Search results for "Workflow"

Next-Generation Sequencing in Clinical Practice

2019

Abstract During the past few decades, Sanger sequencing represented the “gold standard” technique. In order to better define the mutational status of several genes at the same time, next-generation sequencing methodologies have been introduced in the molecular laboratory workflow. In the era of personalized medicine, this technological improvement plays a key role in the comprehensive molecular characterization of cancer patients in order to get a “tile” target therapy. For different cancer patients, different target therapies are available and different genes serve as clinical it relevant biomarkers. This chapter reviews the principal features of these novel technologies and their applicat…

Checkpointing Workflows for Fail-Stop Errors

2017

International audience; We consider the problem of orchestrating the exe- cution of workflow applications structured as Directed Acyclic Graphs (DAGs) on parallel computing platforms that are subject to fail-stop failures. The objective is to minimize expected overall execution time, or makespan. A solution to this problem consists of a schedule of the workflow tasks on the available processors and of a decision of which application data to checkpoint to stable storage, so as to mitigate the impact of processor failures. For general DAGs this problem is hopelessly intractable. In fact, given a solution, computing its expected makespan is still a difficult problem. To address this challenge,…

The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration

2014

Background: In many experimental pipelines, clustering of multidimensional biological datasets is used to detect hidden structures in unlabelled input data. Taverna is a popular workflow management system that is used to design and execute scientific workflows and aid in silico experimentation. The availability of fast unsupervised methods for clustering and visualization in the Taverna platform is important to support a data-driven scientific discovery in complex and explorative bioinformatics applications. Results: This work presents a Taverna plugin, the Biological Data Interactive Clustering Explorer (BioDICE), that performs clustering of high-dimensional biological data and provides a …

Recommendations of a Laboratory Infrastructure for Simulation of Telemedicine Services

2018

In Norway, a health reform targeting coordination and continuity of care has urged municipalities to re-organize their services as there is an increasing use of remote monitoring and sensor technologies in citizens’ homes. In this context, the research project “Telemedicine Agder” is an opportunity to study the implementation, organization and operation of large scale telemedicine services, and identify the service models of the future. As part of the project, simulation of a telemedicine service for remote monitoring of diabetes II was tested in a clinical laboratory with key informants from municipalities, hospital and research partners. This paper presents the technical and physical infr…

Providing timely quality care after-hours: Perceptions of a hospital model of care

2019

Abstract Background Nurses working night shift are key-players in the acute care team, however, their work environment has been characterised by suboptimal leadership, communication inadequacies, limited resources, and a lack of adequate support. Aim The aim of this study was to investigate nurses' perceptions of the Hospital at Night Team, a nursing model of care implemented to provide timely quality nursing care after-hours. Methods The study used a descriptive design. Five focus groups were conducted, with a total of 34 nurses from 14 wards across a 600+ bed tertiary referral teaching hospital in Melbourne, Australia, one year after the Hospital at Night Team implementation. Focus group …

User-Centered Design of a National Medical Registry for Tick-Borne Diseases

2018

Tick-borne diseases are increasing in a global perspective, with Lyme disease and tick-borne encephalitis as the most frequent. The Norwegian National Advisory Unit on Tick-borne Diseases is preparing the development of a national medical registry for clinical follow-up of patients with tick-borne diseases based on the best practice guidelines and for research purposes. This paper presents the methodological approach of a user-centered design process applied in the initial phase of the registry development. A user workshop identified user needs, requirements and proposed a service workflow for the registry operation. As the next step, a simulation of the proposed service workflow was perfor…

Towards MKDA: A Knowledge Discovery Assistant For Researches in Medicine

2007

Nowadays doctors are generating a huge amount of raw data. These data, analyzed with data mining techniques, could be sources of new knowledge. Unluckily such tasks need skilled data analysts, and not so much researchers in Medicine are also data mining experts. In this paper we present a web based system for knowledge discovery assistance in Medicine able to advice a medical researcher in this kind of tasks. The user must define only the experiment specifications in a formal language we have defined. The system GUI helps users in their composition. Then the system plans a Knowledge Discovery Process (KDP) on the basis of rules in a knowledge base. Finally the system executes the KDP and pr…

An Intelligent System for Building Bioinformatics Workflows

2012

In this paper a new intelligent system designed to support the researcher in the development of a workflow for bio informatics experiments is presented. The proposed system is capable to suggest one or more strategies in order to resolve the selected problem and to support the user in the assembly of a workflow for complex experiments, using a a Knowledge base, representing the expertise about the application domain, and a Rule-Based system for decision-making activity. Moreover, the system can represent this workflow at different abstraction layers, freeing the user from implementation details and assisting him in the correct configuration of the algorithms. A sample workflow for protein c…

2018

Epigenetic features such as histone and DNA modifications are important mechanisms for the regulation of gene expression and for cell and tissue development. As a result, extensive efforts are currently undertaken using next-generation sequencing (NGS) to generate vast amounts of data regarding the epigenetic regulation of genomes. Several tools and frameworks for the processing of these NGS data have been developed in the last decade. Nevertheless, each user still bares the challenge to integrate all these tasks to perform the analysis. This procedure is not only tedious but also resource-intensive due to the putative large processing power involved. To automate, standardize and speed up t…

Galaxy LIMS for next-generation sequencing.

2013

Abstract Summary: We have developed a laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. The system provides lab technicians standard and customizable sample information forms, barcoded submission forms, tracking of input sample quality, multiplex-capable automatic flow cell design and automatically generated sample sheets to aid physical flow cell preparation. In addition, the platform provides the researcher with a user-friendly interface to create a request, submit accompanying samples, upload sample quality measurements and access to the sequencing results. As the LIMS is within the Galaxy platform, the …