Edinburgh Data-Intensive Research - DGEMap

An e-Infrastructure for Collaborative Research in Human Embryo Development

Jo.Newman — Thu, 17 Nov 2011 14:25:21 +0000

Using the DCC Lifecycle Model to Curate a Gene Expression Database: A Case Study

Jano.van.Hemert — Tue, 08 Dec 2009 09:09:27 +0000

An E-infrastructure to Support Collaborative Embryo Research

Jano.van.Hemert — Mon, 29 Jun 2009 10:49:57 +0000

New Staff: Dr Laura Valkonen

Jano.van.Hemert — Thu, 11 Jun 2009 13:59:31 +0000

We welcome Laura, who will be working on the DGEMap project until the end of July 2009.

Topic of this submission:

New staff

Projects:

DGEMap

New Staff: Dr Mark Collins

Jano.van.Hemert — Tue, 06 Jan 2009 14:05:10 +0000

We welcome Mark, who is going to work on the DGEMap project. Mark is a CEO of http://www.gulfstream-software.com/ and received his PhD from the School of Informatics.

Topic of this submission:

New staff

Projects:

DGEMap

New staff: Dr Jean O'Donoghue

Jano.van.Hemert — Thu, 21 Aug 2008 09:50:47 +0000

We welcome Jean, who is going to work on the Developmental Gene Expression Map project for the next couple of months. Jean previously worked at the MRC Human Genetics Unit.

Topic of this submission:

New staff

Projects:

DGEMap

An e-Infrastructure to Support Research in Human Embryo Development

Jano.van.Hemert — Fri, 15 Aug 2008 13:25:18 +0000

Speaker(s):

abarker1

Presentation Type:

talk

Characterising gene expression patterns is a crucial part of understanding the molecular determinants of embryonic development and the role of genes in disease. However, gene expression studies in human embryos need to overcome a number of difficulties. These include the sourcing and maintenance of collections of human material suitable for gene expression studies, bridging the expertise in both biological and informatics areas, and amassing and making accessible data from multiple laboratories and studies.

Embryonic gene expression studies are common place in model organisms such as drosophila (fly), mus musculus (mouse) and danio rerio (zebra fish), where procedures such as in-situ hybridisation allow scientists to detect and localise the presence of RNA transcriptomes that are likely to correspond to gene activity. This type of study is less common in humans, and currently only two laboratories are licensed in the UK to collect and analyse human embryonic tissue: the Human Developmental Biology Resource (HDBR) at Newcastle University and the MRC Fetal Tissue Bank (FTB) at University College London (UCL). Human embryonic material is extremely scarce world-wide, dissemination of the results to the wider community is therefore vital for the progression of research.

Date and time:

Tuesday, 9 September, 2008 - 16:00

Location:

e-Science All Hands Meeting 2008, Edinburgh, UK

Web site:

http://www.allhands.org.uk/

Projects:

DGEMap

Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns

Jano.van.Hemert — Fri, 20 Jun 2008 15:39:45 +0000

Speaker(s):

Jano.van.Hemert

Presentation Type:

talk

The Edinburgh Mouse Atlas aims to capture in-situ gene expression patterns in a common spatial framework. In this study, we construct a grammar to define spatial regions by combinations of these patterns. Combinations are formed by applying operators to curated gene expression patterns from the atlas, thereby resembling gene interactions in a spatial context. The space of combinations is searched using an evolutionary algorithm with the objective of finding the best match to a given target pattern. We evaluate the method by testing its robustness and the statistical significance of the results it finds.

Date and time:

Wednesday, 9 July, 2008 - 15:30

Location:

BioInformatics Research and Development 2008, Vienna, Austria.

Web site:

http://www.birdconf.org/

Projects:

DGEMap

Orchestrating Data Centric Workflows

Jano.van.Hemert — Fri, 20 Jun 2008 15:21:49 +0000

Speaker(s):

abarker1

Presentation Type:

talk

Date and time:

Tuesday, 5 February, 2008 - 12:00

Location:

Software Systems and Processes, Centre for Intelligent Systems and their Applications, School of Informatics. Edinburgh, UK.

Projects:

DGEMap

Eliminating the Middle Man: Distributing Dataflow in Scientific Workflows

Jano.van.Hemert — Fri, 20 Jun 2008 15:11:07 +0000

Speaker(s):

abarker1

Presentation Type:

talk

Efficiently executing large-scale, data-intensive workflows such as Montage must take into account the volume and pattern of communication. When orchestrating data-centric workflows, centralised servers common to standard workflow systems can become a bottleneck to performance. However, standards-based workflow systems that rely on centralisation, e.g., Web service based frameworks, have many other benefits such as a wide user base and sustained support.

This paper presents and evaluates a light-weight hybrid architecture which maintains the robustness and simplicity of centralised orchestration, but facilitates choreography by allowing services to exchange data directly with one another. Furthermore our architecture is standards compliment, flexible and is a non-disruptive solution; service definitions do not have to be altered prior to enactment. Our architecture could be realised within any existing workflow framework, in this paper, we focus on a Web service based framework.

Taking inspiration from Montage, a number of common workflow patterns (sequence, fan-in and fan-out), input to output data size relationships and network configurations are identified and evaluated. The performance analysis concludes that a substantial reduction in communication overhead results in a 2--4 fold performance benefit across all patterns. An end-to-end pattern through the Montage workflow results in an 8 fold performance benefit and demonstrates how the advantage of using our hybrid architecture increases as the complexity of a workflow grows.

Date and time:

Wednesday, 25 June, 2008 - 17:30

Location:

ACM/IEEE International Symposium on High-Performance and Distributed Computing

Web site:

http://www.hpdc.org/

Projects:

DGEMap