2008
|
Journal ArticleAbel Gómez, Artur Boronat, José Á. Carsí, Isidro Ramos, Claudia Täubner, Silke Eckstein JISBD2007-03: Biological Data Processing using Model Driven Engineering In: IEEE Latin America Transactions, vol. 6, no. 4, pp. 324-331, 2008, ISSN: 1548-0992. Abstract | Links | BibTeX | Tags: Bioinformatics, Data Migration, Intergenomics, Model Driven Software Development (MDSD), Petri net (PN), Query/View/Transformation (QVT) @article{Gomez:IEEELatAm:2008,
title = {JISBD2007-03: Biological Data Processing using Model Driven Engineering},
author = {Abel G\'{o}mez and Artur Boronat and Jos\'{e} \'{A}. Cars\'{i} and Isidro Ramos and Claudia T\"{a}ubner and Silke Eckstein},
doi = {10.1109/TLA.2008.4815285},
issn = {1548-0992},
year = {2008},
date = {2008-08-01},
journal = {IEEE Latin America Transactions},
volume = {6},
number = {4},
pages = {324-331},
abstract = {This paper shows how model-driven software development (MDSD) can be applied in the bioinformatics field since biological data structures can be easily expressed by means of models. The existence of several heterogeneous data sources is usual in the bioinformatics context. In order to validate the information stored in these data sources, several formalisms and simulation tools have been adopted. The process of importing data from the source databases and introducing it in the simulation tools is usually done by hand. This work describes how to overcome this drawback by applying MDSD techniques (e.g. model transformations). Such techniques allow us to automate the data migration process between source databases and simulation tools, making the transformation process independent of the data persistence format, obtaining more modular tools and generating traceability information automatically.},
keywords = {Bioinformatics, Data Migration, Intergenomics, Model Driven Software Development (MDSD), Petri net (PN), Query/View/Transformation (QVT)},
pubstate = {published},
tppubtype = {article}
}
This paper shows how model-driven software development (MDSD) can be applied in the bioinformatics field since biological data structures can be easily expressed by means of models. The existence of several heterogeneous data sources is usual in the bioinformatics context. In order to validate the information stored in these data sources, several formalisms and simulation tools have been adopted. The process of importing data from the source databases and introducing it in the simulation tools is usually done by hand. This work describes how to overcome this drawback by applying MDSD techniques (e.g. model transformations). Such techniques allow us to automate the data migration process between source databases and simulation tools, making the transformation process independent of the data persistence format, obtaining more modular tools and generating traceability information automatically. Spanish |
ConferenceAbel Gómez, Artur Boronat, José Á. Carsí, Isidro Ramos Biological Data Transformation in Pathway Simulation Actas de las VIII Jornadas Nacionales de Bionformática (JNB 2008), Red Temática Nacional de Bioinformática, Valencia, Spain, 2008. Abstract | Links | BibTeX | Tags: Bioinformatics, Data Migration, Intergenomics, Petri net (PN), Query/View/Transformation (QVT) @conference{Gomez:JNB:2008,
title = {Biological Data Transformation in Pathway Simulation},
author = {Abel G\'{o}mez and Artur Boronat and Jos\'{e} \'{A}. Cars\'{i} and Isidro Ramos},
url = {https://abel.gomez.llana.me/wp-content/uploads/2017/11/gomez-jnb-2008.pdf},
year = {2008},
date = {2008-02-15},
booktitle = {Actas de las VIII Jornadas Nacionales de Bionform\'{a}tica (JNB 2008)},
publisher = {Red Tem\'{a}tica Nacional de Bioinform\'{a}tica},
address = {Valencia, Spain},
abstract = {This work shows how Model-Driven Software Development (MDSD) can be applied in the bioinformatics field since biological data structures can be easily expressed by means of models. The existence of several heterogeneous data sources is usual in the bioinformatics context. In order to validate the information stored in these data sources, several formalisms and simulation tools have been adopted. The process of importing data from the source databases and introducing it in the simulation tools is usually done by hand. This work describes how to overcome this drawback by applying MDSD techniques (e.g. model transformations). Such techniques allow us to automate the data migration process between source databases and simulation tools, making the transformation process independent of the data persistence format, obtaining more modular tools and generating traceability information automatically.},
