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Research Seminar Series

We run a DIR Seminar Series where group members, visitors and guests present their work followed by lively discussions. The seminars are run every Friday at 10am in the Informatics Forum. The organiser of the series is Dr Rosa Filgueira Vicente.

We also list talks relevant to our work in the seminar series from the Centre for Intelligent Systems and their Applications (CISA), the Software Systems and Processes research group (SPP).

Wrapping Tools to Automate Workflows for Gene Therapy in Cystic Fibrosis

NeSC Research Seminar Series
Speaker: 
Rob Kitchen

Currently, the analysis of gene expression data generated by microarray and real-time PCR experiments is a slow process, often taking several weeks to properly process data from a small number of patients. In anticipation of a new clinical trial expected to involve 200 patients it is necessary to improve the efficiency of these analyses, through automation, in order to return meaningful biological data on a much shorter time scale.

Date and time: 
Wednesday, 17 October, 2007 - 11:00
Length: 
45 minutes
Location: 
Cramond
Projects: 

Detection of functional associations in gene expression data

Speaker: 
Attila Gyenesei

The application of mRNA gene expression microarrays has proven to be an invaluable tool for the elucidation of mechanisms of diverse biological processes at the molecular level. In a microarray experiment, several thousands of genes are investigated in parallel. Mainly due to the high costs of the microarrays, gene expression studies are normally carried out with a rather limited set of conditions and repetitions, featuring an experimental design that focuses on a few very specific research questions.

Date and time: 
Wednesday, 10 October, 2007 - 11:00
Length: 
45 minutes
Location: 
Leith

Decentralized Grid Resource Discovery Based on Semantic Similarity of Domain Ontology

Speaker: 
Liangxiu Han

One of open issues in grid computing is efficient resource discovery. Centralized solutions have been proved inefficient for global scale resource discovery. In addition, due to lacking of semantic support, the discovery mechanisms of current solutions do not have the flexibility to perform flexible resource matches for requirements of tasks or jobs.

Date and time: 
Wednesday, 3 October, 2007 - 11:00
Length: 
45 minutes
Location: 
Leith

Job Submission Portlets Described by One XML File

NeSC Research Seminar Series
Speaker: 
Jos Koetsier

We will develop a portlet that allows us to create rapidly and deploy job submissions portlets based on user requirements. The requirements are captured by using the portlet to build a job submission interface. The job submission interface is itself a portlet and can be shown to end-users immediately. More specifically, a designer or software engineer creates a set of parameters with defaults and parameter sweeps. The tool translates this in to a portlet, which the developer is able to deploy dynamically in to the same GridSphere portal.

Date and time: 
Wednesday, 26 September, 2007 - 11:00
Length: 
45 minutes
Location: 
Leith
Projects: 

Grid Computing for Multidisciplinary Optimisation

Speaker: 
Gokop Goteng

Multidisciplinary optimisation (MDO) problems bring together different professionals with diverse backgrounds to collaborate. These professionals are usually distributed in different geographical locations and often need to share resources such as data, information, algorithms, software, hardware, designs and expensive instruments among other things. Grid computing looks suitable for MDO applications with its distributed large-scale computational capabilities that enable virtual organisations to securely work together.

Date and time: 
Wednesday, 19 September, 2007 - 11:00
Length: 
45 minutes
Location: 
Cramond

Harnessing Volunteer Grids

Speaker: 
Jon Weissman

Volunteer Grids represent the most dynamic and unpredictable computing platform in the Grid space. Nodes may come and go, offer varying capabilities, and varying levels of reliability. Despite these "features" this is an attractive platform for scientific computing due to its scale and ease of management. Our research aim is to harness these open systems for a broader class of high performance e-science applications. We discuss one of the main obstacles to achieving this goal - how to effectively manage the inherent unreliability in the system.

Date and time: 
Wednesday, 5 September, 2007 - 11:00
Length: 
45 minutes
Location: 
Leith

The e-Science Institute Public Lecture - "Building a better (fly) brain"

Speaker: 
Douglas Armstrong

Mental Health accounts for 11% of global disease burden, it is growing rapidly yet it is one of the most challenging areas for drug discovery and development. Realistic models that capture the processes (and disorders) of the human brain would provide new insights into the diagnosis and treatment of such disorders. However, to achieve this, we need to begin by working from much simpler, more tractable models. The brain of the fruit-fly Drosophila contains in the region of 100,000 neurons.

Date and time: 
Friday, 2 November, 2007 - 16:00
Length: 
60 minutes
Location: 
Newhaven

Painting with Genes

Speaker: 
Jano van Hemert

The Edinburgh Mouse Atlas aims to capture in-situ gene expression patterns. In this study we construct a grammar to to define spatial regions by combinations of multiple patterns. These combinations are formed by using operators on curated gene expression patterns, which resemble gene interactions in a spatial context. The space of combinations is searched using an evolutionary algorithm with the objective of defining a target pattern.

Date and time: 
Wednesday, 22 August, 2007 - 11:00
Length: 
45 minutes
Location: 
Cramond

Building Gene Homologue Web Services

Speaker: 
Ian Archibald

There are many data resources relating to human and mouse genetics which can be integrated for the matching of specific genes. These resources however are present within various organizations at different locations. Compatibility between these datasets often requires conversions with respect to the gene ID systems in use. To make services such as inter-species homology available to bio-informaticians various methods involving matching genes and converting between different ID formats need to be created.

Date and time: 
Tuesday, 4 September, 2007 - 16:00
Length: 
60 minutes
Location: 
Newhaven

Wrapping Tools to Automate Workflows for Gene Expression Analyses in Cystic Fibrosis

NeSC Research Seminar Series
Speaker: 
Rob Kitchen

Currently, the analysis of gene expression data generated by microarray and real-time PCR experiments is a slow process, often taking several weeks to properly process data from a small number of patients. In anticipation of a new clinical trial expected to involve 200 patients it is necessary to improve the efficiency of these analyses, through automation, in order to return meaningful biological data on a much shorter time scale.

Date and time: 
Tuesday, 4 September, 2007 - 14:00
Length: 
60 minutes
Location: 
Newhaven
Projects: 

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