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Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite

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Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite

dc.contributor.author	Hafez, Ahmed Ibrahem
dc.contributor.author	Soriano, Beatriz
dc.contributor.author	Elsayed, Aya Allah
dc.contributor.author	Futami, Ricardo
dc.contributor.author	Ceprián, Raquel
dc.contributor.author	Ramos-Ruiz, Ricardo
dc.contributor.author	Martínez, Genís
dc.contributor.author	Roig, Francisco Jose
dc.contributor.author	Torres-Font, Miguel Ángel
dc.contributor.author	Naya Catala, Fernando
dc.contributor.author	Calduch-Giner, Josep Alvar
dc.contributor.author	Trilla-Fuertes, Lucia
dc.contributor.author	Gámez-Pozo, Ángelo
dc.contributor.author	Arnau Llombart, Vicente
dc.contributor.author	Sempere-Luna, Jose Maria
dc.contributor.author	Pérez-Sánchez, Jaume
dc.contributor.author	Gabaldón, Toni
dc.contributor.author	Llorens, Carlos
dc.date.accessioned	2023-03-07T15:10:05Z
dc.date.available	2023-03-07T15:10:05Z
dc.date.issued	2023
dc.identifier.citation	Hafez, Ahmed Ibrahem Soriano, Beatriz Elsayed, Aya Allah Futami, Ricardo Ceprián, Raquel Ramos-Ruiz, Ricardo Martínez, Genís Roig, Francisco Jose Torres-Font, Miguel Ángel Naya Catala, Fernando Calduch-Giner, Josep Alvar Trilla-Fuertes, Lucia Gámez-Pozo, Ángelo Arnau Llombart, Vicente Sempere-Luna, Jose Maria Pérez-Sánchez, Jaume Gabaldón, Toni Llorens, Carlos 2023 Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite Genes 14 267 1 20
dc.identifier.uri	https://hdl.handle.net/10550/85702
dc.description.abstract	The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called 'RNASeq' and 'VariantSeq' to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, 'RNASeq' and 'VariantSeq' are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user's PC under any operating system or on remote servers, as a cloud solution. 'RNASeq' and 'VariantSeq' are both available as desktop (RCP compilation) and web (RAP compilation) applications. Each application has two execution modes: a step-by-step mode enables each step of the workflow to be executed independently, and a pipeline mode allows all steps to be run sequentially. 'RNASeq' and 'VariantSeq' also feature an experimental, online support system called GENIE that consists of a virtual (chatbot) assistant and a pipeline jobs panel coupled with an expert system. The chatbot can troubleshoot issues with the usage of each tool, the pipeline jobs panel provides information about the status of each computational job executed in the GPRO Server-Side, while the expert system provides the user with a potential recommendation to identify or fix failed analyses. Our solution is a ready-to-use topic specific platform that combines the user-friendliness, robustness, and security of desktop software, with the efficiency of cloud/web applications to manage pipelines and workflows based on command line interface software.
dc.language.iso	eng
dc.relation.ispartof	Genes, 2023, vol. 14, num. 267, p. 1-20
dc.subject	genomes
dc.title	Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite
dc.type	journal article	es_ES
dc.date.updated	2023-03-07T15:10:05Z
dc.identifier.doi	10.3390/genes14020267
dc.identifier.idgrec	157030
dc.rights.accessRights	open access	es_ES