Edinburgh Data-Intensive Research - Reusable computational models

Universiteit van Amsterdam

Common Operations of Environmental Research Infrastructures

Paul.Martin — Tue, 08 Nov 2011 12:57:25 +0000

From the ENVRI Description of Work: "Frontier environmental research increasingly depends on a wide range of data and advanced capabilities to process and analyse them. The ENVRI project, 'Common Operations of Environmental Research Infrastructures' is a collaboration in the ESFRI Environment Cluster, with support from ICT experts, to develop common e-science components and services for their facilities. The results will speed up the construction of these infrastructures and will allow scientists to use the data and software from each facility to enable multi-disciplinary science."

"The target is on developing common capabilities including software and services of the environmental and e-infrastructure communities. While the ENVRI infrastructures are very diverse, they face common challenges including data capture from distributed sensors, metadata standardisation, management of high volume data, workflow execution and data visualisation. The common standards, deployable services and tools developed will be adopted by each infrastructure as it progresses through its construction phase. Two use cases, led by the most mature infrastructures, will focus the development work on separate requirements and solutions for data pre-processing of primary data and post-processing toward publishing. The project will be based on a common reference model created by capturing the semantic resources of each ESFRI-ENV infrastructure. This model and the development driven by the testbed deployments result in ready-to-use systems which can be integrated into the environmental research infrastructures. The project puts emphasis on synergy between advanced developments, not only among the infrastructure facilities, but also with ICT providers and related e-science initiatives. These links will facilitate system deployment and the training of future researchers, and ensure that the inter-disciplinary capabilities established here remain sustainable beyond the lifetime of the project."

The Data Intensive Group will be working principally on constructing an infrastructure reference model which ensures system interoperability.

Acronym:

ENVRI

Web site:

ENVRI website

Funding body:

EU/FP7

Value:

€5100000

Dates:

1 November 2011 to 31 October 2014

Project members:

Malcolm.Atkinson

Paul.Martin

Partners:

Cardiff University

Umweltbundesamt GmbH, Environment Agency Austria

European Space Agency

Consiglio Nazionale delle Ricerche - Istituto di Scienza e Tecnologie dell'Informazione

Research topics:

Project Status:

In progress

DISPEL Reference Manual

Paul.Martin — Thu, 15 Sep 2011 09:18:13 +0000

Attachment	Size
manual.pdf	794.11 KB

GeoScience meets Informatics

Jano.van.Hemert — Thu, 01 Apr 2010 09:06:14 +0000

NeSC Research Seminar Series

Speaker:

Ian Main, Mark Naylor and Andrew Bell

The agenda of this meeting will be flexible, the aim is to provide the informaticians with an understanding of the specific challenges in monitoring, analysis and modelling of experimental and seismological data.

We will aim to give the geoscientists an idea of what expertise and services we have on offer in the areas of mapping formulations of problems to executable tasks, providing steering of these tasks through intuitive interfaces and facilitating systems for the creation of new challenges and knowledge.

This is also the kick-off meeting for the IDEA Lab project entitled "A scientific gateway for real time geophysical experiments", and we will plan the work for the next month.

Date and time:

Thursday, 1 April, 2010 - 11:00

Length:

120 minutes

Location:

IF116

Projects:

RapidGeo

Research topics:

Intuitive interfaces

http://www.edikt.org.uk/edikt2/Agenda

Edinburgh Data-Intensive Research

Jano.van.Hemert — Tue, 16 Mar 2010 11:50:45 +0000

Speaker(s):

Jano.van.Hemert

Presentation Type:

invited

Data-intensive refers to huge volumes of data, complex patterns of data integration and analysis, and intricate interactions between data and users. Current methods and tools are failing to address data-intensive challenges effectively. They fail for several reasons, all of which are aspects of scalability. The deluge of computational methods and plethora of computational systems prevents effective and efficient use of resources, user interfaces are not adopted at a sufficient rate to satisfy demand for scientific computing and data and knowledge is created outside suitable contexts for collaborative research to be effective.

The Edinburgh Data-Intensive Research group addresses these scalability issues by providing mappings from abstract formulations to concrete and optimised executions of research challenges, by developing intuitive interfaces to enable access to steer these executions and by developing systems to aid in creating new research challenges. In this talk I will present several exemplars where we have dealt with scalability issues in scientific scenarios.

