NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts

Kurs, Jason P; Simi, Maria; Campagne, Fabien

doi:10.1101/041236

Cited by 14 publications

(11 citation statements)

References 18 publications

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“…We aligned reads to the mouse transcriptome downloaded from Ensembl (Mus_musculus.GRCm38.cdna.all.fa.gz). Alignment was run on a MacOS laptop with 16 GB of memory, using the NextflowWorkbench (66) to orchestrate alignment and count aggregation for the analyzed samples. RNA-Seq transcript counts were analyzed with analysis scripts written with the MetaR languages (67).…”

Section: Methodsmentioning

confidence: 99%

Correcting Smad1/5/8, mTOR, and VEGFR2 treats pathology in hereditary hemorrhagic telangiectasia models

Ruíz¹,

Zhao²,

Chandakkar³

et al. 2020

Journal of Clinical Investigation

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Hereditary hemorrhagic telangiectasia (HHT), a genetic bleeding disorder leading to systemic arteriovenous malformations (AVMs), is caused by loss-of-function mutations in the ALK1/ENG/Smad1/5/8 pathway. Evidence suggests that HHT pathogenesis strongly relies on overactivated PI3K/Akt/mTOR and VEGFR2 pathways in endothelial cells (ECs). In the BMP9/10-immunoblocked (BMP9/10ib) neonatal mouse model of HHT, we report here that the mTOR inhibitor, sirolimus, and the receptor tyrosine kinase inhibitor, nintedanib, could synergistically fully block, but also reversed, retinal AVMs to avert retinal bleeding and anemia. Sirolimus plus nintedanib prevented vascular pathology in the oral mucosa, lungs, and liver of the BMP9/10ib mice, as well as significantly reduced gastrointestinal bleeding and anemia in inducible ALK1-deficient adult mice. Mechanistically, in vivo in BMP9/10ib mouse ECs, sirolimus and nintedanib blocked the overactivation of mTOR and VEGFR2, respectively. Furthermore, we found that sirolimus activated ALK2-mediated Smad1/5/8 signaling in primary ECs-including in HHT patient blood outgrowth ECs-and partially rescued Smad1/5/8 activity in vivo in BMP9/10ib mouse ECs. These data demonstrate that the combined correction of endothelial Smad1/5/8, mTOR, and VEGFR2 pathways opposes HHT pathogenesis. Repurposing of sirolimus plus nintedanib might provide therapeutic benefit in patients with HHT.

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Section: Methodsmentioning

confidence: 99%

Correcting Smad1/5/8, mTOR, and VEGFR2 treats pathology in hereditary hemorrhagic telangiectasia models

Ruíz¹,

Zhao²,

Chandakkar³

et al. 2020

Journal of Clinical Investigation

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“…However, certain features described here are also used by existing workflow systems, 6,7,10–12 most notably the support for multiple infrastructures. Additionally, there are certain features not yet implemented in Rabix but which are seen in other systems, such as conditional steps in a workflow, as seen in Toil.…”

Section: Rabix In the Context Of Existing Workflow Models And Enginesmentioning

confidence: 99%

“…It is for this reason that we have developed the Rabix Executor (on GitHub as Project “Bunny”) a , an open-source workflow engine designed to support computational reproducibility/recomputability through the use of standard workflow descriptions, a software model that supports metadata integration, provenance over file organization, the ability to reuse workflows efficiently, and which combines an array of optimizations used separately in existing workflow execution methods. 6–12 …”

Section: Introductionmentioning

confidence: 99%

Rabix: An Open-Source Workflow Executor Supporting Recomputability and Interoperability of Workflow Descriptions

et al. 2016

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As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optimizations1 to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor a , an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions.

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“…It is for this reason that we have developed the Rabix Executor (on GitHub as Project "Bunny") a , an open-source workflow engine designed to support computational reproducibility/recomputability through the use of standard workflow descriptions, a software model that supports metadata integration, provenance over file organization, the ability to reuse workflows efficiently, and which combines an array of optimizations used separately in existing workflow execution methods. [6][7][8][9][10][11][12] For the 1.0 release of the Rabix Executor (or Rabix), we've focused on supporting the Common Workflow Language (CWL), an open, community-driven specification for describing tools and workflows with a focus on features that support reproducibility. 2 The Common Workflow Language is used to describe individual "processes" or "applications", which can be either a single tool or an entire workflow.…”

Section: Introductionmentioning

confidence: 99%

Rabix: an open-source workflow executor supporting recomputability and interoperability of workflow descriptions

Kaushik

Ivkovic

Simonovic

et al. 2016

Preprint

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As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optimizations 1 to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor a , an open-source workflow engine for

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NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts

Cited by 14 publications

References 18 publications

Correcting Smad1/5/8, mTOR, and VEGFR2 treats pathology in hereditary hemorrhagic telangiectasia models

Correcting Smad1/5/8, mTOR, and VEGFR2 treats pathology in hereditary hemorrhagic telangiectasia models

Rabix: An Open-Source Workflow Executor Supporting Recomputability and Interoperability of Workflow Descriptions

Rabix: an open-source workflow executor supporting recomputability and interoperability of workflow descriptions

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