Edinburgh Data-Intensive Research - Rapid

Web Portals for Computational Science

Gary.McGilvary — Sat, 30 Jun 2012 17:15:03 +0000

Speaker(s):

Presentation Type:

tutorial

Not every user knows how to submit a compute job by a remote login or to adapt to different job- submission systems when switching between facilities. In recognition, a recent trend is to provide web portals as an interface, which come in two types, each with its own major drawback. The first type consists of generic job-submission portals, which still require many technical specifics to be supplied by the user and much manual handling of data and results. The second type consists of domain-specific portals, which are expensive and time-consuming to build and maintain. In this tutorial we offer participants an overview of existing toolkits and frameworks for delivering portal solutions. We provide a basic hands-on tutorial on building portals and a more advanced hands-on session to deal with application and resource specific requirements.

Date and time:

Monday, 15 November, 2010 - 13:30

Location:

SC10, New Orleans, LA

Web site:

http://sc10.supercomputing.org/

Projects:

Rapid

New version Rapid 2.0 released!

Jos.Koetsier — Thu, 19 May 2011 14:23:12 +0000

Version:

2.0

With Rapid it is now even easier to develop advanced computational portals in a
very short time. The syntax has been simplified and many powerful features have
been added. A few examples:

- new 'static' variables
- better security options with ssh
- vastly improved 'browser' element
- simplified syntax
- array jobs
- 'id' and 'class' tags can make use of web frameworks
- Many bug fixes and internal changes to improve stability and performance.

Attachment	Size
rapid_basic_tutorial-2.0.pdf	351.05 KB
rapid_manual-2.0.pdf	235.17 KB

Download:

https://downloads.sourceforge.net/project/rapidportlet/rapidportlet-2.0.tgz?r=&t…

Projects:

Rapid

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

Ms Sandra Gesing

Jano.van.Hemert — Tue, 24 Aug 2010 09:33:07 +0000

Affiliation:

University of Tübingen, Germany

Sandra will work with Jano and Jos to develop a portal for mass spectrometry tools using Rapid. She is in room 2.23.

Dates:

15 Sep 2010 to 18 Sep 2010

Projects:

Rapid

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:

Collaborative environments

Intuitive interfaces

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:

Data-intensive computing

Collaborative environments

Intuitive interfaces

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:

Data-intensive computing

Collaborative environments

Intuitive interfaces

Projects:

Rapid

Rapid Version 1.5.1 Released

Jos.Koetsier — Thu, 12 Aug 2010 15:44:25 +0000

Version:

1.5.1

Minor bugfixes

Download:

https://downloads.sourceforge.net/project/rapidportlet/rapidportlet-1.5.1.tgz?r=…

Projects:

Rapid

Rapid Version 1.5.0 Released

Jos.Koetsier — Mon, 02 Aug 2010 18:11:13 +0000

Version:

1.5.0

This new version of Rapid uses a new and faster build system based on Ant and Ivy that generates smaller portlets. File Browsers are improved and can be used to select multiple files at once. Error reporting is improved with the addition of Schematron Rapid now checks a large number of referential constraints. The Code Generation system has been rewritten and a number of bugs have been fixed.

Attachment	Size
rapid_manual-1.5.0.pdf	184.02 KB
rapid_basic_tutorial-1.5.0.pdf	351.29 KB

Download:

https://downloads.sourceforge.net/project/rapidportlet/rapidportlet-1.5.0.tgz?us…

Projects:

Rapid