Date and time:

Wednesday, 28 April, 2010 - 10:30

Location:

edikt2010 Symposium - Using computing in your research, e-Science Institute, 15 South College Street, Edinburgh

Web site:

Research topics:

Intuitive interfaces

http://wikis.nesc.ac.uk/escienvoy/Data-Intensive_Research:_how_should_we_improve…

Edinburgh Data-Intensive Research

Jano.van.Hemert — Mon, 15 Mar 2010 11:06:10 +0000

Speaker(s):

Gagarine.Yaikhom

Liangxiu.Han

Rob.Kitchen

Presentation Type:

demo

We present Edinburgh Data-Intensive Research, a research group in Edinburgh Informatics and part of the UK National e-Science Centre. The demonstration comprises several rounds of 15 minutes, where we briefly introduce the group (2-minutes), then attendees can pick people to talk to for the remaining time. All team members are there and have laptops to provide in-depth demonstrations of our methods and applications of them.

Data-intensive refers to huge volumes of data, complex patterns of data integration and analysis and intricate interactions between combinations of users and systems that deal with these data. Our mission is to advance methods that harness the power of data and computation in collaborative environments. Our goal is to support the life cycle of data to information to knowledge in a multi-disciplinary and multi-organisational context. To achieve this we pursue research in e-Science and Informatics and apply our ideas in several scientific and industrial domains.

Date and time:

Monday, 15 March, 2010 - 14:00

Location:

Data-Intensive Research Workshop, e-Science Institute, UK

Web site:

Research topics:

Intuitive interfaces

An open source toolkit for medical imaging de-identification

Jano.van.Hemert — Mon, 15 Mar 2010 11:01:47 +0000

Assessing the effect of intra-experiment batch-processing variation on gene-expression profiles reported by microarrays

Rob.Kitchen — Mon, 01 Mar 2010 22:08:02 +0000

Speaker(s):

Rob.Kitchen

Presentation Type:

talk

The high cost and difficulty of obtaining high-quality mRNA from primary tissue has led many microarray studies to be conducted based on the analysis of single sample-replicates. The purpose of our study was to quantify the impact of this practice on the quality and reproducibility of reported results by exploiting the multiple-array-per-chip design of the Illumina BeadChip platform. Intra-experiment technical variation in Human WG-8 chips was assessed using 18 repeat hybridisations of universal human reference RNA (UHRR) and 64 duplicate hybridisations of primary breast tumour samples from a clinical study.

A clear batch-specific bias was detected in the measured expressions of both the UHRR and clinical samples. This bias was found to persist following standard microarray normalisation techniques and, following analyses for differential expression using two popular methods, it was observed to have a substantial effect on the reported gene-profiles. In this seminar I will describe the design, analysis, and results of this particular study and provide a brief coverage of batch-processing effects observed in data obtained using other array platforms. I will discuss the mounting evidence in favour of performing specialised batch-corrections on microarray data obtained from a single experiment and also when integrating different datasets at the expression level. Finally, I will introduce valuable batch-correction algorithms that minimise these effects and discuss implications for the design of future experiments employing microarray technologies.

Date and time:

Tuesday, 9 March, 2010 - 09:30

Location:

MRC Human Genetics Unit, Western General Hospital, Edinburgh

Research topics:

Why efforts toward standardisation of data and results from array-based gene-expression studies continue to fall short

Jano.van.Hemert — Wed, 24 Feb 2010 16:32:52 +0000

CISA Seminar Series

Speaker:

Rob Kitchen

High-throughput array-based screens are a popular experimental technique employed by molecular biologists in their endeavour to unravel highly complex gene-interactions. Over the past decade a wealth of research has focused on the development of advanced statistical techniques with which to interrogate these large datasets. Simultaneously, a similar level of effort has been expended in the development of large-scale, open access data repositories and accompanying standards for the reporting of experiment metadata. In disciplines such as mathematics, statistics, and computing these repositories have also become a rich source of data with which to develop and evaluate novel or improved methods of clustering and classification.

Despite these advances towards standardisation and accessibility, the detail of reported experiment metadata remains insufficient to allow the confident re-analyses of the raw data. During the seminar I will discuss recent developments in the following two aspects of the reporting and publication process that promise to improve the quality, depth, and utility of experiment metadata:
1) the need for a greater appreciation for sources of bias in the experiment design and the propensity for noise introduced during sample processing;
2) the need for more rigorous reporting of the statistical treatment of data in 'Methods' sections of journal articles.

Date and time:

Wednesday, 3 March, 2010 - 14:00

Length:

60 minutes

Location:

IF116

Research topics: