Workshops

Workshops

Detailed overview of all workshops at the Conference:

Tuesday, Sept. 3rd

09:00am – 17:00pm (CEST)

Avicenna Day is an annual event focused on collaboration, innovation, and knowledge exchange in the field of in silico practice. You will enjoy the vibrant event features, presentations and round-table discussions by leading experts, showcasing the latest advancements in medical research and technology. Participants will explore the future of digital simulations and their transformative impact on medicine, science, and technology.

Empowering Innovation, Transforming Healthcare

Don’t miss this opportunity to engage with in silico leaders: mark your calendar, register today and join us on September 3rd to be an actor of the healthcare transformation.

Registration fee: 100 EUR

MORE INFORMATION

Tuesday, Sept. 3rd, afternoon

In Silico World is a four-year collaborative project funded by the European Commission to lower the barriers that slow down the adoption of In Silico Trials, the use of computer modelling and simulation in derisking new medical products.  As the project moves to its conclusion in December 2024, the project’s final meeting will be a public event where the consortium will present to the community all the resources (many available in open-access) that we developed to facilitate In Silico Trials.  These include validation data collections, resources to assist with regulatory qualification, resources to simplify communication with specific stakeholders, educational resources, resources for scalability and computational efficiency, and resources to find the appropriate business models and understand the ethical and legal aspects.  The event will conclude with refreshments served within a showcase where the 11 solutions for In Silico Trials developed in the project will be demoed.

Agenda

13:00 – 13:20 In Silico Trials: a SWOT analysis

Marco Viceconti, Alma Mater Studiorum – University of Bologna

13:20 – 13:40 Validation collections

Frans Van der Vosse

13:40 – 14:00 Regulatory resources

Francesco Pappalardo

14:00 – 14:20 Engagement resources

Liesbet Geris

14:20 – 14:40 Computational resources

Maciej Malawski

14:40 – 15:00 Educational resources

Jos vander Sloten

15:00 – 15:20 Business models

Vicenzo Carbone

15:20 – 15:40 Legal resources

Elisabetta Biasin

15:40 – 16:00 Conclusions

Panel discussion with all speakers

16:00 – 18:00 Showcase of the ISW solutions (refreshments will be served)

Target audience & learning objectives

The event interests all those with a professional or educational interest in In Silico Trials.  This includes biomedical engineering and biomedicine students, PhD students in medical technologies, academic researchers, industry experts working in the development and derisking of medical products, medical industry management, specialists in companies developing tools for In Silico Trials, experts in regulatory agencies and notified bodies, experts in legal and ethical issues in computational medicine, and healthcare managers and policymakers.

Friday, Sept. 6th, afternoon

Hands-on introduction to using the open-source CompuCell3D modeling environment to construct and execute compact and sharable multiscale, multicellular Virtual-Tissue models.

Multi-scale, Multicellular Agent-Based Virtual-Tissue models built using modeling frameworks like CompuCell3D are versatile tools for exploring the complex interactions between intracellular signaling and gene-regulatory networks, inter-cellular signaling through contact and diffusible signals, and force generation, cell migration and shape change. Among other applications the open-source modeling environment CompuCell3D has been used successfully to build models of vascular tumor growth and therapy, embryonic development, liver and developmental toxicology, lung infection, immune response and anti-viral therapies. This workshop will explore how CompuCell3D can simplify the construction of complex, extensible and reusable Virtual Tissue models. Members of the audience will build and explore models by downloading the software from (www.compucell3d.org) or run it on-line at (https://nanohub.org/resources/cc3dbase4x; free with required registration). .

Speaker(s)

Joel Vanin and Prof. James A. Glazier, Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47408, USA

Workshop Schedule

Introduction to CompuCell3D—Installing and Running CompuCell3D. Exercise—Angiogenesis simulation.

Principles of CompuCell3D Physics—Cells as spatially-extended computational agents. CPM/GGH Representation of cells, Representation of cell behaviors and interactions as Effective Energies and Constraints. Modified Metropolis Dynamics.

Representing CPM/GGH Models in CompuCell3D Scripts—CC3DML and Python model-specification basics.

Representing and solving complex networks in CompuCell3D. Loading network models into individual cells, specified in SBML, CellML, Antimony or MaBoSS. Coupling subcellular models between cells. Exercise—Cell-Cycle models.

Exercise—Exploring the interaction between subcellular networks and dynamic spatial organization. Building a simulation of Delta-Notch intracellular and juxtacrine signaling. Coupling to Cell-Cycle Models.

Introduction to chemical fields, diffusion, decay, secretion, absorption.

Coupling cells to chemical Fields. Exercise—Chemotaxis and nutrient-limited growth

Compartmental Cells and Links—Building Epithelia and Spatially Complex Cells

Using CompuCell3D as a Callable component in complex modeling workflows

Principles of Model Building and Debugging

Audience

Anyone interested in multicellular Virtual-Tissue modeling or in coupling network models to cell behaviors and dynamic spatial organization. Background: Some experience with basic Python programming helpful.

Learning Outcomes

Ability to use CompuCell3D to design, execute and explore Virtual-Tissue simulations integrating cells, networks and external chemical fields.

