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Tools available to integrate computational modelling and experimental biology

The lab’s publicly available codebases can be found on our Github page.

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The rigor and automation of mathematical and computational approaches can provide a powerful toolset to untangle biological complexity, but mathematical and experimental biology have largely evolved in isolation from one another. My lab follows a 'symbiotic approach' where modellers are encourage to spend time in the wetlab (and vice versa) to design and refine more predictive models based on first-hand experience of the experimental techniques, challenges and limitations as well as the latest biological data and results.

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Cell Simulation Software: the MemAgent-Spring Model is an agent-based model we have utilized and extended across a multitude of collaborations and projects to explore the role of VEGF/Notch signaling dynamics during different aspects of angiogenesis. It is currently available on request from Github) but a more user-friendly version is currently under development to aid its wider use and extendability for the community. 

Image analysis

We also aim to provide open source freely available image analysis software tools for the community, as much of our work is based on visual, spatial cell and tissue shape changes and structures, which can be hard or time consuming to quantify by hand alone.

We are already widely sharing our image analysis Patching software to help other groups quantify individual endothelial junctional patterns in blood vessels, which has resulted in several new collaborative publications. New automated features to this software are currently in development and can be tailored to specific projects on the fly). We are also developing a new image analysis pipeline to analyse blood vessel morphology in 3D by reconstructing from lighsheet microscopy.

Patching Image Analysis Software (Matlab) to analyse differential junction patterns (available on request and full training given).

Funimage: FIJI compatible confocal and lightsheet microscopy mouse retinal analysis software (available through collaboration currently).