Title here
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2023 Oxford Workshop
A workshop on cell-based Chaste: an introduction to basic functionality, and a showcase of the latest additions to the codebase.
Event details
Resources
Links to slides and practical materials are available at https://github.com/Chaste/chaste-workshop-materials-2023
Where
Doctoral Training Centre 1-4 Keble Road Oxford OX1 3NP UK
When
Monday 11 September to Thursday 14 September 2023
Details
We are pleased to announce a workshop on cell-based modelling within Chaste (Cancer, Heart and Soft-Tissue Environment), an open-source multi-scale framework for the computational modelling of biological systems. This software library consists of object-oriented C++ code, developed using an agile approach. All software is tested, robust, reliable and extensible. The library enables general simulations to be undertaken and includes tools to visualise, analyse and automatically curate and store simulation results, thus expediting model development.
The workshop will introduce Chaste’s basic functionality, and showcase the latest additions to the codebase, including more varied cell-based modelling approaches and a Python interface. Through a combination of lectures, case studies, and hands-on practicals, participants will learn how to implement and run simulations of several model biological systems. Time is also reserved for participants to receive help and tuition in how to apply Chaste to novel biological problems, including their own research.
This workshop is aimed at anyone with an interest in developing, or learning more about multi-scale computational cell based models. In order to get the most out of the workshop participants should have a working knowledge of C++ and some experience of mathematical modelling in the life sciences. On completion of the workshop, participants will be able to use Chaste to develop a basic simulation of a biological problem related to their research.
For additional information, please contact Fergus Cooper .
We have funding to cover accommodation and travel within the UK for PhD students and early career researchers attending this workshop.
We look forward to your participation!
Timetable
Monday 11 September (materials)
| Time | Description |
|---|---|
| 10:00-11:00 | Arrivals |
| 11:00-11:15 | Introduction and welcome |
| 11:15-12:30 | Lightning introductions from attendees |
| 12:00-12:45 | Introduction to vertex models, and other cell-based paradigms |
| Lunch | |
| 14:00-14:30 | Accommodation check in (for those staying at Wycliffe Hall, OX2 6PW) |
| 14:30-17:00 | Practical session, using the PyChaste python frontend for Chaste |
| 17:00-17:30 | Getting familiar with Chaste terminology and code structure |
Tuesday 12 September (materials)
| Time | Description |
|---|---|
| 09:30-10:00 | Scientific case study #1: Adrianna Zanca |
| 10:00-11:00 | Get up and running with Chaste in VS Code using Docker and C++ |
| 11:00-12:30 | Practical session, on how to use the C++ interface to make more substantial changes to models |
| 12:30-13:30 | Lunch |
| 13:30-14:00 | Scientific case study #2: Josh Bull |
| 14:00-16:30 | New functionality for implementing more detailed cell shape representations |
| 16:30-17:00 | Overview of the new Chaste infrastructure, and how to access help and support |
| 17:00-17:30 | Aside: an introduction to Research Software Engineering |
| 18:30-20:30 | Dinner at Brasserie Blanc |
Wednesday 13 September (materials)
| Time | Description |
|---|---|
| 09:30-10:00 | Scientific case study #3: Gary Mirams |
| 10:00-12:30 | Coupling cells/tissues to the microenvironment |
| 12:30-13:30 | Lunch |
| 13:30-14:00 | Scientific case study #4: Josh Moore |
| 14:00-16:00 | Modeling cell-environment feedback |
| 16:00-17:00 | Lightning wrapups |
Thursday 14 September (optional hackathon)
- Bring your own project, or
- Get help from the Chaste development team to get started with a model
Registration
We have funding to cover accommodation and travel within the UK for students and early career researchers attending this workshop.