EGI releases the first Unified Middleware Distribution

 The software provisioning team at the European Grid Infrastructure (EGI) has released the first version of the Unified Middleware Distribution (UMD-1). This is a major milestone in providing a consistent platform for all researchers in the European Research Area to gain access to suitable and integrated computing resources.

Every research community has different goals and requirements for their computing and data needs. Many have developed and maintained their own solutions, which work for them. For many years, the European grid has been offering researchers a distributed computing system across different middleware. The goal of the UMD is to provide a system that the community’s existing solutions can easily plug into, not replace, so that these solutions can be deployed at scale across Europe. It will offer a set of well-defined, stable and general-purpose software components to meet their needs.

So for the last year, EGI and its partners have been working with technology providers and users to work out what they need to offer as a sustainable base on which users can build. The chosen components are collectively known as UMD and have been verified to work in the environment used within EGI. Leading the work has been Michel Drescher; EGI’s Technical Manger; he is excited by what they have achieved: “Just getting this far has been a mammoth task. We have consulted a huge range of stakeholders, reviewed every software package on the grid and come up with what we believe provides the best support structure we can. This is however only a first step, we will learn a lot from this initial deployment to improve future releases”.

UMD 1.0.0 is the first release of UMD-1 for the European Grid Infrastructure. This initial release contains the most critical products from EGI's Technology Providers, as agreed by the Technology Coordination Board on behalf of the EGI community. Further versions will be released in the near future incorporating more features, including the full EMI (European Middleware Initiative) software stack and IGE (Initiative for Globus in Europe) components.

EGI releases the first Unified Middleware Distribution

 The software provisioning team at the European Grid Infrastructure (EGI) has released the first version of the Unified Middleware Distribution (UMD-1). This is a major milestone in providing a consistent platform for all researchers in the European Research Area to gain access to suitable and integrated computing resources.

Every research community has different goals and requirements for their computing and data needs. Many have developed and maintained their own solutions, which work for them. For many years, the European grid has been offering researchers a distributed computing system across different middleware. The goal of the UMD is to provide a system that the community’s existing solutions can easily plug into, not replace, so that these solutions can be deployed at scale across Europe. It will offer a set of well-defined, stable and general-purpose software components to meet their needs.

So for the last year, EGI and its partners have been working with technology providers and users to work out what they need to offer as a sustainable base on which users can build. The chosen components are collectively known as UMD and have been verified to work in the environment used within EGI. Leading the work has been Michel Drescher; EGI’s Technical Manger; he is excited by what they have achieved: “Just getting this far has been a mammoth task. We have consulted a huge range of stakeholders, reviewed every software package on the grid and come up with what we believe provides the best support structure we can. This is however only a first step, we will learn a lot from this initial deployment to improve future releases”.

UMD 1.0.0 is the first release of UMD-1 for the European Grid Infrastructure. This initial release contains the most critical products from EGI's Technology Providers, as agreed by the Technology Coordination Board on behalf of the EGI community. Further versions will be released in the near future incorporating more features, including the full EMI (European Middleware Initiative) software stack and IGE (Initiative for Globus in Europe) components.

Framework to diagnose degenerative brain diseases

Stratus Lab logo

 EGI-InSPIRE has signed a Memorandum of Understanding with the DECIDE (Diagnostic Enhancement of Confidence by an International Distributed Environment) project on 6 July 2011. This document defines a framework of collaboration between both parties and formalises the working relationship.

DECIDE aims to set-up a dedicated grid e-infrastructure for use by medical specialists. Users will be able to quickly identify early signs of Alzheimer's disease and schizophrenia (by comparing patients' brain scans with scans from healthy individuals) using computing resources provided by the European grid. As well as analysing medical images, the grid will also securely store and share the data among trusted users.

A key to treating degenerative diseases such as Alzheimer's is an early diagnosis of the condition – analysis on the grid naturally brings advantages because of its ability to process large amounts of data quickly and securely, accessible at any time, from anywhere. "Thanks to the agreement with EGI, the medical community will benefit from a substantial increase in computational resources relying on an homogeneous European distributed infrastructure. This will help in facing the problem of processing huge amount of produced data in order to extract useful biomarkers to enhance confidence in early diagnosis," says Laura Leone, DECIDE project coordinator.

As part of the agreement, EGI-InSPIRE will work with DECIDE to identify user requirements, develop support tools and services, set-up and support Virtual Research Communities. These will be implemented with a view to the long-term sustainability of the services. Progress and results of the collaboration will be clearly communicated to communities from both parties. Finally, aspects of the collaboration will also benefit the wider grid community, for example, in the form of training materials and applications.

"The signing is a significant step forward in establishing a channel for long-term interaction and collaboration, that will allow us to provide an e-infrastructure suitable for the needs of the DECIDE medical community," says Steven Newhouse, Project Director of EGI-InSPIRE. "As many societies face the future of an increasing aging population, the grid can play a significant role in the early diagnosis of degenerative brain diseases, such as Alzheimer's, which affects many people around the world."

