Implementing these approaches into routine laboratory procedures remains challenging, as they require the sequential execution of complex and variable protocols to extract and process the biologically relevant information from the raw sequence data. 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.Īdvances in next-generation sequencing (NGS) have changed the way researchers perform comparative analyses based on RNA-seq and variant-seq resequencing data (for an example review, see ). 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. “ 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. 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” are both available as desktop (RCP compilation) and web (RAP compilation) applications. 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. Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. 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). 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 part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The GPRO suite is an in-progress bioinformatic project for -omics data analysis.

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