arXiv subjects

Tomas Perez-Acle

Publications and source records attributed to Tomas Perez-Acle.

3 recordsLinked to original sources

arXiv2025

The need to implement FAIR principles in biomolecular simulations

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a database that allows findability, accessibility, interoperability, and reusability of molecular dynamics simulation data. Such a development would democratize the field and significantly improve the impact of MD simulations on life science research. This will transform our working paradigm, pushing the field to a new frontier. We invite you to support our initiative at the MDDB community (https://mddbr.eu/community/) Now published as: Amaro, R.E., et al. The need to implement FAIR principles in biomolecular simulations. Nat Methods (2025) https://doi.org/10.1038/s41592-025-02635-0

q-bio.BM↗

arXiv2020

On the interplay between mobility and hospitalization capacity during the COVID-19 pandemic: The SEIRHUD model

Measures to reduce the impact of the COVID-19 pandemic require a mix of logistic, political and social capacity. Depending on the country, different approaches to increase hospitalization capacity or to properly apply lock-downs are observed. In order to better understand the impact of these measures we have developed a compartmental model which, on the one hand allows to calibrate the reduction of movement of people within and among different areas, and on the other hand it incorporates a hospitalization dynamics that differentiates the available kinds of treatment that infected people can receive. By bounding the hospitalization capacity, we are able to study in detail the interplay between mobility and hospitalization capacity.

q-bio.PE↗

arXiv2010

Conan: a platform for complex network analysis

Conan is a C++ library created for the accurate and efficient modelling, inference and analysis of complex networks. It implements the generation and modification of graphs according to several published models, as well as the unexpensive computation of global and local network properties. Other features include network inference and community detection. Furthermore, Conan provides a Python interface to facilitate the use of the library and its integration in currently existing applications. Conan is available at http://github.com/rhz/conan/.

q-bio.QM↗