keywords = {Bioinformatics, Data Migration, Intergenomics, Petri net (PN), Query/View/Transformation (QVT)},
pubstate = {published},
tppubtype = {conference}
}
This work shows how Model-Driven Software Development (MDSD) can be applied in the bioinformatics field since biological data structures can be easily expressed by means of models. The existence of several heterogeneous data sources is usual in the bioinformatics context. In order to validate the information stored in these data sources, several formalisms and simulation tools have been adopted. The process of importing data from the source databases and introducing it in the simulation tools is usually done by hand. This work describes how to overcome this drawback by applying MDSD techniques (e.g. model transformations). Such techniques allow us to automate the data migration process between source databases and simulation tools, making the transformation process independent of the data persistence format, obtaining more modular tools and generating traceability information automatically. Full Text AvailablePreprint |
2007
|
ConferenceAbel Gómez, José Á. Carsí, Artur Boronat, Isidro Ramos, Claudia Täubner, Silke Eckstein Biological Data Migration Using a Model-Driven Approach Proceedings of the 4th International Workshop on Language Engineering (ateM 2007), no. 4/2007, Mainzer Informatik-Berichte Johannes Gutenberg-Universität Mainz Institut für Informatik, 2007, ISSN: 0931-9972, (Nashville, TN, USA). Abstract | Links | BibTeX | Tags: Bioinformatics, Data Migration, Intergenomics, Model Driven Software Development (MDSD), Model Transformation (MT), Model-Driven Engineering (MDE), Petri net (PN), Query/View/Transformation (QVT) @conference{Gomez:ATEM:2007,
title = {Biological Data Migration Using a Model-Driven Approach},
author = {Abel G\'{o}mez and Jos\'{e} \'{A}. Cars\'{i} and Artur Boronat and Isidro Ramos and Claudia T\"{a}ubner and Silke Eckstein},
editor = {Jean-Marie Favre and Dragan Gasevic and Ralk L\"{a}mmel and Andreas Winter},
url = {https://abel.gomez.llana.me/wp-content/uploads/2017/11/gomez-atem-2007.pdf},
issn = {0931-9972},
year = {2007},
date = {2007-09-30},
booktitle = {Proceedings of the 4th International Workshop on Language Engineering (ateM 2007)},
number = {4/2007},
pages = {150--164},
publisher = {Institut f\"{u}r Informatik},
organization = {Johannes Gutenberg-Universit\"{a}t Mainz},
series = {Mainzer Informatik-Berichte},
abstract = {This paper shows how Model-Driven Software Development (MDSD) can be applied in the bioinformatics field since biological data structures can be easily expressed by means of models. The existence of several heterogeneous data sources is usual in the bioinformatics context. In order to validate the information stored in these data sources, several formalisms and simulation tools have been adopted. The process of importing data from the source databases and introducing it in the simulation tools is usually done by hand. This work describes how to overcome this drawback by applying MDSD techniques (e.g. model transformations). Such techniques allow us to automate the data migration process between source databases and simulation tools, making the transformation process independent of the data persistence format, obtaining more modular tools and generating traceability information automatically. },
note = {Nashville, TN, USA},
keywords = {Bioinformatics, Data Migration, Intergenomics, Model Driven Software Development (MDSD), Model Transformation (MT), Model-Driven Engineering (MDE), Petri net (PN), Query/View/Transformation (QVT)},
pubstate = {published},
tppubtype = {conference}
}
