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- Title
Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite.
- Authors
Hafez, Ahmed Ibrahem; Soriano, Beatriz; Elsayed, Aya Allah; Futami, Ricardo; Ceprian, Raquel; Ramos-Ruiz, Ricardo; Martinez, Genis; Roig, Francisco Jose; Torres-Font, Miguel Angel; Naya-Catala, Fernando; Calduch-Giner, Josep Alvar; Trilla-Fuertes, Lucia; Gamez-Pozo, Angelo; Arnau, Vicente; Sempere-Luna, Jose Maria; Perez-Sanchez, Jaume; Gabaldon, Toni; Llorens, Carlos
- 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.
- Subjects
RNA sequencing; EXPERT systems; LINUX operating systems; CHATBOTS; THIRD-party software; STEVEDORES; WEB-based user interfaces
- Publication
Genes, 2023, Vol 14, Issue 2, p267
- ISSN
2073-4425
- Publication type
Article
- DOI
10.3390/genes14020267