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Results for “automated workflows”

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At least 19 recordsLinked to original sources
PubMed2004

High-throughput peptide mass fingerprinting of soybean seed proteins: automated workflow and utility of UniGene expressed sequence tag databases for protein identification.

Identification of anonymous proteins from two-dimensional (2-D) gels by peptide mass fingerprinting is one area of proteomics that can greatly benefit from a simple, automated workflow to minimize sample contamination and facilitate high-throughput sample processing. In this investigation we outline a workflow employing robotic automation at each step subsequent to 2-D gel electrophoresis. As proof-of-concept, 96 protein spots from a 2-D gel were analyzed using this approach. Whole protein (1 mg) from mature, dry soybean (Glycine max [L.] Merr.) cv. Jefferson seed was resolved by high resolution 2-D gel electrophoresis. Approximately 150 proteins were observed after staining with Coomassie Blue. The rather low number of detected proteins was due to the fact that the dynamic range of protein expression was greater than 100-fold. The most abundant proteins were seed storage proteins which in total represented over 60% of soybean seed protein. Using peptide mass fingerprinting 44 protein spots were identified. Identification of soybean proteins was greatly aided by the use of annotated, contiguous Expressed Sequence Tag (EST) databases which are available for public access (UniGene, ftp.ncbi.nih.gov/repository/UniGene/). Searches were orders of magnitude faster when compared to searches of unannotated EST databases and resulted in a higher frequency of valid, high-scoring matches. Some abundant, non seed storage proteins identified in this investigation include an isoelectric series of sucrose binding proteins, alcohol dehydrogenase and seed maturation proteins. This survey of anonymous seed proteins will serve as the basis for future comparative analysis of seed-filling in soybean as well as comparisons with other soybean varieties.

Databases, Genetic↗
PubMed1996

OzCare: a workflow automation system for care plans.

An automated environment for implementing and monitoring care plans and practice guidelines is very important to the reduction of hospital costs and optimization of medical care. The goal of our research effort is to design a general system architecture that facilitates the implementation of (potentially) numerous care plans. Our approach is unique in that we apply the principles and technologies of Oz a multi-user collaborative workflow system that has been used as a software engineering environment framework, to hospital care planning. We utilize not only the workflow modeling and execution facilities of Oz, but also its open-system architecture to interface it with the World Wide Web, the Medical Logic Module server, and other components of the clinical information system. Our initial proof-of-concept system, OzCare, is constructed on top of the existing Oz system. Through several experiments in which we used this system to implement some Columbia-Presbyterian Medical Center care plans, we demonstrated that our system is capable and flexible for care plan automation.

Computer Simulation↗
PubMed2026

Trustworthy Agentic AI in Bioinformatics: From Workflow Automation to Traceable and Validated Biological Inference.

Agentic artificial intelligence is extending bioinformatics beyond conversational assistance by enabling systems to select tools, execute code, revise analytical plans, and interpret biological data. These capabilities may accelerate research, but they also redistribute decisions that determine whether biological conclusions are valid. We conducted a targeted, structured PubMed search in July 2026 and identified 11 peer-reviewed agentic bioinformatics systems for descriptive review based on predefined eligibility criteria for analytical decision-making, tool or code execution, iterative evaluation, or coordinated agent activity. The evidence base covered single-cell transcriptomics, microbial genomics, cancer genomics, and omics applications, together with methodological literature on reproducibility and biological validation. We examined how current systems report delegated authority, provenance, validation, evidence, abstention, and human oversight. Existing platforms implement safeguards such as sandboxed execution, restricted commands, interaction logs, evidence identifiers, automated checks, critic agents, quality scores, and expert assessment. However, published reports rarely provide a connected account linking the original biological question to samples, reference resources, analytical decisions, computational actions, statistical results, supporting evidence, validation outcomes, and final claims. We distinguish inherited bioinformatics errors, errors amplified through autonomous action, and emergent failures arising from memory, retrieval, tool interaction, or agent coordination. We further propose a multidimensional decision-rights profile, consequence-sensitive validation gates, and a claim-to-evidence provenance architecture organized through the Traceable History of Research Evidence, Agent Actions, and Decisions in Bioinformatics (THREAD-Bio) framework. Illustrative cases show that technically successful execution may still support misleading inference. Trustworthy agentic bioinformatics therefore requires claims to remain reconstructible, challengeable, validated, and proportionate to the evidence.

accountable autonomy↗
PubMedDate not supplied

Impact of community pharmacy automation on workflow, workload, and patient interaction.

