Integrating Apache Airavata with Docker, Marathon, and Mesos

Saha, Pankaj; Govindaraju, Madhusudhan; Marru, Suresh; Pierce, Marlon

doi:10.1002/cpe.3708

Cited by 20 publications

(9 citation statements)

References 17 publications

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“…Once packaged, the Docker container is deployed onto a 16-node cluster managed using Apache Mesos ( 35 ). To maximize uptime, Mesosphere's Marathon software is used on top of Apache Mesos as a cluster-wide initialization and control system ( 36 ). The Marathon software automatically controls restarting Enrichr and moving resources across cluster nodes.…”

Section: Enhancements and Updatesmentioning

confidence: 99%

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

Kuleshov¹,

Jones²,

Rouillard³

et al. 2016

Nucleic Acids Res

7,896

6,858

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Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.

show abstract

Section: Enhancements and Updatesmentioning

confidence: 99%

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

Kuleshov¹,

Jones²,

Rouillard³

et al. 2016

Nucleic Acids Res

7,896

6,858

View full text Add to dashboard Cite

show abstract

“…The landing page and each organism web servers are running as separate Docker containers (39) deployed with Apache Mesos (40). Mesosphere Marathon (41) orchestrates these containers by scaling and automatically restoring applications to guarantee high-availability and fault-tolerance. The modEnrichr's ortholog conversion tool is a Flask web server that provides API for a MySQL database of orthologs of selected organisms extracted from OrthoDB v10 (42).…”

Section: Methodsmentioning

confidence: 99%

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

Kuleshov

Diaz

Flamholz

et al. 2019

Nucleic Acids Research

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High-throughput experiments produce increasingly large datasets that are difficult to analyze and integrate. While most data integration approaches focus on aligning metadata, data integration can be achieved by abstracting experimental results into gene sets. Such gene sets can be made available for reuse through gene set enrichment analysis tools such as Enrichr. Enrichr currently only supports gene sets compiled from human and mouse, limiting accessibility for investigators that study other model organisms. modEnrichr is an expansion of Enrichr for four model organisms: fish, fly, worm and yeast. The gene set libraries within FishEnrichr, FlyEnrichr, WormEnrichr and YeastEnrichr are created from the Gene Ontology, mRNA expression profiles, GeneRIF, pathway databases, protein domain databases and other organism-specific resources. Additionally, libraries were created by predicting gene function from RNA-seq co-expression data processed uniformly from the gene expression omnibus for each organism. The modEnrichr suite of tools provides the ability to convert gene lists across species using an ortholog conversion tool that automatically detects the species. For complex analyses, modEnrichr provides API access that enables submitting batch queries. In summary, modEnrichr leverages existing model organism databases and other resources to facilitate comprehensive hypothesis generation through data integration.

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“…The container runs on a HP ProLiant cluster managed using the native Docker support in Apache Mesos ( 21 ). To increase fault tolerance, scalability and uptime is managed via Mesosphere's Marathon ( 22 ). Marathon manages application health checks, balances load, and invokes restarts as well as switching across machines.…”

Section: Methodsmentioning

confidence: 99%

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

Clarke

Kuleshov

Schilder

et al. 2018

Nucleic Acids Research

147

108

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While gene expression data at the mRNA level can be globally and accurately measured, profiling the activity of cell signaling pathways is currently much more difficult. eXpression2Kinases (X2K) computationally predicts involvement of upstream cell signaling pathways, given a signature of differentially expressed genes. X2K first computes enrichment for transcription factors likely to regulate the expression of the differentially expressed genes. The next step of X2K connects these enriched transcription factors through known protein–protein interactions (PPIs) to construct a subnetwork. The final step performs kinase enrichment analysis on the members of the subnetwork. X2K Web is a new implementation of the original eXpression2Kinases algorithm with important enhancements. X2K Web includes many new transcription factor and kinase libraries, and PPI networks. For demonstration, thousands of gene expression signatures induced by kinase inhibitors, applied to six breast cancer cell lines, are provided for fetching directly into X2K Web. The results are displayed as interactive downloadable vector graphic network images and bar graphs. Benchmarking various settings via random permutations enabled the identification of an optimal set of parameters to be used as the default settings in X2K Web. X2K Web is freely available from http://X2K.cloud.

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Integrating Apache Airavata with Docker, Marathon, and Mesos

Cited by 20 publications

References 17 publications

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

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