emergency workflow.

In this paper, the authors introduce a workflow model. The development of computer network technology enables us to share the distributed data in real time. It is a considerable significance in the practical application of network capabilities not only to office work but also to the medical environment. In order to construct a well-connected, managed post (environment, scene), a model is needed to design the workflow. Here we propose a workflow model to cope with the scene of unforeseen events that we usually encounter in daily clinical activities. We give careful consideration to the ability of this model to manage dynamic changes within the workflow and describe its application to a medical scene (triage) and then carry out simulations based on this model. The authors are able to demonstrate the validity of this model through this simulation.

Computer Simulation↗

PubMed2000

Applying workflow analysis tools to assess immunization delivery in outpatient primary care settings.

BACKGROUND: As health care organizations face increasing pressure to institute quality assurance activities, the already-underfunded community clinics that treat the poor and underserved are challenged to perform these activities within tight constraints of human and financial resources. With pediatric immunizations as a marker, a workflow observation tool was used to identify causal processes affecting immunization delivery. METHODS: Ten clinics and five private practices, located in areas designated as health professional shortage areas, participated in the study, gaining access to a tool that would have been unaffordable to them from the private sector. Trained observers followed families through the clinic, using a 127-item workflow observation form--the Observational Checklist of Patient Encounters (OCPE)--assessing discrete activities that families encountered during the checkin/pre-exam, exam, discharge, and billing processes. A convenience sampling of the targeted population--children younger than three years of age--included observations of scheduled acute, scheduled well-child, follow-up, and walk-in visits. In the feedback session, a summary of each clinic's immunization delivery patterns was presented, with an emphasis on the individual health center's operational issues. RESULTS: The workflow observation tool was used to identify operational errors affecting both clinical and fiscal processes in each of the clinics that had not been previously apparent to either clinic management or the quality improvement (QI) teams. DISCUSSION: Feedback addressed and encouraged process-oriented improvements in response to the workflow observations, which were incorporated into the clinics' QI procedures. Twelve of the 15 clinics have formed process action teams to address QI issues on an ongoing basis.

Age Factors↗

PubMedDate not supplied

Dynamic workflow model for complex activity in intensive care unit.

Co-operation is very important in Medical care, especially in the Intensive Care Unit (ICU) where the difficulties increase which is due to the urgency of the work. Workflow systems are considered as well adapted to modelize productive work in business process. We aim at introducing this approach in the Health Care domain. We have proposed a conversation-based workflow in order to modelize the therapeutics plan in the ICU [1]. But in such a complex field, the flexibility of the workflow system is essential for the system to be usable. We have concentrated on three main points usually proposed in the workflow models, suffering from a lack of dynamicity: static links between roles and actors, global notification of information changes, lack of human control on the system. In this paper, we focus on the main points used to increase the dynamicity. We report on affecting roles, highlighting information, and controlling the system. We propose some solutions and describe our prototype in the ICU.

Computer Simulation↗

PubMed2003

[Workflow improvement and efficiency gain with near total digitalization of a radiology department].

PURPOSE: To determine the temporal changes of the workflow caused by digitalization of the radiology department after installation of digital luminescence-radiography (DLR), a radiology information system (RIS) and picture archiving and communication system (PACS) at the Missionsärztliche Klinik in April 2000. MATERIALS AND METHODS: In a comparative study, a workflow analysis by manual registration of different work steps was performed before (1999) and after (2001) digitalization of a radiology department. RESULTS: The digitalization shortened the examination time for patients from a mean of 8 min to 5 min. The time the patient is absent from the emergency room did not change. Reporting radiographic examinations including comparison with previous studies begins earlier from a mean of 2 h 37 min to 17 min. Using PACS, 85.9 % of all cases could be interpreted on the day of the examination (without PACS 41.2 %) and 87.2 % of the reports were completed the day after the examination (without PACS 64.5 %). No time differences were found between reading conventional studies on the monitor or as soft-copy. CONCLUSION: Compared to conventional film-screen systems, complete digitalization of a radiology department is time saving at nearly all steps of the workflow, with expected positive effects on the workflow quality of the entire hospital.

Efficiency, Organizational↗

PubMed2026

A modular class-aware workflow for small RNA sequencing analysis using mouse sperm as a case study.

