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Automated Experimentation (1)
Database: The Journal of Biological Databases and Curation (1)
Lurgi, Miguel (2)
Arús, Carles (1)
Barceló, Anna (1)
Candiota, Ana Paula (1)
Celda, Bernardo (1)
Estanyol, Francesc (1)
Ferrer-Luna, Rubén (1)
García, Alina (1)
Julià-Sapé, Margarida (1)
Martínez-Bisbal, M. Carmen (1)
Mier, Mariola (1)
Moreno-Torres, Àngel (1)
Rafael, Xavier (1)
Robertson, David (1)
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Strategies for annotation and curation of translational databases: the eTUMOUR project
Candiota, Ana Paula
Martínez-Bisbal, M. Carmen
Database: The Journal of Biological Databases and Curation
The eTUMOUR (eT) multi-centre project gathered in vivo and ex vivo magnetic resonance (MR) data, as well as transcriptomic and clinical information from brain tumour patients, with the purpose of improving the diagnostic and prognostic evaluation of future patients. In order to carry this out, among other work, a database—the eTDB—was developed. In addition to complex permission rules and software and management quality control (QC), it was necessary to develop anonymization, processing and data visualization tools for the data uploaded. It was also necessary to develop sophisticated curation strategies that involved on one hand, dedicated fields for QC-generated meta-data and specialized queries and global permissions for senior curators and on the other, to establish a set of metrics to quantify its contents. The indispensable dataset (ID), completeness and pairedness indices were set. The database contains 1317 cases created as a result of the eT project and 304 from a previous project, INTERPRET. The number of cases fulfilling the ID was 656. Completeness and pairedness were heterogeneous, depending on the data type involved.
Automated experimentation in ecological networks
In ecological networks, natural communities are studied from a complex systems perspective by representing interactions among species within them in the form of a graph, which is in turn analysed using mathematical tools. Topological features encountered in complex networks have been proved to provide the systems they represent with interesting attributes such as robustness and stability, which in ecological systems translates into the ability of communities to resist perturbations of different kinds. A focus of research in community ecology is on understanding the mechanisms by which these complex networks of interactions among species in a community arise. We employ an agent-based approach to model ecological processes operating at the species' interaction level for the study of the emergence of organisation in ecological networks.
We have designed protocols of interaction among agents in a multi-agent system based on ecological processes occurring at the interaction level between species in plant-animal mutualistic communities. Interaction models for agents coordination thus engineered facilitate the emergence of network features such as those found in ecological networks of interacting species, in our artificial societies of agents.
Agent based models developed in this way facilitate the automation of the design an execution of simulation experiments that allow for the exploration of diverse behavioural mechanisms believed to be responsible for community organisation in ecological communities. This automated way of conducting experiments empowers the study of ecological networks by exploiting the expressive power of interaction models specification in agent systems.
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