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At least 19 recordsLinked to original sources
PubMed2000

Workflow management with systems approach: anticipated and ad-hoc workflow for scientific applications.

While workflow management has mostly been considered in business applications so far, the focus of the Workflow Management with Systems Approach (WOMASA) is on scientific applications such as geoprocessing, molecular biology, or laboratory environments. In particular, WOMASA aims at flexible and platform-indepented workflow support, with respect to both specification and execution of workflows. It turns out that the modeling and execution of workflows in traditional and in scientific applications exhibit significant differences. In particular, the need for dynamic modifications of workflow models while workflows are running is an important feature in scientific applications. The conceptual design and functionality of a WOMASA prototype is outlined, in particular that of its core workflow engine, and it is shown how the requirements of flexibility in modeling and executing workflows, imposed by scientific applications, are met.

DNA↗
PubMed2005

Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator.

BACKGROUND: Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. RESULTS: We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. AVAILABILITY: http://if-web1.imb.uq.edu.au/Pise/5.a/gpipe.html (interactive), ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/ (download). CONCLUSION: From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous analytical tools.

Algorithms↗
PubMed2002

Workflow optimization: current trends and future directions.

In an attempt to maximize productivity within the medical imaging department, increasing importance and attention is being placed on workflow. Workflow is the process of analyzing individual steps that occur during a single event, such as the performance of an MRI exam. The primary focus of workflow optimization within the imaging department is automation and task consolidation, however, a number of other factors should be considered including the stochastic nature of the workload, availability of human resources, and the specific technologies being employed. The purpose of this paper is to determine the complex relationship that exists between information technology and the radiologic technologist, in an attempt to determine how workflow can be optimized to improve technologist productivity. This relationship takes on greater importance as more imaging departments are undergoing the transition from film-based to filmless operation. A nationwide survey was conducted to compare technologist workflow in film-based and filmless operations, for all imaging modalities. The individual tasks performed by technologists were defined, along with the amount of time allocated to these tasks. The index of workflow efficiency was determined to be the percentage of overall technologist time allocated to image acquisition, since this is the primary responsibility of the radiologic technologist. Preliminary analysis indicates technologist workflow in filmless operation is enhanced when compared with film-based operation, for all imaging modalities. The specific tasks that require less technologist time in filmless operation are accessing data and retake rates (due to both technical factors and lost exams). Surprisingly, no significant differences were reported for the task of image processing, when comparing technologist workflow in film-based and filmless operations. Additional research is planned to evaluate the potential workflow gains achievable through workflow optimization software, improved systems integration, and automation of advanced image processing techniques.

Efficiency, Organizational↗
PubMed2006

The critical path method to analyze and modify OR-workflow: integration of an image documentation system.

Intraoperative image documentation is becoming more and more important for quality management in medicine, in terms of forensic documentation, research and teaching. Up to now, no software-based OR-image-documentation system fits satisfactorily into an OR-workflow. The objective of this study is to transparently show system integration in a clinical workflow for evaluating demands on future system developments. An example of the OR-workflow is presented for the department of obstetrics and gynecology at the University of Tuebingen (Germany). Twelve representative gynecologic laparoscopic surgeries were analyzed by using the critical path method (CPM). CPM network diagrams are shown for an actual laparoscopic workflow and for a workflow including an OR-image-documentation system. With the objective not to increase the total time of actual workflow, the maximum system operation time can be calculated for each period of time. Before surgery the maximum system operation time is x(max) = 7,3 minutes. After surgery it has to be assumed that system operation will increase total workflow time. Using the CPM to analyze requirements for system integration in a medical workflow has not yet been investigated. It is an appropriate method to transparently show integration possibilities and to define workflow-based requirements for the development process of new systems.

Critical Pathways↗
PubMed2026

A portable recalibration workflow for reference-based variant calling in non-human genomes.

A key computational step in reference-based variant calling is distinguishing true genetic variants from sequencing errors. Advanced tools and workflows have been developed to handle this by computational modelling of technical errors from the sequencing machines. However, these recalibration workflows have largely been evaluated for human data only and its exact applicability for non-human data remains unknown. Here, we conducted a systematic evaluation of variant calling on human, rice, sheep, and chickpea data, and found that existing workflows introduce unexpected statistical bias, thus leading to suboptimal variant calls for non-human data. To address this problem, we present simple guidelines for constructing a "pseudo-"database (pseudoDB) of genetic variants as a scalable and portable solution for recalibration and variant calling. With human data, our pseudoDB-based workflow performs comparably to existing dbSNP-based GATK3 workflows and those using DeepVariant, Strelka2, and FreeBayes. We extend this to other non-human genomes, namely cattle, brown bear, swan goose, African oil palm, Komodo dragon, and stevia, altogether resulting in the identification of up to 242.0% unique genetic variants. The majority of newly identified variants are within the non-coding regions, hinting at the rich diversity of genome regulation in the non-human population. Our pseudoDB-based workflow is agnostic to reference genomes and modular for easy integration with other computational workflows for human and non-human resequencing data.

