Group project for 3rd year Programming 3 module (Biomedical Engineering - Imperial College London) Team members: Andreas Polydorides, Marios Theodorou, Nestoras Neofytou, Nikolaos Katsis
Project title: Development of web-based database platform for translational systems biology and reduction of animal experiments
Project description as set by clients, Dr. Reiko Tanaka and PhD students Natasha Motsi and Tara Hameed:
" A translational systems biology approach has been successfully applied to diverse diseases, including cancers (Anderson & Quaranta 2008 Nat Rev Cancer) and trauma (Brown et al. 2015 Sci Trans Med), and contributed to the rational design of personalised treatment strategies based on mechanistic understanding. The key element of this approach is the development of mathematical models, i.e. mathematical description of the relevant biological processes and reactions. Systematic computational simulation of the mathematical models provides insights into the complex pathophysiological mechanisms.
A key step in the development of mathematical models for translational systems biology is model calibration using time-course data using animal experiments. However, locating and collecting data from the literature that is useful for model calibration is often very challenging because the focus of the experimentalists and the focus of quantitative computational modellers do not often overlap.
This project aims to develop a web-based platform for a database of the experimental data collated by our group and our collaborators to develop a mathematical model to understand the efficacy of novel immunotherapies for lung fungal infection. The website should allow and support the experimentalists to input their own time-course data from their animal experiments, along with their experimental set-up (meta-data). This will encourage increased interdisciplinary collaboration for translational systems biology, with a focus on making the data useable for mathematical modelling.
The website will also act as an interactive viewer for experimental data, equipped with a search engine and rudimentary data analysis. It will highlight whether the results sourced from different experimental labs, or even within labs, concur. Having a readily accessible, shared platform for viewing experimental data increases awareness of what data is missing from the field and reduces unnecessary animal experiments. "
The project is following an agile software development plan with an iterative lifecycle heavily influenced by frequent requirement gathering and attention to user stories.