AIBench: a rapid application development framework for translational research in biomedicine
Autor(a) principal: | |
---|---|
Data de Publicação: | 2010 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/24302 |
Resumo: | Applied research in both biomedical discovery and translational medicine today often requires the rapid development of fully featured applications containing both advanced and specific functionalities, for real use in practice. In this context, new tools are demanded that allowfor efficient generation, deployment and reutilization of such biomedical applications as well as their associated functionalities. In this context this paper presents AIBench, an open-source Java desktop application framework for scientific software development with the goal of providing support to both fundamental and applied research in the domain of translational biomedicine. AIBench incorporates a powerful plug-in engine, a flexible scripting platform and takes advantage of Java annotations, reflection and various design principles in order to make it easy to use, lightweight and non-intrusive. By following a basic input–processing–output life cycle, it is possible to fully develop multiplatform applications using only three types of concepts: operations, data-types and views. The framework automatically provides functionalities that are present in a typical scientific application including user parameter definition, logging facilities, multi-threading execution, experiment repeatability and user interface workflow management, among others. The proposed framework architecture defines a reusable component model which also allows assembling new applications by the reuse of libraries from past projects or third-party software. |
id |
RCAP_b8a505acb5056e932ba0a05a139eaaff |
---|---|
oai_identifier_str |
oai:repositorium.sdum.uminho.pt:1822/24302 |
network_acronym_str |
RCAP |
network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository_id_str |
7160 |
spelling |
AIBench: a rapid application development framework for translational research in biomedicineScientific software developmentBiomedical informaticsOpen softwareReusable component modelApplication frameworkScience & TechnologyApplied research in both biomedical discovery and translational medicine today often requires the rapid development of fully featured applications containing both advanced and specific functionalities, for real use in practice. In this context, new tools are demanded that allowfor efficient generation, deployment and reutilization of such biomedical applications as well as their associated functionalities. In this context this paper presents AIBench, an open-source Java desktop application framework for scientific software development with the goal of providing support to both fundamental and applied research in the domain of translational biomedicine. AIBench incorporates a powerful plug-in engine, a flexible scripting platform and takes advantage of Java annotations, reflection and various design principles in order to make it easy to use, lightweight and non-intrusive. By following a basic input–processing–output life cycle, it is possible to fully develop multiplatform applications using only three types of concepts: operations, data-types and views. The framework automatically provides functionalities that are present in a typical scientific application including user parameter definition, logging facilities, multi-threading execution, experiment repeatability and user interface workflow management, among others. The proposed framework architecture defines a reusable component model which also allows assembling new applications by the reuse of libraries from past projects or third-party software.This work was partially supported by the Integrated Action Development of computational tools for cancer diagnosis using gene expression data (HP2006-0125) between Portugal (University of Minho) and Spain (University of Vigo), the project Development of biomedical applications (09VIB10) from University of Vigo and the project MEDICAL-BENCH: Platform for the development and integration of knowledge-based data mining techniques and their application to the clinical domain (TIN2009-14057-C03-02) from Ministry of Science and Innovation. D. Glez-Peria acknowledges Xunta de Galicia (Spain) for the program Maria Barbeito. We would also like to thank all those involved in the implementation of the OptFlux, @Note and GOABench applications referred to in Section 4, namely: Isabel Rocha, Analia Lourenco, Eugenio Ferreira, Pedro Evangelista, Rafael Carreira, Jose P. Pinto, Ruben Romero, Pablo Ferreiro and Jose R. Mendez.ElsevierElsevier BVUniversidade do MinhoRocha, MiguelGlez-Peña, DanielReboiro-Jato, M.Maia, P.Díaz, FernandoFdez-Riverola, Florentino20102010-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/24302eng0169-260710.1016/j.cmpb.2009.12.00320047774info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:52:05Zoai:repositorium.sdum.uminho.pt:1822/24302Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:51:08.653382Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
AIBench: a rapid application development framework for translational research in biomedicine |
title |
AIBench: a rapid application development framework for translational research in biomedicine |
spellingShingle |
AIBench: a rapid application development framework for translational research in biomedicine Rocha, Miguel Scientific software development Biomedical informatics Open software Reusable component model Application framework Science & Technology |
title_short |
AIBench: a rapid application development framework for translational research in biomedicine |
title_full |
AIBench: a rapid application development framework for translational research in biomedicine |
title_fullStr |
AIBench: a rapid application development framework for translational research in biomedicine |
title_full_unstemmed |
AIBench: a rapid application development framework for translational research in biomedicine |
title_sort |
AIBench: a rapid application development framework for translational research in biomedicine |
author |
Rocha, Miguel |
author_facet |
Rocha, Miguel Glez-Peña, Daniel Reboiro-Jato, M. Maia, P. Díaz, Fernando Fdez-Riverola, Florentino |
author_role |
author |
author2 |
Glez-Peña, Daniel Reboiro-Jato, M. Maia, P. Díaz, Fernando Fdez-Riverola, Florentino |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Rocha, Miguel Glez-Peña, Daniel Reboiro-Jato, M. Maia, P. Díaz, Fernando Fdez-Riverola, Florentino |
dc.subject.por.fl_str_mv |
Scientific software development Biomedical informatics Open software Reusable component model Application framework Science & Technology |
topic |
Scientific software development Biomedical informatics Open software Reusable component model Application framework Science & Technology |
description |
Applied research in both biomedical discovery and translational medicine today often requires the rapid development of fully featured applications containing both advanced and specific functionalities, for real use in practice. In this context, new tools are demanded that allowfor efficient generation, deployment and reutilization of such biomedical applications as well as their associated functionalities. In this context this paper presents AIBench, an open-source Java desktop application framework for scientific software development with the goal of providing support to both fundamental and applied research in the domain of translational biomedicine. AIBench incorporates a powerful plug-in engine, a flexible scripting platform and takes advantage of Java annotations, reflection and various design principles in order to make it easy to use, lightweight and non-intrusive. By following a basic input–processing–output life cycle, it is possible to fully develop multiplatform applications using only three types of concepts: operations, data-types and views. The framework automatically provides functionalities that are present in a typical scientific application including user parameter definition, logging facilities, multi-threading execution, experiment repeatability and user interface workflow management, among others. The proposed framework architecture defines a reusable component model which also allows assembling new applications by the reuse of libraries from past projects or third-party software. |
publishDate |
2010 |
dc.date.none.fl_str_mv |
2010 2010-01-01T00:00:00Z |
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.uri.fl_str_mv |
http://hdl.handle.net/1822/24302 |
url |
http://hdl.handle.net/1822/24302 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
0169-2607 10.1016/j.cmpb.2009.12.003 20047774 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Elsevier Elsevier BV |
publisher.none.fl_str_mv |
Elsevier Elsevier BV |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
|
_version_ |
1799133098618650624 |