BACKGROUND: Small RNA sequencing analysis is challenging because RNA classes differ in biogenesis, sequence redundancy, genomic organization, and annotation reliability. Integrated workflows accommodating these constraints remain limited, particularly for fragment-level and cluster-level analysis. METHODS: We present a reproducible, containerized, class-aware workflow for small RNA sequencing analysis, using mouse sperm as a case study. The workflow combines standardized preprocessing with complementary annotation and quantification strategies for microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), ribosomal RNA-derived small RNAs (rsRNAs), and PIWI-interacting RNA (piRNA)-enriched genomic clusters. Using sperm small RNA data from offspring of lipopolysaccharide (LPS)-exposed male mice, we compared integrated-reference mapping, multi-class annotation, fragment-level tsRNA profiling, and genome-based piRNA cluster analysis, with custom modules for locus-aware harmonization and condition-specific cluster analysis. RESULTS: Integrated-reference mapping aligned 88.17% of reads and retained 690 features after filtering. It identified 11 differentially expressed miRNAs between LPS and controls, while other classes showed limited signal. Fragment-level profiling improved tsRNA resolution. piRNA cluster analysis identified 958 control and 940 LPS clusters, with 18 control-specific and no LPS-specific clusters. CONCLUSION: This workflow supports transparent, reproducible, class-aware interpretation of small RNA sequencing data while emphasizing cautious interpretation of piRNA-enriched signals from total small RNA sequencing.

Small non-coding RNA analysis↗

PubMed2006

Observations of residents' work activities for 24 consecutive hours: implications for workflow redesign.

PURPOSE: To examine resident workflow as part of an institutional approach to redesigning the processes of health care delivery. METHOD: In 2003 the authors observed the workflows for 24 hours of seven residents who were at various levels of training (two each from the internal medicine, pediatrics, and obstetrics and gynecology programs, and one from general surgery) at Denver Health Medical Center, an urban, public teaching hospital. RESULTS: Although the residents spent varying proportions of their time in various activities, all had extremely fragmented workflows as they engaged in from 5.0 to 11.3 different activities per hour of nonsleeping time, many of which required only minutes to complete. All residents experienced frequent interruptions and changes in focus. The internal medicine and surgery residents spent large amounts of time traveling, covering three and six miles, respectively, during their 24-hour shifts. Three of the residents slept between one-quarter and one-third of their time on duty (one without any interruption). CONCLUSIONS: The authors suggest that fragmented workflow exists in all residency programs and that applying the same work limitations to all residents in all training programs (to reduce fatigue-related errors) may be overly restrictive. Improving these processes of care will be difficult and will likely require analytic skills and knowledge of systems engineering that most physicians do not have.

Delivery of Health Care↗

PubMedDate not supplied

Workflow technology: the new frontier. How to overcome the barriers and join the future.

Hospitals are catching up to the business world in the introduction of technology systems that support professional practice and workflow. The field of case management is highly complex and interrelates with diverse groups in diverse locations. The last few years have seen the introduction of Workflow Technology Tools, which can improve the quality and efficiency of discharge planning by the case manager. Despite the availability of these wonderful new programs, many case managers are hesitant to adopt the new technology and workflow. For a myriad of reasons, a computer-based workflow system can seem like a brick wall. This article discusses, from a practitioner's point of view, how professionals can gain confidence and skill to get around the brick wall and join the future.

Adult↗

PubMed2006

Modeling of workflow-engaged networks on radiology transfers across a metro network.

Radiology metro networks bear the challenging proposition of interconnecting several hospitals in a region to provide a comprehensive diagnostic imaging service. Consequences of a poorly designed and implemented metro network could cause delays or no access at all when health care providers try to retrieve medical cases across the network. This could translate into limited diagnostic services to patients, resulting in negative impacts to the patients' medical treatment. A workflow-engaged network (WEN) is a new network paradigm. A WEN appreciates radiology workflows and priorities in using the network. A WEN greatly improves the network performance by guaranteeing that critical image transfers experience minimal delay. It adjusts network settings to ensure the application's requirements are met. This means that high-priority image transfers will have guaranteed and known delay times, whereas lower-priority traffic will have increased delays. This paper introduces a modeling to understand the benefits that WEN brings to a radiology metro network. The modeling uses actual data patterns and flows found in a hospital metro region. The workflows considered are based on the Integrating the Healthcare Enterprise profiles. This modeling has been applied to metropolitan workflows of a health region. The modeling helps identify the kind of metro network that supports data patterns and flows in a metro area. The results of the modeling show that a 155-Mb/s metropolitan area network (MAN) with WEN operates virtually equal to a normal 622-Mb/s MAN without WEN, with potential cost savings for leased line services measured in the millions of dollars per year.

Canada↗

PubMed2006

Optimising workflow in andrology: a new electronic patient record and database.

