eDIKT Technical Workshop

 Date:   Tuesday March 20th 2007
 Start:  13:30
 Finish: 17:00
 Venue:  NeSC, Glasgow. Room 243f of the Kelvin Building.
         Also available via Access Grid in Edinburgh:
          - rm 3303, JCMB, King Buildings
          - Leith Room, NeSC, Old College

Purpose of Workshop

This eDIKT workshop will feature four talks from a variety of scientific research areas that make heavy use of computational resources. The speakers are Dr. Andrew Turner (School of Chemistry, University of Edinburgh), Dr. Paul Armitage (SFC Brain Imaging Research Centre, University of Edinburgh), Dr. Javier Santoyo-Lopez (GTI, University of Edinburgh) and Dr Russell Hamilton (Institute of Cell Biology, University of Edinburgh). Abstracts for the talks are included below.

The purpose of the workshop is for researchers to exchange knowledge and experience in research computing amongst interested parties.

The eDIKT (eScience Data, Information and Knowledge Transformation) project has been running since May 2002 and is using computational science to extract knowledge from vast datasets and simulation models. eDIKT is funded by the Scottish Funding Council.

For more information on eDIKT, see the project web site at http://www.edikt.org.

Preliminary Agenda

1330 Welcome. Mr Terry Sloan Terry_Sloan_edikt2_March_2007.ppt
1350 Chemistry. Dr. Andrew Turner Andrew_Turner_edikt2_March_2007.ppt , and two movies: azolink_water.wmv and cys_water.wmv
1430 Brain Imaging. Dr. Paul Armitage Paul_Armitage_edikt2_March_2007.ppt
1510 Coffee.
1530 GTI. Dr Javier Santoyo-Lopez Javier_Santoyo_edikt2_March_2007.ppt
1610 Cell Biology. Dr Russell Hamilton Russell_Hamilton_edikt2_March_2007.ppt
1650 Discussions and Wrap-up.
1700 Close.

Workshop Venue

The workshop will take place in Room 243f at the National e-Science Centre Hub at the University of Glasgow. Alternatively you can participate via Access Grid in virtual meeting room. If you would like further details on the Access Grid, please contact Jon Hill ( J.Hill@epcc.ed.ac.uk , 0131 651 3396). Edinburgh-based researchers can use the Access Grid facilities at either NeSC or EPCC.

Registration

Attendance at the workshop is free with no prior registration required however the organisers would appreciate it if you could contact Jon Hill ( J.Hill@epcc.ed.ac.uk , 0131 651 3396) beforehand with your name and the location you wish to attend from.

Useful Information

Kelvin Building (B8 on map): http://www.gla.ac.uk/general/maps/colourmap.pdf

Google Map of Kelvin Building: http://maps.google.co.uk/maps?f=q&hl=en&q=G12+8QQ&ie=UTF8&z=16&om=1&iwloc=addr

EPCC Access Grid Room (Room 3303): http://www.ed.ac.uk/maps/kings-buildings/james-clerk-maxwell-building/?sort=name&order=asc

Leith Room: http://www.ed.ac.uk/maps/central-area/old-college/?sort=name&order=asc

For more information please contact Jon Hill: J.Hill@epcc.ed.ac.uk 0131 651 3396

Abstracts

EaStCHEM Research Computing Facility: Computational chemistry for all

Dr Andrew Turner, School of Chemistry University of Edinburgh

Computational chemistry tools and the associated hardware have now reached the level where they can routinely investigate systems that are of direct interest to experimental chemists. Unfortunately, the majority of chemistry researchers lack the knowledge or skills to effectively exploit these tools. The EaStCHEM Research Computing Facility (RCF) is the first in-house service designed to address these problems. We aim to provide a route into computational chemistry for general chemistry researchers by providing access to the hardware, the software and, most importantly, the expertise that they need. The facility allows researchers to pursue their own research within an integrated environment that is designed to provide the support and tools they need.

In this presentation I will give an introduction to the EaStCHEM RCF, including a discussion of the ideas behind the service and how we have implemented them. I will also give examples of the types of problems that researchers have been investigating using the facility.

White Matter Tractography in the Human Brain

Dr Paul Armitage, SFC Brain Imaging Research Centre University of Edinburgh

Diffusion tensor magnetic resonance imaging (DT-MRI) is a non-invasive technique that produces images of molecular water diffusion in human tissues. DT-MRI provides information about the magnitude and directionality of diffusion in each component voxel of the image. This directionality information can be utilised to assess white matter connectivity in the brain by application of tractography algorithms that identify optimum white matter pathways connecting together different brain regions. In this talk, some of the issues surrounding tractography data management, visualisation and algorithm implementation will be discussed and the added value that research computing techniques can bring to solving these problems will be highlighted.

Development and implementation of novel software and hardware infrastructure to annotate and archive biological images and other digital biological information

Dr Russell Hamilton, Wellcome Trust Centre for Cell Biology University of Edinburgh

Researchers in Cell Biology are generating digital data requiring systematic storage, annotation and cataloguing. For example, Prof. Ilan Davis and his lab are using high resolution and rapid image capture microscopy to study RNA localization [1]. Several terabytes of multidimensional microscope images are captured per year and must be catalogued and stored in a reliable manner, moving away from the DVD and lab book systems currently used. The Open Microscopy Environment (OME)[2] is being investigated for the management of the microscope data. We have also been investigating the feasibility of implementing a data grid for cell biology, in conjunction with QCDGrid [3] and OME, as a means of making microscope image data available to collaborators. We are also starting to generate large amounts of microarray data and are addressing methods of managing and storing this data with the BioArray Software Environment (BASE2)[4].

Further to the management and storage of data we are providing software and tools to aid researchers. Recently we have developed ParticleStats to provide analysis of RNA particles tracked from microscope images. We have also provided tools to aid with the de-blurring of microscope images.

References;

Developing standards for high throughput RNA interference experiments

Dr Javier Santoyo-Lopez, Scottish Centre for Genomic Technology and Informatics University of Edinburgh

RNA interference (RNAi) is a natural post-transcriptional gene-silencing phenomenon that is being exploited to inhibit the expression of particular genes. Currently these experiments are carried out at a genome scale in a high- throughput fashion generating vast volumes of data. In this context standards and reporting guidelines are needed to describe unambiguously the experiments and to allow data exchange. To that end the Minimum Information About and RNAi Experiment (MIARE) has been created. Other technologies particularly those in the field of functional genomics have developed standards, like the Minimum Information about a Microarray Experiment (MIAME), that have fostered the mining of data making possible new discoveries.

MIARE aims to provide bioinformatics tools and scientific standards to support RNAi high throughput experiments. In particular MIARE core activities are the development of reporting guidelines, ontologies, object models and data exchange standards in order to enhance the accurate interpretation and mining of RNAi- based findings and to enable cross-discipline analysis. Currently the development of an object model using the Functional Genomics Experiment Object Model (FuGE) framework is in progress.