Humans↗
PubMed2006

[Workflow analysis to assess the efficiency of intraoperative technology using the example of functional endoscopic sinus surgery].

Evaluation of the efficiency of surgical technology systems has to date been largely subjective. The aim of this study was to develop an ontology for surgical procedures usable workflow structures, and the evaluation of surgical workflow analysis using the example of functional endoscopic sinus surgery (FESS). A total of 38 procedures (20 patients) were included. Surgery was carried out by seven different surgeons with different degrees of training. Description of the surgical procedures and resources is based on the standard EN1828/2001 (Structure for Classification and Coding Systems for Surgical Procedures). In addition the requirements of the Workflow Reference Models (document no. Tc00-1003), Workflow Management Coalition (WfMC) were integrated. The workflow recorded the position, frequency of change of position, use time, cleaning time and concept based instrument changes. A total of 293 items were used to define FESS. A total of 1,029 different endoscopic positions were documented. These could be combined into five major endoscopic positions. The frequency of position changes was 27.1 per side, the period spent in an endoscopic position is about 1.31 min. Time for the concept-caused instrument changing was 6.44 min per side. This study demonstrates the need for assistance in guiding the endoscope in FESS. Using the workflow-data, the concept of an assistant system is possible. We offer a basis for discussion of the development of an ontology, recording and analysing surgical workflows and their practical application.

Biotechnology↗
PubMedDate not supplied

SOMA--workflow for small molecule property calculations on a multiplatform computing grid.

We present the concept of the SOMA workflow developed at the Finnish IT Center for Science CSC. The SOMA workflow unites multiplatform UNIX/LINUX computing resources and third-party software for calculating molecular structure and properties. The presented workflow components consist of the computing program XML descriptions, the core workflow program Grape, the toolkit for parsing program input and output, and the extranet interface. The program Grape and the developed XML descriptions of scientific programs allow researchers to link molecular modeling software into highly sophisticated computational workflows. SOMA collects the calculated data produced by the workflow and stores the computed information in the Chemical Markup Language (CML) format. The extranet interface is used for user authentication, building of the program interfaces and the workflows, and for sorting, filtering, and visualizing the results.

Journal Article↗
PubMed2005

High performance workflow implementation for protein surface characterization using grid technology.

BACKGROUND: This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence to the exposed residues of the protein surface. The implementation of this workflow is based on the Italian Grid.it project infrastructure, that is a network of several computational resources and storage facilities distributed at different grid sites. METHODS: Workflows are very common in Bioinformatics because they allow to process large quantities of data by delegating the management of resources to the information streaming. Grid technology optimizes the computational load during the different workflow steps, dividing the more expensive tasks into a set of small jobs. RESULTS: Grid technology allows efficient database management, a crucial problem for obtaining good results in Bioinformatics applications. The proposed workflow is implemented to integrate huge amounts of data and the results themselves must be stored into a relational database, which results as the added value to the global knowledge. CONCLUSION: A web interface has been developed to make this technology accessible to grid users. Once the workflow has started, by means of the simplified interface, it is possible to follow all the different steps throughout the data processing. Eventually, when the workflow has been terminated, the different features of the protein, like the amino acids exposed on the protein surface, can be compared with the data present in the output database.

Automation↗
PubMed2000

[Computer support of workflow in the hospital: concepts, technology and application].

For a variety of reasons, hospitals are developing a growing interest in changing their information systems to support patient processes in a more direct way. This means to actively deliver the tasks to be performed to the right persons at the right point in time with the necessary information and the application functions needed for performing these tasks. Process-oriented workflow technology is a very interesting candidate to achieve this goal. It offers components for the computer-based analysis, modeling, animation, coordination and monitoring of (hospital) processes. In this paper we discuss the perspectives offered by workflow-based, clinical information systems. We survey key features of today's business process modeling tools and of workflow management systems, and we show how they can be applied in the clinical domain. To illustrate the huge potential offered by workflow technology, we present results from the project "Using Workflow Management Systems for Clinical Applications". Within this project we thoroughly analyzed and redesigned core processes from the University's Women hospital and we proto-typically implemented a workflow-based application system for the support of processes from the division day clinic. Although our work shows that current workflow technology is still lacking some important features, in the long run, it may strongly influence information processing within hospitals.

Computers↗
PubMed2026

A streamlined workflow for high throughput metaproteomic analysis of the rumen microbiome.

