Dataset Information

Watchdog - a workflow management system for the distributed analysis of large-scale experimental data.

ABSTRACT: BACKGROUND:The development of high-throughput experimental technologies, such as next-generation sequencing, have led to new challenges for handling, analyzing and integrating the resulting large and diverse datasets. Bioinformatical analysis of these data commonly requires a number of mutually dependent steps applied to numerous samples for multiple conditions and replicates. To support these analyses, a number of workflow management systems (WMSs) have been developed to allow automated execution of corresponding analysis workflows. Major advantages of WMSs are the easy reproducibility of results as well as the reusability of workflows or their components. RESULTS:In this article, we present Watchdog, a WMS for the automated analysis of large-scale experimental data. Main features include straightforward processing of replicate data, support for distributed computer systems, customizable error detection and manual intervention into workflow execution. Watchdog is implemented in Java and thus platform-independent and allows easy sharing of workflows and corresponding program modules. It provides a graphical user interface (GUI) for workflow construction using pre-defined modules as well as a helper script for creating new module definitions. Execution of workflows is possible using either the GUI or a command-line interface and a web-interface is provided for monitoring the execution status and intervening in case of errors. To illustrate its potentials on a real-life example, a comprehensive workflow and modules for the analysis of RNA-seq experiments were implemented and are provided with the software in addition to simple test examples. CONCLUSIONS:Watchdog is a powerful and flexible WMS for the analysis of large-scale high-throughput experiments. We believe it will greatly benefit both users with and without programming skills who want to develop and apply bioinformatical workflows with reasonable overhead. The software, example workflows and a comprehensive documentation are freely available at www.bio.ifi.lmu.de/watchdog.

SUBMITTER: Kluge M

PROVIDER: S-EPMC5850912 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundSAM (Self-help for Anxiety Management) is a mobile phone app that provides self-help for anxiety management. Launched in 2013, the app has achieved over one million downloads on the iOS and Android platform app stores. Key features of the app are anxiety monitoring, self-help techniques, and social support via a mobile forum ("the Social Cloud"). This paper presents unique insights into eMental health app usage patterns and explores user behaviors and usage of self-help techniques.ObjectiveThe objective of our study was to investigate behavioral engagement and to establish discernible usage patterns of the app linked to the features of anxiety monitoring, ratings of self-help techniques, and social participation.MethodsWe use data mining techniques on aggregate data obtained from 105,380 registered users of the app's cloud services.ResultsEngagement generally conformed to common mobile participation patterns with an inverted pyramid or "funnel" of engagement of increasing intensity. We further identified 4 distinct groups of behavioral engagement differentiated by levels of activity in anxiety monitoring and social feature usage. Anxiety levels among all monitoring users were markedly reduced in the first few days of usage with some bounce back effect thereafter. A small group of users demonstrated long-term anxiety reduction (using a robust measure), typically monitored for 12-110 days, with 10-30 discrete updates and showed low levels of social participation.ConclusionsThe data supported our expectation of different usage patterns, given flexible user journeys, and varying commitment in an unstructured mobile phone usage setting. We nevertheless show an aggregate trend of reduction in self-reported anxiety across all minimally-engaged users, while noting that due to the anonymized dataset, we did not have information on users also enrolled in therapy or other intervention while using the app. We find several commonalities between these app-based behavioral patterns and traditional therapy engagement.

Dataset Information

Watchdog - a workflow management system for the distributed analysis of large-scale experimental data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets