Edinburgh Data-Intensive Research - Intuitive interfaces

Multi-Workflow Systems and Editors

Sandra.Gesing — Thu, 27 Jun 2013 11:39:10 +0000

Speaker(s):

Sandra.Gesing

Presentation Type:

talk

Researchers often need to use workflows that have been developed by other experts in their field to handle specific parts of their work. Sooner or later they find that they want to use workflows from multiple sources that are written in different languages. Enacting multi-lingual workflows (or meta workflows) has been pioneered in a group of European projects. The next step is to be able to change them when they don’t do exactly what you want. But that is not easy if you need to learn a different editor for each workflow language. The talk will conclude with the status of research underway to address this problem.

Attachment	Size
osdc2013WorkflowsSandraGesing.pdf	1.72 MB

Date and time:

Wednesday, 19 June, 2013 - 11:30

Location:

OSDC PIRE Workshop 2013, Edinburgh, UK

Web site:

OSDC PIRE Workshop

Research topics:

Biological/Medical Image Processing

MoSGrid - Molecular Simulations in a Distributed Environment

Sandra.Gesing — Thu, 27 Jun 2013 11:33:02 +0000

Speaker(s):

Sandra.Gesing

Presentation Type:

talk

Molecular simulations are indispensable methods in areas like material science, structural biology, and drug design. These methods address data-intensive and compute-intensive problems, which demand high-performance computing to allow data analysis in an acceptable time. The project MoSGrid (Molecular Simulation Grid) offers a workflow-enabled grid portal allowing access to molecular simulation tools on distributed resources in an intuitive manner. Users are able to exchange workflows and data via repositories and, thus, to exchange knowledge about the specific application domain. The talk will give an overview on the current MoSGrid portal, the underlying infrastructure, and an outlook on the next steps.

Attachment	Size
osdc2013MoSGridSandraGesing.pdf	4.77 MB

Date and time:

Tuesday, 18 June, 2013 - 12:00

Location:

OSDC PIRE Workshop 2013, Edinburgh, UK

Web site:

OSDC PIRE Workshop

Research topics:

RapidBrain: Developing a Portal for Brain Research Imaging

David.Rodriguez — Fri, 30 Sep 2011 10:46:02 +0000

Speaker(s):

David.Rodriguez

Presentation Type:

talk

Brain imaging researchers execute complex multistep workflows in their computational analysis. Those workflows often include applications that have very different user interfaces and sometimes use different data formats. A good example is the brain perfusion quantification workflow used at the BRIC (Brain Research Imaging Centre) in Edinburgh.
Rapid provides an easy method for creating portlets for computational jobs, and at the same it is extensible.
We have exploited this extensibility with additions that stretch the functionality beyond the original limits. These changes can be used by other projects to create their own portals, but it should be noted that the development of such portals involve a greater effort than the required in the regular use of Rapid for creating portlets. In our case it has been used to provide a user-friendly interface for perfusion analysis that covers from volume reconstruction to results visualisation.

Date and time:

Wednesday, 28 September, 2011 - 13:40

Location:

All Hands Meeting 2011, York

Projects:

SINAPSE

Research topics:

Generating web-based user interfaces for computational science

Jano.van.Hemert — Fri, 18 Feb 2011 09:31:04 +0000

Special Issue: Portals for life sciences---Providing intuitive access to bioinformatic tools

Jano.van.Hemert — Fri, 18 Feb 2011 09:22:33 +0000

Next Generation Embryology goes live

Jano.van.Hemert — Tue, 21 Sep 2010 15:02:53 +0000

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

Students will be able to query an anatomical component, for example the forebrain, and then navigate a 3D model of the embryo to zoom in on a specific area in the forebrain to find information on that area that has been deposited.

A version of the software is now live and can be found here http://aberlour.hgu.mrc.ac.uk/ngembryo/

Topic of this submission:

News

Research topics:

Projects:

NextGenerationEmbryology

Screencast: A Rapid portal for Parallel TCoffee running on HECToR

Jano.van.Hemert — Tue, 24 Aug 2010 08:30:01 +0000

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.

Topic of this submission:

Screen capture

Research topics:

Projects:

Rapid

Surfing for earthquakes

Jano.van.Hemert — Fri, 20 Aug 2010 18:33:50 +0000

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.

Seismologists measure vibrations in the Earth at hundreds of observatories across Europe which allows them to study earthquakes as they travel across countries and continents. By measuring the speed and strength of the vibrations at different sites, deductions can be made about the type of ground they have travelled through. From this information, the structure of the Earth can be constructed. The problem with earthquakes is that they don't occur when and where you need them.

Earthquakes aren't the only things that cause vibrations: road traffic, waves pounding on the beach and even wind and thunder can cause detectable vibrations. These vibrations – known as noise – may lack the strength of earthquakes, but they compensate by being available in huge numbers. If enough noise is analysed, it is possible to build up information about the Earth's structure. The analysis is not without problems "You can use noise to analyse the Earth's structure, but you need to analyse huge amounts of data and that's nearly impossible on standard [computers]" explained Andreas Rietbrock, who helped develop the new system with the Rapid team and is Professor of Seismology at the University of Liverpool.

The Orfeus foundation collects seismic data from around Europe and makes it available for analysis through websites like the Earthquake Data Portal (www.seismicportal.eu). Only a few organisations have the resources and technical know-how needed to process this vast store of data. Orfeus asked the Rapid team to develop a system that would allow any seismologist to analyse seismic data using powerful computers located around Europe. "We don't want [seismologists] to have to study how to access [remote] computer power and data" said Torild van Eck, Secretary General of Orfeus "Rapid is, for us, a tool to hide the tricky part of getting, steering and manipulating data".

The Rapid team have developed a reputation for helping scientists use their data, and have worked with everyone from chemists to medics and biologists to engineers. "It's been great working with the seismologists, because as a community they're very open to trying out new ways of working. And they have really pushed the boundaries of our technology" said Jano van Hemert, leader of the Rapid team. For Orfeus, the team developed a web portal. This takes all the complex computing needed for seismic analysis and hides it behind a standard web browser. By presenting all of the analysis tools in such a familiar environment, any seismologist—even the most technophobic ones—can use the system. One of the first applications for the Rapid web portal is to allow seismologists to study noise for the analysis of the Earth's structure. Rapid will build on this work with help from a grant from the UK's Natural Environment Research Council, which has provided funding to explore whether it is possible to predict earthquakes and volcanic eruptions.

The Rapid web portal allows even the smallest seismology groups to perform the kind of analysis that was previously limited to organisations that could afford their own supercomputers. By making this analysis easy, Rapid and Orfeus have brought complex research programmes into the hands of many more seismologists. More seismologists working together means that results are produced faster, and that means we could soon benefit from a better understanding of the ground beneath our feet.

(source: http://www.eurekalert.org/pub_releases/2010-08/uoe-sfe082010.php)

Topic of this submission:

Success story

Research topics:

Projects:

Rapid

Screencast:A Rapid portal for computational chemistry on HECToR, the UK-national academic supercomputer

Jano.van.Hemert — Fri, 13 Aug 2010 11:30:49 +0000

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

Topic of this submission:

Screen capture

Research topics: