TY - GEN
T1 - Considerations of graph-based concepts to manage of computational biology models and associated simulations
AU - Henkel, Ron
AU - Le Novère, Nicolas
AU - Wolkenhauer, Olaf
AU - Waltemath, Dagmar
N1 - Publisher Copyright:
© 2012 Gesellschaft fur Informatik (GI). All rights reserved.
PY - 2012
Y1 - 2012
N2 - Over the past years various databases in Life Sciences have been developed, among them databases to handle computational models of biological systems. Exchange formats that represent these models are typically XML-based; they encode models as networks. Models are published together with supplementary materials such as annotations, simulation experiment descriptions, or result sets. In consequence, not only model files need to be managed, but also the associated simulation setups, and highly linked meta-information. We discuss here the use of graph databases for model storage as they well reflect this interrelated nature. They can also enhance the integrated management of computational models and associated meta-information, as they handle connections between models, simulation descriptions and result data files, as well as external knowledge. This property enhances version control, retrieval and ranking, thereby resulting in improved model reuse and result reproducibility.
AB - Over the past years various databases in Life Sciences have been developed, among them databases to handle computational models of biological systems. Exchange formats that represent these models are typically XML-based; they encode models as networks. Models are published together with supplementary materials such as annotations, simulation experiment descriptions, or result sets. In consequence, not only model files need to be managed, but also the associated simulation setups, and highly linked meta-information. We discuss here the use of graph databases for model storage as they well reflect this interrelated nature. They can also enhance the integrated management of computational models and associated meta-information, as they handle connections between models, simulation descriptions and result data files, as well as external knowledge. This property enhances version control, retrieval and ranking, thereby resulting in improved model reuse and result reproducibility.
KW - Computational biology model
KW - Graph database
KW - Standards
KW - XML
UR - https://www.scopus.com/pages/publications/84904718597
M3 - Conference contribution
AN - SCOPUS:84904718597
T3 - Lecture Notes in Informatics (LNI), Proceedings - Series of the Gesellschaft fur Informatik (GI)
SP - 1545
EP - 1551
BT - Informatik 2012 - 42. Jahrestagung der Gesellschaft fur Informatik e.V. (GI)
A2 - Goltz, Ursula
A2 - Magnor, Marcus A.
A2 - Appelrath, Hans-Jurgen
A2 - Matthies, Herbert K.
A2 - Balke, Wolf-Tilo
A2 - Wolf, Lars C.
PB - Gesellschaft fur Informatik (GI)
T2 - 42. Jahrestagung der Gesellschaft fur Informatik e.V. ,GI, Informatik 2012 - 42nd Annual Meeting of the German Informatics Society (GI), Informatics 2012
Y2 - 16 September 2012 through 21 September 2012
ER -