AIM: To improve workflow and usability by introduction of a new electronic patient record (EPR) and database. METHODS: Establishment of an EPR based on open source technology (MySQL database and PHP scripting language) in a tertiary care andrology center at a university clinic. Workflow analysis, a benchmark comparing the two systems and a survey for usability and ergonomics were carried out. RESULTS: Workflow optimizations (electronic ordering of laboratory analysis, elimination of transcription steps and automated referral letters) and the decrease in time required for data entry per patient to 71%+/-27%, P<0.05, lead to a workload reduction. The benchmark showed a significant performance increase (highest with starting the respective system: 1.3+/-0.2 s vs. 11.1+/-0.2 s, mean+/-SD). In the survey, users rated the new system at least two ranks higher over its predecessor (P<0.01) in all sub-areas. CONCLUSION: With further improvements, today's EPR can evolve to substitute paper records, saving time (and possibly costs), supporting user satisfaction and expanding the basis for scientific evaluation when more data is electronically available. Newly introduced systems should be versatile, adaptable for users, and workflow-oriented to yield the highest benefit. If ready-made software is purchased, customization should be implemented during rollout.

Andrology↗

PubMedDate not supplied

Approach for workflow modeling using pi-calculus.

As a variant of process algebra, Pi-calculus can describe the interactions between evolving processes. By modeling activity as a process interacting with other processes through ports, this paper presents a new approach: representing workflow models using Pi-calculus. As a result, the model can characterize the dynamic behaviors of the workflow process in terms of the LTS (Labeled Transition Semantics) semantics of Pi-calculus. The main advantage of the workflow model's formal semantic is that it allows for verification of the model's properties, such as deadlock-free and normal termination. Moreover, the equivalence of workflow models can be checked through weak bisimulation theorem in the Pi-calculus, thus facilitating the optimization of business processes.

Decision Support Techniques↗

PubMed1997

Enhancing quality and controlling costs: using Internet technology to apply workflow to health care.

The pressures associated with the competitive, quickly changing health care marketplace require the use of all available tools to deliver the highest quality care at the lowest cost. Workflow, as employed by other industries, delivers significant increases in both productivity and quality of services. Likewise, the application of automated workflow techniques to the health care industry offers measurable and immediate benefits. The very nature of a workflow product requires that it be available as widely as possible and be customized to fit the working patterns of the people who use it. To gain the advantages of customization and wide platform access, it is mandatory that the burgeoning technologies of the Internet be used in the creation of any modern networked computer application. Automated health care workflow provides the necessary information technology for caregivers to deliver efficient and effective high-quality care.

Computer Communication Networks↗

PubMed2006

[Integration of PACS and HIS into the workflow of a nuclear medicine department. Experience in Regensburg].

AIM: The development of new diagnostic techniques and the implementation of a modern quality control management system requires the continuous adaptation of existing data processing tools to the nuclear medicine diagnostic workflow. Furthermore, PACS connected to HIS facilitates and enhances the transfer of data and pictures, and satisfies the legal requirements for data retention as regulated by law. Therefore, the aim of this work is to present the architecture, structure and results of such a system newly installed in a department of nuclear medicine. METHODS: Initially, the nuclear medicine workflow was carefully analyzed and each step was correlated to the corresponding module. The standard SAP R/3 and IS-H/IS-H(*)med based software used for patient administration at the University of Regensburg Hospital was adapted to the needs of the Nuclear Medicine Department. The networking of the imaging systems was done by integration of a PACS. Finally, the PACS was connected to the HIS to allow the attachment of images to the medical report. RESULTS, CONCLUSION: By connecting the HIS to the nuclear medicine PACS, the workflow was significantly improved. The data management sequence starting at the reception desk, continuing through the nuclear medical examination, to the physician's final written and image report is clearly structured. Although high demands exist on technical support and administration the integration of PACS and HIS into the nuclear medicine workflow leads to enhanced efficiency and reduction in hospital costs. Patient and data management are considerably improved in this way.

Documentation↗

PubMed2006

Context-aware workflow management of mobile health applications.

We propose a medical application management architecture that allows medical (IT) experts readily designing, developing and deploying context-aware mobile health (m-health) applications or services. In particular, we elaborate on how our application workflow management architecture enables chaining, coordinating, composing, and adapting context-sensitive medical application components such that critical Quality of Service (QoS) and Quality of Context (QoC) requirements typical for m-health applications or services can be met. This functional architectural support requires learning modules for distilling application-critical selection of attention and anticipation models. These models will help medical experts constructing and adjusting on-the-fly m-health application workflows and workflow strategies. We illustrate our context-aware workflow management paradigm for a m-health data delivery problem, in which optimal communication network configurations have to be determined.

