ArticleGigaScience2020
Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
7 citing papers in PubMed, 12 citations in OpenAlex.
- A scoping review of approaches to evaluating workflow management systems for bioinformatics users.Briefings in bioinformatics · 2026Article
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- 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
- RegCFinder: targeted discovery of genomic subregions with differential read density.Bioinformatics advances · 2023Article
- HSV-1 and influenza infection induce linear and circular splicing of the long NEAT1 isoform.PloS one · 2022Article
- Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution.GigaScience · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAdvances in high-throughput methods have brought new challenges for biological data analysis, often requiring many interdependent steps applied to a large number of samples. To address this challenge, workflow management systems, such as Watchdog, have been developed to support scientists in the (semi-)automated execution of large analysis workflows. IMPLEMENTATION: Here, we present Watchdog 2.0, which implements new developments for module creation, reusability, and documentation and for reproducibility of analyses and workflow execution. Developments include a graphical user interface for semi-automatic module creation from software help pages, sharing repositories for modules and workflows, and a standardized module documentation format. The latter allows generation of a customized reference book of public and user-specific modules. Furthermore, extensive logging of workflow execution, module and software versions, and explicit support for package managers and container virtualization now ensures reproducibility of results. A step-by-step analysis protocol generated from the log file may, e.g., serve as a draft of a manuscript methods section. Finally, 2 new execution modes were implemented. One allows resuming workflow execution after interruption or modification without rerunning successfully executed tasks not affected by changes. The second one allows detaching and reattaching to workflow execution on a local computer while tasks continue running on computer clusters.
conclusionsWatchdog 2.0 provides several new developments that we believe to be of benefit for large-scale bioinformatics analysis and that are not completely covered by other competing workflow management systems. The software itself, module and workflow repositories, and comprehensive documentation are freely available at https://www.bio.ifi.lmu.de/watchdog.
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What OpenQuestion holds
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.