Computational Biology at EBD

Institution: Estación Biológica de Doñana (EBD)

Members (researchers): Miguel Angel Fortuna

Home page: https://fortunalab.org
Contact email: fortuna@ebd.csic.es

Tools: Avida: a digital evolution software platform for studying evolution, OntoAvida, avidaR

There are no service units associated with this research group.

We do interdisciplinary research by combining mathematical and computational approaches with database analysis to harness the evolution of asexual populations of malignant cells, pathogens, and entire microbial communities.

Research topics:

Analysis packages (R, Python, etc.), Bioinformatics education, Biological Databases, Biological Ontologies, Cloud Computing, Computational models and simulations, Computational Techniques, Containers Computing, Data Repositories, Deep Learning in Biology, Ecological modelling, Evolutionary modelling, FAIRfication, High-performance Computing, Knowledge graphs, Microbial Communities, Phylogenetic Analysis, Population dynamics, Systems Biology, Web-service

Publications

Ortega, R., Wulff, E., & Fortuna, M. A. (2023). Ontology for the Avida digital evolution platform. Scientific Data, 10(1). https://doi.org/10.1038/s41597-023-02514-3

Ortega, R., & Fortuna, M. A. (2023). avidaR: an R library to perform complex queries on an ontology-based database of digital organisms. PeerJ Computer Science, 9, e1568. Portico. https://doi.org/10.7717/peerj-cs.1568

Fortuna, M. A. (2022). The phenotypic plasticity of an evolving digital organism. Royal Society Open Science, 9(9). https://doi.org/10.1098/rsos.220852

Fortuna, M. A., Beslon, G., & Ofria, C. (2022). Editorial: Digital evolution: Insights for biologists. Frontiers in Ecology and Evolution, 10. https://doi.org/10.3389/fevo.2022.1037040

Fortuna, M. A., Zaman, L., Wagner, A., & Bascompte, J. (2017). Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms. Philosophical Transactions of the Royal Society B: Biological Sciences, 372(1735), 20160431. https://doi.org/10.1098/rstb.2016.0431

Fortuna, M. A., Zaman, L., Wagner, A. P., & Ofria, C. (2013). Evolving Digital Ecological Networks. PLoS Computational Biology, 9(3), e1002928. https://doi.org/10.1371/journal.pcbi.1002928

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HPC Resources: We lead the Bioinformatics and Computational Biology (BCB) lab at the Estación Biológica de Doñana (EBD-CSIC), where we provide computational support for genomics and large-scale data analysis to researchers in ecology and evolutionary biology. In parallel, we are committed to advancing high-quality education and training programs in bioinformatics and data science (https://bcb.ebd.csic.es).