Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy

Detalhes bibliográficos
Autor(a) principal: Pires, Jorge Guerra
Data de Publicação: 2021
Outros Autores: Silva, Gilberto Ferreira da, Weyssow, Thomas, Conforte, Alessandra Jordano, Pagnoncelli, Dante, Silva, Fabrício Alves Barbosa da, Carels, Nicolas
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/59580
Resumo: Oswaldo Cruz Foundation. Center for Technology Development in Health. Plataforma de Modelagem de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil.
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spelling Pires, Jorge GuerraSilva, Gilberto Ferreira daWeyssow, ThomasConforte, Alessandra JordanoPagnoncelli, DanteSilva, Fabrício Alves Barbosa daCarels, Nicolas2023-07-13T23:49:14Z2023-07-13T23:49:14Z2021PIRES, Jorge Guerra et al. Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy. Frontiers in Genetics, Switzerland, v. 12, p. 1-26, Feb. 2021.1664-8021https://www.arca.fiocruz.br/handle/icict/5958010.3389/FGENE.2021.6242591664-8021engFrontiers Media S.A.Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapyinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleOswaldo Cruz Foundation. Center for Technology Development in Health. Plataforma de Modelagem de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Center for Technology Development in Health. Plataforma de Modelagem de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil.Informatic Department. Free University of Brussels (ULB). Brussels, Belgium.Oswaldo Cruz Foundation. Center for Technology Development in Health. Plataforma de Modelagem de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil / Oswaldo Cruz Foundation. Presidency. Scientific Computing Program. Laboratório de Modelagem Computacional de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil.Instituto COI. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Presidency. Scientific Computing Program. Laboratório de Modelagem Computacional de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil.Oswaldo Cruz Foundation. Center for Technology Development in Health. Plataforma de Modelagem de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil.Fundação Oswaldo Cruz. Centro de Desenvolvimento Tecnológico em Saúde. Rio de Janeiro, RJ, Brasil.One aspect of personalized medicine is aiming at identifying specific targets for therapy considering the gene expression profile of each patient individually. The real-world implementation of this approach is better achieved by user-friendly bioinformatics systems for healthcare professionals. In this report, we present an online platform that endows users with an interface designed using MEAN stack supported by a Galaxy pipeline. This pipeline targets connection <i>hubs</i> in the subnetworks formed by the interactions between the proteins of genes that are up-regulated in tumors. This strategy has been proved to be suitable for the inhibition of tumor growth and metastasis <i>in vitro</i>. Therefore, Perl and Python scripts were enclosed in Galaxy for translating RNA-seq data into protein targets suitable for the chemotherapy of solid tumors. Consequently, we validated the process of target diagnosis by (i) reference to subnetwork entropy, (ii) the critical value of density probability of differential gene expression, and (iii) the inhibition of the most relevant targets according to TCGA and GDC data. Finally, the most relevant targets identified by the pipeline are stored in MongoDB and can be accessed through the aforementioned internet portal designed to be compatible with mobile or small devices through Angular libraries.Systems biologyTranslational oncologyPersonalized medicineGalaxyMEAN stackAngularProtein–protein networkShannon entropyinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txttext/plain1748https://www.arca.fiocruz.br/bitstream/icict/59580/1/license.txt8a4605be74aa9ea9d79846c1fba20a33MD51ORIGINAL10.3389_fgene.2021.624259.pdfapplication/pdf6038613https://www.arca.fiocruz.br/bitstream/icict/59580/2/10.3389_fgene.2021.624259.pdf0be67d028caec8ba099cbec399ea696bMD52icict/595802023-07-13 21:45:30.202oai:www.arca.fiocruz.br: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Repositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-07-14T00:45:30Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.en_US.fl_str_mv Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy
title Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy
spellingShingle Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy
Pires, Jorge Guerra
Systems biology
Translational oncology
Personalized medicine
Galaxy
MEAN stack
Angular
Protein–protein network
Shannon entropy
title_short Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy
title_full Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy
title_fullStr Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy
title_full_unstemmed Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy
title_sort Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy
author Pires, Jorge Guerra
author_facet Pires, Jorge Guerra
Silva, Gilberto Ferreira da
Weyssow, Thomas
Conforte, Alessandra Jordano
Pagnoncelli, Dante
Silva, Fabrício Alves Barbosa da
Carels, Nicolas
author_role author
author2 Silva, Gilberto Ferreira da
Weyssow, Thomas
Conforte, Alessandra Jordano
Pagnoncelli, Dante
Silva, Fabrício Alves Barbosa da
Carels, Nicolas
author2_role author
author
author
author
author
author
dc.contributor.author.fl_str_mv Pires, Jorge Guerra
Silva, Gilberto Ferreira da
Weyssow, Thomas
Conforte, Alessandra Jordano
Pagnoncelli, Dante
Silva, Fabrício Alves Barbosa da
Carels, Nicolas
dc.subject.en.en_US.fl_str_mv Systems biology
Translational oncology
Personalized medicine
Galaxy
MEAN stack
Angular
Protein–protein network
Shannon entropy
topic Systems biology
Translational oncology
Personalized medicine
Galaxy
MEAN stack
Angular
Protein–protein network
Shannon entropy
description Oswaldo Cruz Foundation. Center for Technology Development in Health. Plataforma de Modelagem de Sistemas Biológicos. Rio de Janeiro, RJ, Brazil.
publishDate 2021
dc.date.issued.fl_str_mv 2021
dc.date.accessioned.fl_str_mv 2023-07-13T23:49:14Z
dc.date.available.fl_str_mv 2023-07-13T23:49:14Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv PIRES, Jorge Guerra et al. Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy. Frontiers in Genetics, Switzerland, v. 12, p. 1-26, Feb. 2021.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/59580
dc.identifier.issn.en_US.fl_str_mv 1664-8021
dc.identifier.doi.none.fl_str_mv 10.3389/FGENE.2021.624259
dc.identifier.eissn.none.fl_str_mv 1664-8021
identifier_str_mv PIRES, Jorge Guerra et al. Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy. Frontiers in Genetics, Switzerland, v. 12, p. 1-26, Feb. 2021.
1664-8021
10.3389/FGENE.2021.624259
url https://www.arca.fiocruz.br/handle/icict/59580
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Frontiers Media S.A.
publisher.none.fl_str_mv Frontiers Media S.A.
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/59580/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/59580/2/10.3389_fgene.2021.624259.pdf
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
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