Thursday 20th May
G47A, Flowers Building
Imperial College London,
The Flowers building is number 33 on the Campus map. It is swipe card access but I will be there outside to make sure you can all get in.
Catherine Canevet – Ondex: Data integration and visualisation
Ondex (http://ondex.org/) is a data integration platform which enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques. This talk describes its functionalities and a few application cases.
Christopher Barnes – ABC-SysBio – Approximate Bayesian Computation in Python with GPU support
Mathematical modelling has become ubiquitous in systems biology and there are many tools available to model biological systems. The Systems Biology Markup Language (SBML) framework, in which models are encoded in xml, has greatly aided this progression. However the models used in systems biology are usually of high dimension with many unknown parameters. Measuring parameter values in vivo can be difficult and measurements taken in vitro are often not applicable. Therefore, in a growing number of cases, the parameter values must be inferred from data such as time series measurements. Additionally there is often a set of competing models proposed to describe a process and the most appropriate model must be chosen given a set of measurements.
ABC-SysBio implements approximate Bayesian computation (ABC) methods for inference and model selection in dynamical systems. It is designed to work with models written in SBML and can perform inference for models described by ordinary differential equations (ODE), stochastic differential equations (SDE) and Markov jump processes (MJP). Algorithms for integrating these different types of processes have been implemented in CUDA which is an extension of the C language for execution on Nvidia graphical processing units (GPUs) which greatly reduces execution time.
In this talk I will give an overview of ABC methodology and then discuss its suitability for implementation on GPUs. I will talk about the features of GPU architecture and programming and in particular the use of different memory types. Finally I will discuss some examples from my research.
N Purswani, L. Tweedy, Z. Patel, C.Suriel-Melchor – DASbrick: A cloud based Rich internet application for Synthetic Biology Parts Registries.
Biobricks are an important standard in the emerging field of synthetic biology. These standardised genetic parts are essentially lego for geneticists (or at least the ones who don’t play with actual lego). They allow for an easy, modular approach to genetic engineering and their component-like nature is a valuable starting point for the computer aided design of complete genetic systems.
Such tools rely on informatics tool and a well-kept database is vital. The current repository for biobrick information is at MIT, and has been around since the inception of the idea. As such, it contains parts of multiple standards, and the quality of their annotation is extremely variable. There is a need for alternative tools, and DASBrick, a client-server system employing the widely used Distributed Annotation System, aims to address this need.
Location: Eastside Bar – Imperial College