OBJECTIVE: To compare workload productivity, workflow efficiency, and pharmacist-patient interaction in automated and nonautomated community pharmacies. DESIGN: Observational study. SETTING: Four community pharmacy sites within a regional pharmacy chain. STUDY PARTICIPANTS: 173 patients and 11 pharmacists. INTERVENTIONS: Patient surveys, pharmacist surveys, and direct observation. MAIN OUTCOME MEASURES: Patient satisfaction, frequency of pharmacist-patient interactions, and prescription dispensing productivity and efficiency. RESULTS: Results from the three nonautomated pharmacies were averaged and compared with results from the automated pharmacy. Patient satisfaction was generally favorable for both automated and nonautomated pharmacies, but scores for the automated site were significantly better on items measuring one domain, technical competence of pharmacy staff. No association was found between patient counseling and prescription workload in automated or nonautomated sites. Personnel at the automated site made significantly more offers to counsel patients, but the number of patients who received counseling did not differ significantly. Automation was associated with a higher number of prescriptions dispensed per full-time equivalent pharmacist and fewer technical dispensing tasks performed by pharmacists. CONCLUSION: Patient satisfaction was not related to the presence of an automated dispensing system. Automation was associated with higher prescription productivity, but actual counseling rates were no different from those observed in nonautomated pharmacies. The likelihood that a patient would receive counseling was not related to staffing levels, automation, or workload. Whether counseling occurred appeared to depend on factors other than automation.

Automation↗
PubMed2026

Systematic performance evaluation and application validation of an end-to-end NGS workstation.

Next-generation sequencing (NGS) library preparation is a core component of precision genomics, but it is commonly constrained by inefficiency, variability, and low throughput of manual protocols. To address these limitations, we developed and systematically evaluated a fully automated NGS workstations and further validated its performance across representative application scenarios. The automated system reduced total processing time from 8 to 10 to 4–6 h. At the same time, it maintained similar performance in pre-library metric, including DNA yield and fragment size, as well as post-capture sequencing metrics (Q30 > 90%, mapping rates > 95%, on-target rates 85–90%). The duplication rate was reduced to 5–8%, compared with 10–15% for manual methods, indicating increased library complexity. Bioinformatic evaluation of inter-species read mapping showed minimal cross-contamination, with a maximum contamination ratio of 0.0003%, indicating effective sample isolation in the automated workflow. High concordance in variant detection was observed between automated and manual workflows. Overall, this automated workstation provides a standardized and reproducible workflow that supports scalable precision genomics applications.

High-Throughput Nucleotide Sequencing↗
PubMed1993

Electronic forms: a next step in hospital automation.

Information consists of two parts, facts and communication. It is not enough for one person to know a fact; the fact must be communicated for it to be of any value to anyone else. Forms were invented to do just that--communicate facts in a systematic manner from one party to the next. Automating forms with computers on a local area network or a wide area network allows for hospital personnel to input a patient's information once and electronically share the information from one department to another, simultaneously. Switching from a paper-based forms system to a fully automated workflow forms system or combining the two can save a healthcare institution money, errors, time and even lives. The levels of an automated forms system include: electronic forms design, demand printing, typewriter replacement, intelligent forms, intelligent mail and true workflow automation.

Communication↗
PubMed2003

Emergency healthcare process automation using workflow technology and web services.

Emergency healthcare delivery involves a variety of interrelated activities performed from the time of a call to the ambulance service until the time of patient's exit from the emergency department of a hospital. As these activities can be viewed as parts of inter-organizational healthcare processes that involve at least two organizations (e.g. an ambulance service and a hospital), there is a need to provide the appropriate technological infrastructure for automating and managing these processes even in cases where the organizations involved use heterogeneous systems to support their internal services. Web-based workflow systems in conjunction with web services present a new way for service-oriented integration (SOI) of disparate systems and for developing distributed applications within and between organizations. Thus, process automation with the use of web services can provide an appropriate infrastructure for the integration of pre-hospital and in-hospital emergency healthcare. A prototype development of such a system is presented in this paper.

Ambulances↗
PubMed2026

'PePApipe': A complete bioinformatics analysis pipeline for African Swine Fever Virus genome.

