Last week I was invited by Prof. Werner Seiler to travel to Kassel (Hessen, Germany). I gave a talk about "Studying biosystems robustness, uncertainty, and other properties through symmetry analysis" at the research training group Multiscale Clocks. Lots of interesting discussions -- and ideas for future collaborations!
"Controllability and accessibility analysis of nonlinear biosystems" has been published at Computer Methods and Programs in Biomedicine: doi:10.1016/j.cmpb.2023.107837. In this paper we provide implementations of algorithms for testing nonlinear accessibility and controllability, and apply them to several systems of biomedical interest.
SELDOMpy is a python version of SELDOM, a method for building predictive signalling models. SELDOMpy has been developed by Luis Prado López under the supervision of David Henriques and Alejandro F. Villaverde. It is available in PyPI and GitHub.
Today, Gemma Massonis Feixas has successfully defended her PhD thesis. Entitled "Contributions to mechanistic modelling in systems biology: identifiability, symmetries and uncertainty quantification", it was co-supervised by Julio R. Banga and Alejandro F. Villaverde. Congratulations, Dr. Massonis!
Today, Sandra and Xabier are presenting posters at the CINBIO 6AM, which is the Annual Meeting of the Centre for Biomedical Research at the Universidade de Vigo.
This week, Alejandro F Villaverde is attending the SIAM conference in Algebraic Geometry ( SIAM AG23) in Eindhoven, to give a talk entitled "How Often Do We Encounter Locally-But-Not-Globally-Identifiable Parameters in Systems Biology, and Why?".
"On the origins and rarity of locally but not globally identifiable parameters in biological modeling" has been accepted at IEEE Access: doi:10.1109/ACCESS.2023.3288998. In this paper, Xabier Rey Barreiro and Alejandro F Villaverde investigate the difference between local and global identifiability in systems biology models.
This week we are hosting two visitors from Uni-Kassel: Prof. Werner Seiler and Meskerem Abebaw Mebratie. Today, Werner gave a talk titled "(Approximate) Symmetries of Differential Equations". Lots of intriguing stuff, with connections to identifiability and other structural properties. Looking forward to a fruitful collaboration!
Titled "Structural Identifiability and Observability of Microbial Community Models", it is included in a special issue of Bioengineering on "Role of Computational Methods for Living Systems at Different Scales": doi:10.3390/bioengineering10040483.
The BICO team will travel to Madrid to attend the "II Simposio Conjunto Grupos Temáticos CEA Ingeniería de Control y Modelado, Simulación y Optimización" (website), where Sandra and Xabier will discuss the progress of their PhD theses and present early results.
I (Alex) will participate in CITMAga CoLab days, an event that seeks to engage researchers from CITMAga in new collaborations. The topic I will propose is the possible use of symmetries for reachability analysis of dynamical biosystems. Looking forward to a fruitful exchange of ideas!
Titled "Distilling identifiable and interpretable dynamic models from biological data", it reports the latest results of a collaboration with Gemma Massonis and Julio R. Banga (MBG-CSIC). Check it out at bioRxiv here: doi:10.1101/2023.03.13.532340.
Dr. Alexander Browning (Mathematical Institute, University of Oxford) will visit the BICO team next monday, March 27th. At 11:00 he will give a talk about Identifying cell-to-cell variability using mathematical and statistical modelling at the "Aula de Grao", Escola de Enxeñaría Industrial, sede Campus (42.16803077019169, -8.689819747823226). Everybody is welcome to attend!
Sandra will talk about Propiedades estructurales en sistemas biológicos para control óptimo on March 1st, 17:00, as part of CITMAga's "seminarios de iniciación á investigación". More info here.
Our comparison of software tools that analyse structural identifiability and observability, which until now was only available as an arxiv preprint, has now been published in Bioinformatics.
The January 2023 issue of Bioinformatics includes two papers from our group: the first paper by Sandra and Xabo and a collaboration with Gemma Massonis and Julio Banga from MBG-CSIC.
The new release of the STRIKE-GOLDD toolbox avoids some approximation errors that might appear when analysing models with complex output functions. As always, it can be downloaded from its GitHub website.