Computer Communication Networks↗

PubMed1996

Workflow computing. Improving management and efficiency of pathology diagnostic services.

Traditionally, information technology in health care has helped practitioners to collect, store, and present information and also to add a degree of automation to simple tasks (instrument interfaces supporting result entry, for example). Thus commercially available information systems do little to support the need to model, execute, monitor, coordinate, and revise the various complex clinical processes required to support health-care delivery. Workflow computing, which is already implemented and improving the efficiency of operations in several nonmedical industries, can address the need to manage complex clinical processes. Workflow computing not only provides a means to define and manage the events, roles, and information integral to health-care delivery but also supports the explicit implementation of policy or rules appropriate to the process. This article explains how workflow computing may be applied to health-care and the inherent advantages of the technology, and it defines workflow system requirements for use in health-care delivery with special reference to diagnostic pathology.

Ambulatory Care↗

PubMed2025

Triage and workflow optimization with artificial intelligence in pediatric imaging.

Artificial intelligence (AI) is being increasingly utilized in various aspects by the radiology department. With an ever-increasing burden on the healthcare system, particularly in emergency units, the need to incorporate AI in patient triage and workflow optimization cannot be overstated. Machine learning (ML)-based algorithms form the core of AI-based software, aiding healthcare professionals at nearly every step in delivering appropriate patient care. Regarding the radiology section of the hospital, AI-based algorithms have proven exceptionally useful in assisting radiologists and technicians with image acquisition. From accurate clinical referrals to scheduling computed tomography/magnetic resonance imaging scan appointments, from ensuring the lowest radiation exposure to offering timely follow-up reminders, ML-based software has indeed revolutionized the concept of modern image acquisition, especially in the pediatric radiology section. Although the implementation of these algorithms is swift, several technical challenges and the limited availability of pediatric datasets preclude their widespread use. The utility of multimodal pediatric datasets, which combine imaging, genomics, and clinical data, for comprehensive AI triage models can help AI systems evolve toward greater adaptability and integration, resulting in enhanced efficiency, reduced turnaround times, and improved patient outcomes in pediatric radiology departments in the future. In this article, we highlight and review the utility of AI and machine learning-based algorithms in efficiently aiding triage and streamlining the workflow in the pediatric radiology section, thereby ensuring an overall improvement in the departmental workflow.

Triage↗

PubMed2024

optiPRM: A Targeted Immunopeptidomics LC-MS Workflow With Ultra-High Sensitivity for the Detection of Mutation-Derived Tumor Neoepitopes From Limited Input Material.

Personalized cancer immunotherapies such as therapeutic vaccines and adoptive transfer of T cell receptor-transgenic T cells rely on the presentation of tumor-specific peptides by human leukocyte antigen class I molecules to cytotoxic T cells. Such neoepitopes can for example arise from somatic mutations and their identification is crucial for the rational design of new therapeutic interventions. Liquid chromatography mass spectrometry (LC-MS)-based immunopeptidomics is the only method to directly prove actual peptide presentation and we have developed a parameter optimization workflow to tune targeted assays for maximum detection sensitivity on a per peptide basis, termed optiPRM. Optimization of collision energy using optiPRM allows for the improved detection of low abundant peptides that are very hard to detect using standard parameters. Applying this to immunopeptidomics, we detected a neoepitope in a patient-derived xenograft from as little as 2.5 × 106 cells input. Application of the workflow on small patient tumor samples allowed for the detection of five mutation-derived neoepitopes in three patients. One neoepitope was confirmed to be recognized by patient T cells. In conclusion, optiPRM, a targeted MS workflow reaching ultra-high sensitivity by per peptide parameter optimization, makes the identification of actionable neoepitopes possible from sample sizes usually available in the clinic.

Humans↗

PubMed2025

Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly.

MOTIVATION: De novo assembly creates reference genomes that underpin many modern biodiversity and conservation studies. Large numbers of new genomes are being assembled by labs around the world. To avoid duplication of efforts and variable data quality, we desire a best-practice assembly process, implemented as an automated portable workflow. RESULTS: Here, we present Colora, a Snakemake workflow that produces chromosome-scale de novo primary or phased genome assemblies complete with organelles using Pacific Biosciences HiFi, Hi-C, and optionally Oxford Nanopore Technologies reads as input. Colora is a user-friendly, versatile, and reproducible pipeline that is ready to use by researchers looking for an automated way to obtain high-quality de novo genome assemblies. AVAILABILITY AND IMPLEMENTATION: The source code of Colora is available on GitHub (https://github.com/LiaOb21/colora) and has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576. Colora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora).

Software↗