PerMedCoE’s work will also be showcased in different activities at the 29th Conference on Intelligent Systems for Molecular Biology and 20th European Conference on Computational Biology (ISMB/ECCB 2021), which will be held virtually on 25-30 July 2021.


Virtual Booth

PerMedCoE’s virtual booth includes project resources, the opportunity to have a chat with our researchers and runs four sessions with live Q&A:

  • The HPC/Exascale Centre of Excellence in Personalised Medicine (Monday 26 July @ 15:20-16:20 UTC / 17:20-18:20 CEST)
  •  Building blocks and workflows (Tuesday 27 July @ 15:20-16:20 UTC / 17:20-18:20 CEST)
  • PerMedCoE Core Applications: PhysiCell-MPI, PhysiBoSS, COBREXA and CellNOpt/CARNIVAL (Wednesday 28 July @ 15:20-16:20 UTC / 17:20-18:20 CEST)
  • PerMedCoE Competency Hub and upcoming training (Thursday 29 July @ 15:20-16:20 UTC / 17:20-18:20 CEST)


PerMedCoE: A roadmap to scalability in Personalised Medicine

(Technology Track, Friday 30 July @ 13.20-14.00 UTC /15.20-16.00 CEST)

Author: José Carbonell-Caballero


PerMedCoE is a recently created European Center of Excellence (CoE) in personalized medicine. The main goal of the PerMedCoE project is to provide an efficient and sustainable roadmap to scale up a collection of relevant computational biology tools to leverage the next generation of HPC exascale platforms. This work will provide an ecosystem of tools and workflows that computational biology researchers will be able to apply to propose and test new and more complex biological hypotheses.

The selected core applications represent a set of open-source reference solutions for modelling and simulating different essential aspects of cell biology. Three tools aim at the simulation of intracellular models: MaBoSS and CellNOpt to simulate molecular signalling pathways through the use of Boolean models, and COBRA to simulate cellular metabolism as a constrained linear problem. The fourth one, PhysiCell, provides a physics-based framework designed to simulate the evolution and dynamics of a heterogeneous population of cells.

To achieve its goals, PerMedCoE will contribute to an extensive refactoring of these core applications, thus producing a considerable increase in speed-up and scalability. As a consequence, the new developments will support more complex and realistic cellular scenarios that usually demand a higher number of cells in multi-scale modelling simulations, more complex signalling pathways to properly address cell-type specificity, or the implementation of larger-scale models in metabolic studies, among others. At the end of the project, we will provide a rich computational framework to translate omics analyses into actionable models of cellular functions, with great importance to build patient-specific models in the context of emerging paradigms such as targeted therapy or personalised medicine.

In this presentation, we will summarize the main strategies we are following to scale up the selected core applications. As an example of the PerMedCoE approach, we will detail the ongoing work on PhysiCell, whose roadmap focuses on refactoring the official version to use the MPI protocol to address the simulation of real-sized tumours.


The PerMedCoE competency framework to guide the training programme

(Education COSI, Monday 26 July @ 11.40-12.00 UTC / 13.40-14.00 CEST)

Authors: Marta Lloret-Llinares, Joaquim Calbo, José Carbonell-Caballero, Javier Conejero, Esther Dorado-Ladera, Damjana Kastelic, Vera Matser, Ana M. Morales, Henrik Nortamo, Daniel Thomas-Lopez, Miguel Vazquez, Alessandra Villa


One of PerMedCoE’s goals is to organised a training programme to educate professionals in life sciences and HPC communities about the capabilities of PerMedCoE developments. We created a competency framework to define the training needs and, based on them, implement a training programme. A competency is an observable ability of any professional, integrating multiple components such as knowledge, skills and behaviours. The PerMedCoE framework lists the competencies for professionals within the scope of the CoE: developing cell-level simulation tools with the long-term vision of using them in the clinical context.

The competency framework will enable the definition of different professional profiles within its area of application, which can help people identify the abilities needed for working in a specific role (e.g. bioinformatician, tool developer), and therefore, inform their professional development. We will present the structure of the PerMedCoE competency framework, the first profiles created within it and how to explore it in the EMBL-EBI Competency Hub.

Click here to access the PerMedCoE Competency Framework.


Multiscale model of the different modes of invasion

(6th Annual SysMod Meeting, Thursday 29 July @ 12.40-12.55 UTC / 14.40-14.55 CEST)

Authors: Marco Ruscone, Arnau Montagud, Emmanuel Barillot, Andrei Zinovyev, Laurence Calzone and Vincent Noël


Mathematical models of biological processes are often represented as complex networks of signaling pathways, describing intracellular behaviors of specific cell types (epithelial, T cells, etc.). However, this representation prevents us from describing spatial information or cell-cell interactions, that plays an important role in the dynamics and gives a more complete view of a biological process. To test the effectiveness that comes from merging models of signalling pathways with spatial models of cell populations, we present a model of cell invasion made with PhysiBoSS, a multiscale framework which combines agent-based simulation and continuous time Markov processes applied on Boolean network.

The purpose of this model is to study the different modes of cell migration through an extracellular matrix by combining the spatial information obtained from the agent simulation and the intracellular information obtained from the possible stable states of the transcription factors signaling network. This includes different pathways involved in cell fates processes that can lead to death, proliferation, quiescence and invasion.

The model allows to simulate different initial conditions and mutations, as well as monitoring each cell behaviors using 2D and 3D representations, successfully reproducing single, collective and trail migration processes.


Interfacing systems biology standards with the Julia ecosystem

(Bioinformatics Open Source Conference BOSC 2021, poster)

Authors: Miroslav KratochvĂ­l, Laurent Heirendt, Samuel Isaacson, Paul F. Lang, Shahriar Iravanian, Anand Jain, Christopher Rackauckas, Christophe Trefois, Wei Gu and Reinhard Schneider


Julia is a general purpose programming language designed for simplifying and accelerating numerical analysis and computational science. Thanks to the efficiency of the high-level program representation and the tools available in the ecosystem for numerical physics and mathematics, the language is well suited for work on biochemical reaction systems.

We describe a set of three open source software packages that provide the systems biology community access to the high performance tools in Julia: Catalyst.jl, SBML.jl and CellMLToolkit.jl. Catalyst.jl is a domain specific language to create dynamic models of chemical reaction networks in Julia de novo. SBML.jl and CellMLToolkit.jl import SBML and CellML models, which are XML-based community standards for exchange and storage of biological models. Importing the data into Julia enables leveraging the available functionality for simulating and analyzing these models.

Importantly, the new library implementations provide us with major gains of efficiency and program simplicity, allowing rapid development and large-scale data processing that has not been feasible before. For example, we demonstrate that combined community models consisting of tens of millions total metabolic reactions may be constructed interactively on off-the-shelf hardware, and show the new applications of SciML on the imported datasets.


Panel Discussion: Online and hybrid education post-COVID

(Education COSI, Tuesday 27 July @ 14.20-15.20 UTC / 16.20-17.20 CEST)

PerMedCoE Panellist: Vera Matser

The PerMedCoE Training Work Package Leader, Vera Matser (EMBL-EBI), will participate in the panel discussion of the Education COSI.

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