Metaproteomics can provide direct functional insights into complex microbial communities, yet its application in rumen research remains limited due to labor-intensive and low-throughput sample preparation workflows before the MS analysis. This work aimed to develop and characterize a streamlined, high throughput metaproteomic workflow optimized for rumen samples. Key steps, including microbial cell extraction, cell lysis, protein digestion, and LC-MS/MS acquisition, were systematically assessed and optimized to reduce hands-on time while maintaining deep proteome coverage. The optimized workflow integrates a minimized cell extraction protocol using 0.5 g starting material and in-solution tryptic digestion. Application of the final workflow to 72 samples from in vitro fermentation revealed that biological variability between inocula dominated technical variability, which remained moderate (median CV of 21-24% across batches). Overall, the optimized workflow supports robust taxonomic and functional characterization of the rumen microbiome with improved scalability. These advances provide a foundation for applying metaproteomics to larger experimental designs, including nutritional trials and cohort studies, thereby enabling broader functional interrogation of rumen microbial ecosystems. SIGNIFICANCE: This study addresses current limitations in the application of metaproteomics to rumen microbiome research by developing a streamlined and scalable sample preparation workflow. By optimizing key steps and reducing sample input while maintaining reproducibility and proteome coverage, this work enables more efficient processing of larger sample sets. These advances support the broader use of metaproteomics in rumen studies and facilitate functional investigations relevant to animal nutrition and sustainable livestock production.

Animals↗
PubMed2004

Taverna: a tool for the composition and enactment of bioinformatics workflows.

MOTIVATION: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. RESULTS: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application.

Computational Biology↗
PubMed2005

Wildfire: distributed, Grid-enabled workflow construction and execution.

BACKGROUND: We observe two trends in bioinformatics: (i) analyses are increasing in complexity, often requiring several applications to be run as a workflow; and (ii) multiple CPU clusters and Grids are available to more scientists. The traditional solution to the problem of running workflows across multiple CPUs required programming, often in a scripting language such as perl. Programming places such solutions beyond the reach of many bioinformatics consumers. RESULTS: We present Wildfire, a graphical user interface for constructing and running workflows. Wildfire borrows user interface features from Jemboss and adds a drag-and-drop interface allowing the user to compose EMBOSS (and other) programs into workflows. For execution, Wildfire uses GEL, the underlying workflow execution engine, which can exploit available parallelism on multiple CPU machines including Beowulf-class clusters and Grids. CONCLUSION: Wildfire simplifies the tasks of constructing and executing bioinformatics workflows.

Algorithms↗
PubMed2006

BioMoby extensions to the Taverna workflow management and enactment software.

BACKGROUND: As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface. RESULTS: The exposed BioMoby functionality aids in the design of "sensible" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s) that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate. CONCLUSION: With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional Web Services.

Biology↗
PubMed2026

Comparative performance of portable DNA extraction protocols and bioinformatics workflows for rapid detection of gram-negative bacteria and antimicrobial resistance using Oxford Nanopore sequencing.

Oxford Nanopore Technology (ONT) enables rapid, portable pathogen identification and antimicrobial resistance (AMR) detection, but the reliability of downstream genomic analyses is highly dependent on DNA extraction quality, particularly in resource-limited settings. This study comparatively evaluated four portable bacterial DNA extraction protocols derived from three commercial kits to determine their impact on nanopore sequencing performance, bioinformatics workflow completion, and field deployability. Six gram-negative bacterial isolates (Escherichia coli, n = 4; Pseudomonas sp., n = 1; and Salmonella sp., n = 1) were processed using four extraction protocols: SwiftX DNA, SwiftX DNA with proteinase K (ProtK), SwiftX ParaBact, and NucleoSpin Microbial. Twenty-four resulting DNA extracts were sequenced on a single multiplexed MinION R10.4.1 flow cell. Sequencing data were analyzed using validated Galaxy-based generic and species-specific pipelines. Workflow completion was defined as successful progression through quality control, assembly, virulence, plasmid, and AMR detection modules. DNA purity varied substantially by extraction protocol and was strongly associated with successful workflow completion (Kruskal-Wallis, P = 0.0006). Accordingly, NucleoSpin Microbial achieved 100% workflow completion, and SwiftX ParaBact achieved 83%, while both SwiftX DNA-based protocols failed to complete full workflows. Importantly, key AMR genes required to classify isolates as multidrug-resistant were consistently detected using both NucleoSpin Microbial and SwiftX ParaBact extractions. However, NucleoSpin Microbial assemblies showed significantly higher contiguity and enabled a broader, more complete detection of virulence factors, pathogenicity islands, plasmid replicons, and accessory AMR genes, reflecting enhanced genomic resolution.IMPORTANCERapid whole-genome sequencing is increasingly used to detect antimicrobial resistance and guide public health responses, but its reliability depends strongly on how bacterial DNA is extracted. In this study, we have shown that DNA extraction method choice has a major impact on Oxford Nanopore sequencing performance across clinically relevant gram-negative bacteria. While silica column-based extraction maximized genomic completeness and analytical depth, paramagnetic bead-based reverse purification offered superior portability with sufficient resolution for frontline AMR surveillance. These findings highlight a practical trade-off between field deployability and high-resolution genomic characterization in low-resource settings.

DNA extraction↗