ArticleBMC bioinformatics2018
Watchdog - a workflow management system for the distributed analysis of large-scale experimental data.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Retention of embryonic positional identity signatures in the adult sheep tail: evidence from HOXB13 spatial RNA expression gradients.Scientific reports · 2026Article
- CDK7-CDK11 axis in spliceosome regulation and pre-mRNA splicing.Nucleic acids research · 2025Article
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- HSV-1 infection induces a downstream shift of the +1 nucleosome.Journal of virology · 2025Article
- Whole blood RNA profiling in cats dissects the host immunological response during recovery from feline infectious peritonitis.PloS one · 2025Article
- The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes.Nature communications · 2023Article
- HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes.Journal of virology · 2023Article
- P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway.Nucleic acids research · 2023Article
- RegCFinder: targeted discovery of genomic subregions with differential read density.Bioinformatics advances · 2023Article
- RelB contributes to the survival, migration and lymphomagenesis of B cells with constitutively active CD40 signaling.Frontiers in immunology · 2022Article
- nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data.South African computer journal = Suid-Afrikaanse rekenaartydskrif · 2021Article
- Impact of concurrency on the performance of a whole exome sequencing pipeline.BMC bioinformatics · 2021Article
- Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution.GigaScience · 2020Article
- DolphinNext: a distributed data processing platform for high throughput genomics.BMC genomics · 2020Article
- Immunostimulatory RNA leads to functional reprogramming of myeloid-derived suppressor cells in pancreatic cancer.Journal for immunotherapy of cancer · 2019Article
- CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes.EMBO reports · 2019Article
- Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment.EBioMedicine · 2019Article
- MIR sequences recruit zinc finger protein ZNF768 to expressed genes.Nucleic acids research · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundThe 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.
resultsIn 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.
conclusionsWatchdog 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.