We are delighted to welcome Donald MacDonald who is joining the Rapid-OMERO project developing its story from where Jos Koestier is leaving it.
He brings with him the experience of working in the OMERO team with Professor Jason Swedlow in Dundee, and earlier experience of data mining in Paisley.
NG Embryo aims to create an educational repository of developmental biology models that is:
- Accessible to researchers, teachers and students
- Searchable via annotated images rather than keywords and free text
- Able to map results onto 3D models of developing embryos
- Updated and enhanced with materials from researchers and lecturers throughout the world
- Free and available online
We show a screencast of a portlet created for Parallel TCoffee—the first parallel implementation of the TCoffee multiple sequence alignment tool. The portlet was developed using our Rapid technology and shows how TCoffee can be run on the UK National Academic Supercomputer HECToR. To see this demo you require Flash to be installed.
A better understanding of the ground beneath our feet will result from research by seismologists and Rapid—a group of computer scientists at the University of Edinburgh. The Earth's structure controls how earthquakes travel and the damage they can cause. A clear picture of this structure would be extremely valuable to earthquake planners, but it requires the analysis of huge amounts of data. The Rapid team developed a system that performs the seismologists' data-crunching, and have made it easy to use by relying on an interface familiar to all scientists – a web browser.
Below a screencast where Rapid was used to develop a portal for the UK-national academic supercomputer HECToR. The portal shows how to setup an advanced compute job involving computational chemistry. You need Flash installed in the browser to watch the video below. Click here for a large version
The inherent limits to the predictability of brittle failure events such as earthquakes and volcanic eruptions are important, unknown, and much debated. We will establish techniques to determine what this limit is in the ideal case of controlled laboratory tests, for the first time in real-time, prospective mode, meaning before failure has occurred.
Edinburgh Data-Intensive Research Data-intensive refers to huge volumes of data, complex patterns of data integration and analysis, and intricate interactions between data and users. Current methods and tools are failing to address data-intensive challenges effectively. They fail for several reasons, all of which are aspects of scalability.
Date and time:
Tuesday, 1 June, 2010 - 14:00
iDEA lab bio-medical data day, Informatics Forum, Edinburgh, UK
Modern cell and developmental biology and the now-established domain of systems biology use quantitative imaging methods to measure the location, dynamics and interaction of molecules in fixed and living cells, and at increasingly high spatial and temporal resolution. Quantitative imaging depends on the development, delivery, and use of sophisticated image processing and analysis algorithms. The availability of these data analysis tools is commonly cited as a major bottleneck in scientific discovery.
The Next Generation Embryology project is funded by JISC (Joint Information Systems Committee), a sponsor that supports education and research by promoting innovation in new technologies. The attached PDF flyer provides a brief introduction to the main aims of the project.
3D developmental atlases are used in research for capture, collation and analysis of spatio‐ temporal data such as in situ gene‐expression. The most advanced systems are based on a temporal series of 3D models. Examples are the EADHB human embryo atlas in Newcastle and the e‐MouseAtlas in Edinburgh. In this project, we use the 3D spatio‐temporal frameworks in conjunction with a repository to deliver research and educational materials directly in the context of the developing embryo.
Date and time:
Tuesday, 11 May, 2010 - 13:20
The Influence and Impact of Web 2.0 on Various Applications, e-Science Institute, Edinburgh, UK