Reactive Boolean Networks
Universidade de Aveiro –
In the context of biological regulatory networks, the connection between Piecewise-linear (PWL) models and Boolean networks is well-known, since Boolean networks can be seen as simplifications of PWL models. However, due to the abstraction of BN models, some asymptotic dynamics can be lost. This is observed since some steady states of a PWL model can be forgotten by the corresponding BN, not being signaled by terminals. Reactive Boolean networks (RBN) are an intermediary kind of model which is based on the notion of switch graph, as introduced by Marcelino and Gabbay. A switch graph is a generalized graph which includes special edges which grants a notion of “memory” to a usual graph. An adapted notion of terminal is obtained for RBN and it is shown that this class of model can recover asymptotic dynamics than Boolean networks.
Finally the concept of switch graph is generalized to include weights in edges. This produces a more general class of model and its application to model biological regulatory networks is explored.
Daniel Figueiredo is a final year PhD student of Applied Mathematics at Universidade de Aveiro, supervised by Manuel Antonio Martins (Dep. Mathematics – Universidade de Aveiro) and co-supervised by Luis Soares Barbosa (Dep. Computer Science – Universidade do Minho).
Date: 2019-Nov-07 Time: 10:00:00 Room: 336
For more information:
Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
The workshop is open to all members of these two projects but also, importantly, to the community in general.
The program and more details are available here.