African Swine Fever Virus (ASFV) is of high concern in porcine livestock across the world due to both the high mortality rates and the trade restrictions imposed on affected regions. The viral genome is large and complex, and genomic analysis is essential for tracing its origin and evolution. Although several bioinformatics tools exist for genome assembly and analysis, no single platform integrates all necessary steps in an accessible and systematic way. In this study the authors developed 'PePApipe', a custom-built, user-friendly pipeline that enables rapid, complete, and efficient ASFV genome analysis. It is specifically designed for laboratory professionals with limited bioinformatics experience, requiring only basic command-line knowledge. Starting from raw sequencing data, PePApipe integrates thirteen software tools into one automated workflow, covering quality control and pre-processing of raw reads, de novo genome assembly and variant calling. Programmed in Python, it can be executed locally through bash scripts, or using a Slurm protocol for batch processing of multiple samples. The main outputs are the ASFV consensus genome sequence and a file listing its putative variants compared to the selected reference genome. PePApipe classifies generated files into structured folders and produces intermediate files that can be used as inputs for further or parallel analyses; users can also enable or disable specific steps in each particular case. This pipeline is adaptable and complementary to downstream steps such as viral genome annotation or genome visualization. By consolidating all stages of viral genome analysis into a single automated workflow, PePApipe reduces the likelihood of user error, and enhances reproducibility and efficiency. This user-friendly pipeline facilitates the transition from sequencing to assembly and downstream analysis of viral genomes, ensuring a fast and reliable response to molecular analysis demands. Finally, the pipeline can be easily adapted to the study of other viral species, expanding its application in infectious diseases surveillance.

African Swine Fever Virus↗
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↗
PubMed2002

Impact of speech recognition on radiologist productivity.

A survey was conducted of radiology practices with productivity data from at least 3 of the following 4 workflows: film with manual transcription, filmless with manual transcription, film with speech recognition, and filmless with speech recognition. Two surveys were submitted to candidate sites. The first was used to ascertain suitable available data for follow-up. The second survey requested data for report turn around times, full-time equivalent (FTE) staffing levels, and report volume. Data were collected and stored in a Microsoft Access database and statistical analysis performed in Excel. Whereas several metrics were used, the normalized figure of reports-per-day/FTE was found to have improved an average of 1.9 (for filmless with speech recognition) and 2.3 (for film with speech recognition) over the film with manual transcription case. Filmless with manual transcription was only 1.4 times the value of the all manual case. At the 10% confidence level, both filmless with manual transcription and film with speech recognition workflows were found to have statistically significant enhanced productivity. Insufficient data exist to show if the fully automated workflow (filmless with speech recognition) offers benefits over 2 previous semiautomated workflows.

Data Collection↗
PubMed2004

Picture archiving and communication systems.

Picture archiving and communication systems (PACS) are highly versatile data storage and retrieval systems that facilitate the transfer of digital images and patient data throughout a healthcare enterprise. Typically, they process images from diagnostic imaging modalities and are interfaced to radiology information systems (RISs) and hospital information systems (HISs) to improve overall workflow. For this Evaluation, we tested six PACS from six suppliers. Ideally, a PACS should allow the healthcare facility to achieve a fully automated workflow, in which patient image data is shared seamlessly from one system to another within a single electronic medical record (EMR). Although our testing found that this ideal has not yet been completely realized, many of the evaluated systems have taken significant steps in that direction. This Evaluation was limited to radiology PACS; however, more and more facilities are considering single PACS solutions to cover the needs of all their imaging departments.

Humans↗
PubMed2002

Picture archiving and communication systems.

Picture archiving and communication systems (PACS) are highly versatile data storage and retrieval systems that facilitate the transfer of digital images and patient data throughout a healthcare enterprise. Typically, they process images from diagnostic imaging modalities and are interfaced to radiology information systems (RISs) and hospital information systems (HISs) to help create a single patient record and improve overall workflow. For this Update Evaluation, we tested eight PACS from eight major suppliers. Ideally, a PACS should allow the facility to achieve a fully automated workflow, in which patient data could move seamlessly from one system to another in a single electronic medical record. Although our testing found that this ideal has not yet been realized, many of the evaluated systems have taken significant steps in that direction. Three of the systems covered in this issue were originally tested for our November 2000 Evaluation. Because PACS technology evolves so rapidly, we haven't simply provided updated data on these three systems, as we customarily would for an Update Evaluation. Instead, we have reexamined the systems from top to bottom and are presenting the results in brand-new Product Profiles, alongside the profiles for the five other systems evaluated here for the first time.

Computer Communication Networks↗