This paper shows how Model-Driven Software Development (MDSD) can be applied in the bioinformatics field since biological data structures can be easily expressed by means of models. The existence of several heterogeneous data sources is usual in the bioinformatics context. In order to validate the information stored in these data sources, several formalisms and simulation tools have been adopted. The process of importing data from the source databases and introducing it in the simulation tools is usually done by hand. This work describes how to overcome this drawback by applying MDSD techniques (e.g. model transformations). Such techniques allow us to automate the data migration process between source databases and simulation tools, making the transformation process independent of the data persistence format, obtaining more modular tools and generating traceability information automatically. Full Text AvailablePreprint |
ConferenceAbel Gómez, Artur Boronat, José Á. Carsí, Isidro Ramos, Claudia Täubner, Silke Eckstein Recuperación y procesado de datos biológicos mediante Ingeniería Dirigida por Modelos Actas de las XII Jornadas de Ingeniería del Software y Bases de Datos (JISBD 2007), Zaragoza, Spain, September 11-14, 2007., Thomson Editorial, 2007, ISBN: 978-84-9732-595-0. Abstract | Links | BibTeX | Tags: Bioinformatics, Data Migration, Intergenomics, Model Driven Software Development (MDSD), Model-Driven Development (MDD), Query/View/Transformation (QVT) @conference{Gomez:JISBD:2007,
title = {Recuperaci\'{o}n y procesado de datos biol\'{o}gicos mediante Ingenier\'{i}a Dirigida por Modelos},
author = {Abel G\'{o}mez and Artur Boronat and Jos\'{e} \'{A}. Cars\'{i} and Isidro Ramos and Claudia T\"{a}ubner and Silke Eckstein},
editor = {Xavier Franch},
url = {https://abel.gomez.llana.me/wp-content/uploads/2017/11/gomez-jisbd-2007.pdf},
isbn = {978-84-9732-595-0},
year = {2007},
date = {2007-09-11},
booktitle = {Actas de las XII Jornadas de Ingenier\'{i}a del Software y Bases de Datos (JISBD 2007), Zaragoza, Spain, September 11-14, 2007.},
pages = {275--284},
publisher = {Thomson Editorial},
abstract = {Este art\'{i}culo muestra c\'{o}mo el proceso de desarrollo de software dirigido por modelos (DSDM) es aplicable al campo de la bioinform\'{a}tica ya que la estructura de los datos biol\'{o}gicos se puede expresar mediante modelos de forma muy natural. En el contexto de la bioinform\'{a}tica es com\'{u}n la existencia de fuentes de datos (rellenadas de forma manual) heterog\'{e}neas. Con el objetivo de validar la informaci\'{o}n de estas fuentes de datos, se han adaptado diversos formalismos y herramientas de simulaci\'{o}n. El proceso de introducci\'{o}n de datos ---obtenidos de estas bases de datos--- en las herramientas de validaci\'{o}n se realiza tradicionalmente de forma manual. Este trabajo describe c\'{o}mo se ha resuelto este problema siguiendo una metodolog\'{i}a de DSDM empleando transformaciones de modelos. Esto permite automatizar el proceso de migraci\'{o}n de datos, obtener herramientas modulares, aislar el proceso de transformaci\'{o}n de datos de los formatos de persistencia de estos, y disponer de informaci\'{o}n de trazabilidad.},
keywords = {Bioinformatics, Data Migration, Intergenomics, Model Driven Software Development (MDSD), Model-Driven Development (MDD), Query/View/Transformation (QVT)},
pubstate = {published},
tppubtype = {conference}
}
Este artículo muestra cómo el proceso de desarrollo de software dirigido por modelos (DSDM) es aplicable al campo de la bioinformática ya que la estructura de los datos biológicos se puede expresar mediante modelos de forma muy natural. En el contexto de la bioinformática es común la existencia de fuentes de datos (rellenadas de forma manual) heterogéneas. Con el objetivo de validar la información de estas fuentes de datos, se han adaptado diversos formalismos y herramientas de simulación. El proceso de introducción de datos ---obtenidos de estas bases de datos--- en las herramientas de validación se realiza tradicionalmente de forma manual. Este trabajo describe cómo se ha resuelto este problema siguiendo una metodología de DSDM empleando transformaciones de modelos. Esto permite automatizar el proceso de migración de datos, obtener herramientas modulares, aislar el proceso de transformación de datos de los formatos de persistencia de estos, y disponer de información de trazabilidad. Full Text AvailablePreprintSpanish |