For more information: see https://www.compucell3d.org or contact jaglazier@gmail.com or joelvanin@gmail.com.

After Workshop Support: After the workshop we provide support for user’s further model development.

Computer Requirements

Any Windows or Mac computer. CompuCell3D is open-source and free. It also runs on many LINUX deployments (see www.compucell3d.org for details). CompuCell3D can also be run in a browser-based deployment on the nanoHUB public servers without a local installation.

Friday, Sept. 6th, afternoon

This 2-hour workshop on the importance of Public and Patient Involvement (PPI) in the field of in silico medicine aims to enhance the understanding of critical concepts among the research community, as well as the general public. When designed through extensive interdisciplinary collaboration, PPI can significantly enhance research and innovation (R&I). This approach ensures that outcomes and products are better aligned with the needs, concerns, and expectations of the society they are designed to benefit. The workshop will focus on three key objectives: increasing the general awareness of key concepts like PPI, co-creation, and in silico medicine, while highlighting the significant impact PPI can have on research and innovation (R&I) through real-life examples and testimonies of successful co-creation, and encouraging the participants to reflect on effective methods for involving patients in their research and innovation process. By the end of this hands-on session, attendees will gain valuable insights into the benefits of PPI and acquire the practical tools for meaningful patient engagement.

Tuesday, Sept. 3rd, afternoon

Introduction to Tellurium and Related Tools for Systems Biology Modeling

This workshop session is designed for systems biology modelers who wish to leverage the capabilities of Tellurium, a Python-based modeling environment. Participants will be introduced to the basics of Tellurium, including its installation, key features, and applications in systems biology. The session will cover essential concepts such as model construction via the simple Antimony model description language, simulation, and analysis using Tellurium’s intuitive syntax and integrated tools. Attendees will learn how to create models using SBML (Systems Biology Markup Language) and perform time-course simulations, and steady-state analysis. The tutorial will also delve into more advanced topics, such as model fitting, sensitivity analysis, and network visualization. By the end of the session, participants will have hands-on experience in building and analyzing systems biology models, enabling them to apply these skills to their research projects. This session is suitable for beginners with no prior experience in Tellurium, as well as for more experienced modelers looking to enhance their toolset. Some experience with Python is required. 

Organizers

Herbert M Sauro, Lucian Smith (University of Washington, Bioengineering, Seattle, USA)

Target Audience

VPH community and modelers in general (keywords: systems and synthetic biology modelers)

Agenda/ Learning Objectives

By the end of this tutorial, participants will be able to:
1. Install and Set Up Tellurium:
– Successfully install Tellurium.
– Navigate the Tellurium environment and its key features.
2. Understand Core Concepts of Systems Biology Modeling:
– Understand how biochemical network models are built.
3. Construct and Simulate Models:
– Create models using Antimony and generating the Systems Biology Markup Language (SBML).
– Execute time-course simulations to analyze dynamic behaviors of biological systems.
4. Perform Model Analysis:
– Conduct parameter scans to explore model behavior under varying conditions.
– Execute sensitivity analysis to identify key parameters influencing model outcomes.
5. Advanced Model Analysis:
– Examine the dynamic stability of some key model configurations.
– Draw network models using the SBML standard and annotate the diagram
6. Describe additional third-party tools that modelers can add to their toolbox
– Recommendations for parameter fitting
– Web-based tools such as makeSBML and the Antimony Web annotation tool
– Network drawing tools such as Alcuin

 

Friday, Sept. 6th, afternoon

Further information will follow soon.

Friday, Sep. 6th, afternoon

We have the ambition of developing virtual human models for clinical applications, both for populations (such as in virtual clinical trials) and for individuals – the so-called ‘Virtual Human Twin’, or VHT, which is often linked with continuously updated data from implantable and wearable devices. Along with many others, we are particularly interested in the development of virtual human models that are based on multiscale biophysically-based models that incorporate physiological function from the molecular level to the organ and organ system level in order that they can interpret clinical measurements from genetic testing, blood biomarkers, clinical imaging and physiological function testing. This is a huge undertaking that requires global collaboration and coordination. The European EDITH project, the New Zealand 12 Labours project, and the NIH funded SPARC portal are all contributing to this global effort. The goal of this workshop is to showcase plans and progress towards developing software tools, computational models, devices, datasets, and clinical applications to support these initiatives.

Organisers

Peter Hunter, David Nickerson, Prasad Babarenda Gamage, Greg Sands (Auckland Bioengineering Institute, University of Auckland, New Zealand)

Target audience

VPH community (keywords: multiscale modellers, digital twin developers and users, wearable device and clinical applications)

Agenda/Learning objectives

In the first part of the workshop, we will lead introductory discussion sessions to ensure all attendees are given a common starting point from which to launch into the examples and tutorials. We will discuss how the standards, tools, and practices used across these projects are being developed and could be applied in your projects. Throughout the discussions we will endeavour to point to the specific tools being used and where the capability is available via API or service for integration into other tools. In the second part, attendees will be encouraged to pick and choose from the range of guided tutorials that will be available in the following sections and work their way through the material on their own or in groups. We will provide guidance on specific pathways through the tutorials that aim to address specific use-cases, and instructors will be on hand to advise and discuss. The available instructors will include expert software developers and researchers.