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

Ahmed Ibrahem Hafez; Beatriz Soriano; Aya Allah Elsayed; Ricardo Futami; Raquel Ceprian; Ricardo Ramos-Ruiz; Genis Martinez; Francisco Jose Roig; Miguel Angel Torres-Font; Fernando Naya-Catala; Josep Alvar Calduch-Giner; Lucia Trilla-Fuertes; Angelo Gamez-Pozo; Vicente Arnau; Jose Maria Sempere-Luna; Jaume Perez-Sanchez; Toni Gabaldon; Carlos Llorens

doi:10.3390/genes14020267

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

Genes (Basel). 2023 Jan 19;14(2):267. doi: 10.3390/genes14020267.

Authors

Ahmed Ibrahem Hafez^{1

2

3}, Beatriz Soriano^{1

4

5}, Aya Allah Elsayed^{1

6}, Ricardo Futami¹, Raquel Ceprian¹, Ricardo Ramos-Ruiz⁷, Genis Martinez¹, Francisco Jose Roig⁸, Miguel Angel Torres-Font^{1

9}, Fernando Naya-Catala⁴, Josep Alvar Calduch-Giner⁴, Lucia Trilla-Fuertes¹⁰, Angelo Gamez-Pozo^{10

11}, Vicente Arnau⁵, Jose Maria Sempere-Luna⁶, Jaume Perez-Sanchez⁴, Toni Gabaldon^{2

12

13

14}, Carlos Llorens¹

Affiliations

¹ Biotechvana, Parc Científic Universitat de València, 46980 Paterna, Spain.
² Faculty of Biomedical and Life Sciencies, Universitat Pompeu Fabra, 08002 Barcelona, Spain.
³ Faculty of Computers and Information, Minia University, Minia 61519, Egypt.
⁴ Institute of Aquaculture Torre de la Sal (IATS), Consejo Superior de Investigaciones Cientificas (CSIC), 12595 Castellón, Spain.
⁵ Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia y CSIC, UVEG-CSIC, 46980 Paterna, Spain.
⁶ Valencian Research Institute for Artificial Intelligence (VRAIN-UPV), Universitat Politècnica de València, 46022 Valencia, Spain.
⁷ Genomics Unit Cantoblanco, Parque Científico de Madrid, 28049 Madrid, Spain.
⁸ Facultad de Ciencias de la Salud, Universidad San Jorge, 50830 Zaragoza, Spain.
⁹ Escola Tècnica Superior d'Enginyeria, Universitat de València, 46100 Burjassot, Spain.
¹⁰ Biomedica Molecular Medicine SL, Parque Científico de Madrid, 28049 Madrid, Spain.
¹¹ Molecular Oncology and Pathology Lab, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain.
¹² Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.
¹³ Life Sciences, Barcelona Supercomputing Centre (BSC-CNS), 08034 Barcelona, Spain.
¹⁴ Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.

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.

Keywords: RNASeq; VariantSeq; artificial intelligence; interface environments; pipelines; resequencing; server-side; workflows.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
Databases, Factual
Humans
Software*
User-Computer Interface*
Workflow

Grants and funding

This work was supported by the Marie Sklodowska-Curie OPATHY project grant agreement 642095, the pre-doctoral research fellowship from MINECO Industrial Doctorates (Grant 659 DI-17-09134); Grant TSI-100903-2019-11 from the Secretary of State for Digital Advancement from Ministry of Economic Affairs and Digital Transformation, Spain; the Expedient IDI-2021-158274-a from the Ministry of Science and Innovation, Spain; and the ThinkInAzul program supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat Valenciana (THINKINAZUL/2021/024).