ESNW : A Centre for Collaborative Multidisciplinary e-Research in the North West
Lead Research Organisation:
University of Manchester
Department Name: Computer Science
Abstract
This proposal is to build a centre for collaborative multidisciplinary research building on the existing successes of e-Science North-West (ESNW). ESNW was established to provide support for Grid and e-Science activities in the region and to provide effort in building a UK National Grid. ESNW also has a strong specialism in bio-medical e-Science. We have succeeded in gaining substantial additional funding from the University and the North-West region and are now seeking further funding to provide a transition to a sustainable centre that will be a permanent part of the national and international e-Science activities in the UK. We are also intending to use the funding to promote knowledge transfer from our current portfolio of projects to new projects in new application areas and disciplines. We are establishing a Virtual Campus at the University linking researchers to tools and infrastructure for solving problems at the frontiers of research. The sheer volume and range of formats for research data and the need for massive computing power for simulation and data analysis are the identifying areas of e-Science so our proposal invests heavily in effort for robust software engineering.We also wish to play a key role in technology transfer of e-Science techniques to industry and other stakeholders in the North-West. Consequently our proposal includes the activities of a business manager to provide this liaison, arrange seminars, workshops and demonstrations of technology. We will utilise our world-class expertise in Access Grid both to diffuse our courses and seminars more widely and to make available other courses and seminars given by international partners. Our participation in the World Universities Network will be leveraged here. Our bio-medical e-Science will grow, and ESNW will be responsible for extracting commonality of Grid middleware and techniques from these projects and liaising with organisations such as the UK Open Middleware Infrastructure Initiative to make these robust and widely available. Thus we will augment the UK Grid middleware stack. We liaise closely with the UK Grid Operations Support Centre and provide effort and consultancy as part of this national support effort. We are founding members of North-West Grid and will use our contacts and projects to ensure that this is productively used to grow the knowledge economy in the North-West.
Organisations
Publications
Jameson D
(2008)
Data capture in bioinformatics: requirements and experiences with Pedro.
in BMC bioinformatics
Missier P
(2010)
Scientific and Statistical Database Management
Peters M
(2017)
The JWS online simulation database.
in Bioinformatics (Oxford, England)
Wilkinson MD
(2016)
The FAIR Guiding Principles for scientific data management and stewardship.
in Scientific data
Wolstencroft K
(2017)
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.
in Nucleic acids research
| Description | The main aims of the activities of the North-West e-Science Centre were to: 1. Continue to develop and implement e-Infrastructure in the North-West. E-Infrastructure refers to the hardware and software required for collaborative research enabled by the internet, most particularly research that needs to process very large amounts of data. 2. To develop and nurture research collaborations that can use such infrastructure to develop new research methods and new knowledge. 3. To provide technology transfer activities to enable use of e-Science methods in industry. The main achievement towards 1 was the development of software that made the use of the UK e-Infrastructure easier by a) allowing users to be checked for validity by checking the records of their home institution instead of them having to manage their own credentials and b) the development of accounting software that allowed the sites that provided resources to the UK e-Infrastructure with information about who was using it. This allowed checks that the resources provided were being shared fairly. The main achievement towards 2 was to prepare the developments of an Informatics network at the University of Manchester, Manchester Informatics, which continues to support research collaborations in data-intensive science, most particularly in medical informatics. ESNW pioneered the facilitation of research collaborations via advanced video conferencing. ESNW delivered a seminar series on topics in e-Infrastructure research via advanced videoconferencing, with 53 seminars, 789 local participants and 48 remote sites participating. The specialist expertise in supporting research utilizing e-Infrastructure has been adopted as part of the working practice of the University of Manchester IT services, contributing towards support for research data management and access to high-performance computing, locally via the University of Manchester ecosystem for Computational Science and regionally in the N8 distributed computational facility. ESNW also developed methods and educational material for enabling research students to acquire the skills for utilising e-Infrastructure via an e-Science taught MSc module Computer Science; 6 Masters dissertations on e-Science and; e-Science support and training for PhD students In terms of aim 3, technology transfer to industry, ESNW provided project management support to the development of a project to transfer expertise from the University of Manchester School of Computer Science to Siemens, involving the use of semantic technology to enhance the use of medical records, resulting in $3.2 million investment from Siemens US to develop this research. |
