BioPipeline Creator—a user-friendly Java-based GUI for managing and customizing biological data pipelines
Abstract Bioinformatics tools are essential for performing analyses in the omics sciences. Given the numerous experimental opportunities arising from advances in the field of omics and easier access to high-throughput sequencing platforms, these tools play a fundamental role in research projects. De...
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Nature Portfolio
2024-07-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-024-67409-8 |
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| author | Cléo Maia Cordeiro Gislenne da Silva Moia Mônica Silva de Oliveira Lucas da Silva e Silva Maria Paula Cruz Schneider Sávio S. Costa Rafael Azevedo Baraúna Diego Assis das Graças Artur Silva Adonney Allan de Oliveira Veras |
| author_facet | Cléo Maia Cordeiro Gislenne da Silva Moia Mônica Silva de Oliveira Lucas da Silva e Silva Maria Paula Cruz Schneider Sávio S. Costa Rafael Azevedo Baraúna Diego Assis das Graças Artur Silva Adonney Allan de Oliveira Veras |
| author_sort | Cléo Maia Cordeiro |
| collection | DOAJ |
| description | Abstract Bioinformatics tools are essential for performing analyses in the omics sciences. Given the numerous experimental opportunities arising from advances in the field of omics and easier access to high-throughput sequencing platforms, these tools play a fundamental role in research projects. Despite the considerable progress made possible by the development of bioinformatics tools, some tools are tailored to specific analytical goals, leading to challenges for non-bioinformaticians who need to integrate the results of these specific tools into a customized pipeline. To solve this problem, we have developed the BioPipeline Creator, a user-friendly Java-based GUI that allows different software tools to be integrated into the repertoire while ensuring easy user interaction via an accessible graphical interface. Consisting of client and server software components, BioPipeline Creator provides an intuitive graphical interface that simplifies the use of various bioinformatics tools for users without advanced computer skills. It can run on less sophisticated devices or workstations, allowing users to keep their operating system without having to switch to another compatible system. The server is responsible for the processing tasks and can perform the analysis in the user's local or remote network structure. Compatible with the most important operating systems, available at https://github.com/allanverasce/bpc.git . |
| format | Article |
| id | doaj-art-a5e9c9bdb2ef4c8ba6a1dc4b5e8c661a |
| institution | OA Journals |
| issn | 2045-2322 |
| language | English |
| publishDate | 2024-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-a5e9c9bdb2ef4c8ba6a1dc4b5e8c661a2025-08-20T02:17:50ZengNature PortfolioScientific Reports2045-23222024-07-011411810.1038/s41598-024-67409-8BioPipeline Creator—a user-friendly Java-based GUI for managing and customizing biological data pipelinesCléo Maia Cordeiro0Gislenne da Silva Moia1Mônica Silva de Oliveira2Lucas da Silva e Silva3Maria Paula Cruz Schneider4Sávio S. Costa5Rafael Azevedo Baraúna6Diego Assis das Graças7Artur Silva8Adonney Allan de Oliveira Veras9Faculty of Computing, Federal University of Pará campus CastanhalPostgraduate Program in Applied Computing, Federal University of Pará campus Tucuruí ParáFederal Institute of Pará campus TucuruíCenter of Genomics and System Biologics, Federal University of ParáCenter of Genomics and System Biologics, Federal University of ParáBiological Engineering Laboratory, Guamá Science and Technology ParkBiological Engineering Laboratory, Guamá Science and Technology ParkBiological Engineering Laboratory, Guamá Science and Technology ParkBiological Engineering Laboratory, Guamá Science and Technology ParkBiological Engineering Laboratory, Guamá Science and Technology ParkAbstract Bioinformatics tools are essential for performing analyses in the omics sciences. Given the numerous experimental opportunities arising from advances in the field of omics and easier access to high-throughput sequencing platforms, these tools play a fundamental role in research projects. Despite the considerable progress made possible by the development of bioinformatics tools, some tools are tailored to specific analytical goals, leading to challenges for non-bioinformaticians who need to integrate the results of these specific tools into a customized pipeline. To solve this problem, we have developed the BioPipeline Creator, a user-friendly Java-based GUI that allows different software tools to be integrated into the repertoire while ensuring easy user interaction via an accessible graphical interface. Consisting of client and server software components, BioPipeline Creator provides an intuitive graphical interface that simplifies the use of various bioinformatics tools for users without advanced computer skills. It can run on less sophisticated devices or workstations, allowing users to keep their operating system without having to switch to another compatible system. The server is responsible for the processing tasks and can perform the analysis in the user's local or remote network structure. Compatible with the most important operating systems, available at https://github.com/allanverasce/bpc.git .https://doi.org/10.1038/s41598-024-67409-8Research reproducibilityCustomized pipelineBioinformatics |
| spellingShingle | Cléo Maia Cordeiro Gislenne da Silva Moia Mônica Silva de Oliveira Lucas da Silva e Silva Maria Paula Cruz Schneider Sávio S. Costa Rafael Azevedo Baraúna Diego Assis das Graças Artur Silva Adonney Allan de Oliveira Veras BioPipeline Creator—a user-friendly Java-based GUI for managing and customizing biological data pipelines Scientific Reports Research reproducibility Customized pipeline Bioinformatics |
| title | BioPipeline Creator—a user-friendly Java-based GUI for managing and customizing biological data pipelines |
| title_full | BioPipeline Creator—a user-friendly Java-based GUI for managing and customizing biological data pipelines |
| title_fullStr | BioPipeline Creator—a user-friendly Java-based GUI for managing and customizing biological data pipelines |
| title_full_unstemmed | BioPipeline Creator—a user-friendly Java-based GUI for managing and customizing biological data pipelines |
| title_short | BioPipeline Creator—a user-friendly Java-based GUI for managing and customizing biological data pipelines |
| title_sort | biopipeline creator a user friendly java based gui for managing and customizing biological data pipelines |
| topic | Research reproducibility Customized pipeline Bioinformatics |
| url | https://doi.org/10.1038/s41598-024-67409-8 |
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