| Exploitation Route | The expertise and software developed by ESNW, and by projects that it incubated were, and still are used, in the operation of the UK e-Infrastructure that provided the UK contribution to the EU wide e-Infrastructure. This was carried out by the UK NGS during the period of this grant and until 2013, and then was continued by the GridPP project (the UK particle physics e-Infrastructure). ESNW and the GridPP node at Manchester established a close working relationship from the start of this grant that has continued via other projects funded by JISC and STFC. Part of the recent UK investment in e-Infrastructure has been the funding of regional facilities for High Performance Computing. ESNW staff developed expertise in the operation of such regional facilities by its close collaboration with the North West Grid project, linking computational resource at the Universities of Manchester, Liverpool and Lancaster and at STFC Daresbury. Developing from this and from the White Rose Grid formed by the Universities in the North East, the N8 consortium of Northern Universities successfully bid for facilities for High Performance Computing (n8hpc.org.uk) to back the N8 collaborative research (www.n8research.org.uk). Staff employed on the ESNW project play leading technical roles in supporting this infrastructure. ESNW developed the use of advanced video-conferencing for delivering research seminars to geographically distributed participants. This expertise and equipment was contributed to successful bids for EPSRC funding by the School of Mathematics at the University of Manchester to develop the MAGIC consortium, which currently delivers postgraduate mathematics courses across 20 UK Universities (www.maths-magic.ac.uk). Postgraduate mathematics education is very specialised, and cohorts in the sub-disciplines can be very small (this is particularly true in pure mathematics). Thus it is not cost-effective for each institution to supply the full range of expertise in-house and the MAGIC distributed courses have greatly extended the postgraduate curriculum. It is important that conventional video-conferencing methods cannot cope with such a number of participants, nor can they deliver a virtual classroom of sufficient quality. In terms of technology transfer, ESNW played a key role in transferring research in Semantic Web and Scientific Workflows into the international development of virtual astronomy, via EU Framework 7 Project HELIO (www.helio-vo.eu). HELIO is a working infrastructure that uses scientific workflows and ontologies for data integration as part of an integrated Virtual Observatory for Heliophysics linking European and US research in heliophysics and space weather. Space weather warning systems are of immense importance to the space industry. ESNW effort developed the groundwork in the original HELIO proposal for integrating workflow and semantic technologies produced in other EPSRC and JISC projects at Manchester. These technologies, Taverna and myExperiment, became key components of the HELIO infrastructure. IT Services at the University of Manchester has built on work begun in ESNW, to develop services for research data management in partnership with the Library Service and with the Faculty of Life Sciences, via the MADAM and MISS projects partly funded by JISC and now wholly funded within the University IT Services. |
| Sectors | Aerospace, Defence and Marine,Digital/Communication/Information Technologies (including Software),Education |
| URL | http://www.manchester.ac.uk/informatics |
| Description | The work of ESNW was mainly to build and operate e-Infrastructure and to foster collaborations to exploit the use of such infrastructure. The collaborations established in projects supported by ESNW, in particular the building of the North-West Grid (2005-8) have continued in the N8 consortium of Northern Universities and in links to the Hartree Centre, a £37.5 million investment in e-Infrastructure from the UK e-Infrastructure programme, which has particular emphasis on the transfer to industry of methods of simulation and visualization. The impact of such infrastructure is still unfolding, however a concrete result of the collaborations established by ESNW is the interest of IBM (who are partners with STFC in the Hartree Centre) in interfaces on mobile devices to supercomputing resources to allow monitoring and steering of simulations. IBM adapted the RealityGrid steering library, developed in the e-Science project RealityGrid and promoted via ESNW in the context of North-West infrastructure. to provide lightweight steering clients to the BlueGene machine at Hartree from iPads. This iPad app is being developed in a project with Unilever to use high performance computing and visualization in the rapid development of new products, see http://www.stfc.ac.uk/files/1795/1795_res_12.pdf Such lightweight interfaces are also being integrated into the engineering practice of water companies. A collaboration between the University of Manchester and WRc Ltd (www.wrcplc.co.uk) is integrating this software into the working practice of several water companies who have subscribed to WRc project CP540 "Proactive Management of Water Distribution Systems", augmented with a KTP Fellowship funded by Innovate UK, "To develop a real time management package for water distribution networks", to run from 2015 to 2017. WRc intend to adopt the results of the project as a "Software as a Service" offering to their water industry clients. A second area of impact is the use of medical ontologies in clinical practice. ESNW assisted in the creation of a project between Siemens Health Services US and the Bio-Health Informatics research group at the University of Manchester to develop next generation clinical documentation tools. A lecturer from the University of Manchester who is a specialist in ontologies is currently on two years secondment to Siemens Health US to develop the outputs of this project. |
| First Year Of Impact | 2012 |
| Sector | Environment,Healthcare |
| Impact Types | Societal,Economic |
| Description | EPSRC Establishment of BIRN nodes at Edinburgh and Manchester |
| Amount | £44,835 (GBP) |
| Funding ID | EP/D030471/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2006 |
| End | 08/2007 |
| Description | EPSRC Research Cluster for Novel Hardware for the Digital Economy |
| Amount | £40,100 (GBP) |
| Funding ID | EP G00210X/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2008 |
| End | 03/2009 |
| Description | HELIO - EU Framework 7 INFRA-2008-1.2.2 Scientific Data Infrastructure |
| Amount | € 429,924 (EUR) |
| Funding ID | 238969 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 06/2009 |
| End | 12/2012 |
| Description | Intelligent Decision Support Tools - EPSRC Pathways to Impact |
| Amount | £24,529 (GBP) |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2012 |
| End | 03/2013 |
| Description | JISC National e-Infrastructure for Social Science Simulation |
| Amount | £165,358 (GBP) |
| Funding ID | IRDEVRDI |
| Organisation | Jisc |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2009 |
| End | 03/2012 |
| Description | JISC Shibboleth Resources to the National Grid Service |
| Amount | £183,168 (GBP) |
| Organisation | Jisc |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2008 |
| End | 01/2009 |
| Description | Online Water Modelling - KTP Associate |
| Amount | £100,343 (GBP) |
| Funding ID | KTP009629 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2015 |
| End | 03/2017 |
| Description | Siemens Health US project for next generation clinical documentation tools |
| Amount | $3,200,000 (USD) |
| Organisation | Siemens Health Services US |
| Sector | Private |
| Country | United States |
| Start | |
| Title | myExperiment |
| Description | First and arguably only public sharing platform for computational workflows that supports over 20 workflows management systems. this resource was further developed in this award |
| Type Of Material | Database/Collection of data |
| Year Produced | 2008 |
| Provided To Others? | Yes |
| Impact | First and arguably only public sharing platform for any workflow system. Over 500 citations (combined, google scholar) of 3 main myExperiment papers. on 13/03/2017 myExperiment has: 10472 registered members, 392 groups, 3811 workflows, 1223 files, 470 packs Used by several EU projects (e.g. BioVeL, SCAPE, HELIO, VPH), US (e.g. FLOSS) and companies (e.g. RapidMiner) as their workflow repository. over 22 workflow systems represented in repository. in the 30 days in Oct 2014, 2391 unique users (logged in and anonymous), which we can extrapolate. |
| URL | http://www.myexperiment.org |
| Title | UTOPIA protein analysis suite |
| Description | A collection of interoperable desktop tools for exploration and analysis of protein sequences and structures. |
| Type Of Technology | Software |
| Open Source License? | Yes |
| Impact | The suite of tools has formed the basis of bi-annual training courses on protein sequence alignment and analysis held at the EBI since 2004, with an estimated 1200 participants to date. |
| URL | http://utopia.cs.man.ac.uk/utopia/ |
| Description | Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015. The project ran this workshop with colleagues in Rostock and HITS aimed at researchers in Systems Biology The meeting spawned contact with LifeGlimmer, and also Jon Olav Vik from Norway. As a result FAIRDOM gained a new large-scale project (GenoSysFat), and also a new contributing partner which they support for data and model management (DigiSal) which led onto a close partnership with Norway's Digital Life programme and ELIXIR-Norway |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://fair-dom.org/2015/09/22/reproducible-and-citable-data-and-models-workshop/ |