Framework to diagnose degenerative brain diseases

Stratus Lab logo

 EGI-InSPIRE has signed a Memorandum of Understanding with the DECIDE (Diagnostic Enhancement of Confidence by an International Distributed Environment) project on 6 July 2011. This document defines a framework of collaboration between both parties and formalises the working relationship.

DECIDE aims to set-up a dedicated grid e-infrastructure for use by medical specialists. Users will be able to quickly identify early signs of Alzheimer's disease and schizophrenia (by comparing patients' brain scans with scans from healthy individuals) using computing resources provided by the European grid. As well as analysing medical images, the grid will also securely store and share the data among trusted users.

A key to treating degenerative diseases such as Alzheimer's is an early diagnosis of the condition – analysis on the grid naturally brings advantages because of its ability to process large amounts of data quickly and securely, accessible at any time, from anywhere. "Thanks to the agreement with EGI, the medical community will benefit from a substantial increase in computational resources relying on an homogeneous European distributed infrastructure. This will help in facing the problem of processing huge amount of produced data in order to extract useful biomarkers to enhance confidence in early diagnosis," says Laura Leone, DECIDE project coordinator.

As part of the agreement, EGI-InSPIRE will work with DECIDE to identify user requirements, develop support tools and services, set-up and support Virtual Research Communities. These will be implemented with a view to the long-term sustainability of the services. Progress and results of the collaboration will be clearly communicated to communities from both parties. Finally, aspects of the collaboration will also benefit the wider grid community, for example, in the form of training materials and applications.

"The signing is a significant step forward in establishing a channel for long-term interaction and collaboration, that will allow us to provide an e-infrastructure suitable for the needs of the DECIDE medical community," says Steven Newhouse, Project Director of EGI-InSPIRE. "As many societies face the future of an increasing aging population, the grid can play a significant role in the early diagnosis of degenerative brain diseases, such as Alzheimer's, which affects many people around the world."

Re-writing the digital landscape

the CLARIN logo

the DARIAH logo

Earlier this month EGI.eu signed a Letter of Intent with two European Commission funded projects aiming to provide the arts and humanities with an e-Infrastructure of their own. The two projects, DARIAH and CLARIN, both signed the three-way agreement, which has the express intention of ensuring that technology developed by the two projects and the European Grid Infrastructure (EGI) are compatible and provides the best service to their users. The agreement also provides a blueprint for similar arrangements between EGI.eu and other user communities that are interested in exploring grid technology but are temporarily constrained from establishing a Virtual Research Community.

While there is a wide range of research using the European grid, the arts and humanities are currently under represented but both DARIAH and CLARIN aim to remedy this. CLARIN (Common Language Resources and Technology Infrastructure) is focussed on creating tools and resources for the language community, while DARIAH (Digital Research Infrastructure for the Arts and Humanities) supports the wider humanities and arts community. The two projects are part of the European Strategy Forum on Research Infrastructures (ESFRI) programme. This initiative helps to support a coherent approach to policy-making on research infrastructures in Europe so that researchers get the resources/technologies they need.

This latest agreement cements the relationship between the 2 ESFRI projects and EGI.eu, helping all three to develop common tools and technologies while exploring further opportunities for collaboration. Connecting EGI with the infrastructures developed by these two projects will have benefits for the sites within partner countries providing the resources, benefits for the countries themselves in terms of integrating the resource centres with the EGI monitoring and support services and finally, benefits for the research communities in terms of support, advice and influence over the evolving infrastructure. The first priority however is to understand the needs of the communities that DARIAH and CLARIN represent so that they can build and manage an infrastructure for their users. The areas of greatest concern are; data storage and availability, the hosting and monitoring of services as well as authentication and authorisation issues.

Chief Community Officer, Steve Brewer said: “For EGI this is the first step in establishing and welcoming a valuable new user community onto the European grid, DARIAH and CLARIN represent a broad range of interests across the arts, humanities and social sciences with, between them, a wealth of digitally-enabled methods and tools to integrate with the infrastructure.”

Outside the agreement with EGI, CLARIN and DARIAH have also agreed to co-organise the SDH 2011 conference in Copenhagen later in the year. The meeting, the full name of which is “Supporting the Digital Humanities: Answering the unaskable”, will be held in the Danish capital on the 17th and 18th of November. It will provide a forum for discussing the benefits of the e-Infrastructures to the arts and humanities alongside how new forms of research can be facilitated and supported. 

Re-writing the digital landscape

the CLARIN logo

the DARIAH logo

Earlier this month EGI.eu signed a Letter of Intent with two European Commission funded projects aiming to provide the arts and humanities with an e-Infrastructure of their own. The two projects, DARIAH and CLARIN, both signed the three-way agreement, which has the express intention of ensuring that technology developed by the two projects and the European Grid Infrastructure (EGI) are compatible and provides the best service to their users. The agreement also provides a blueprint for similar arrangements between EGI.eu and other user communities that are interested in exploring grid technology but are temporarily constrained from establishing a Virtual Research Community.

While there is a wide range of research using the European grid, the arts and humanities are currently under represented but both DARIAH and CLARIN aim to remedy this. CLARIN (Common Language Resources and Technology Infrastructure) is focussed on creating tools and resources for the language community, while DARIAH (Digital Research Infrastructure for the Arts and Humanities) supports the wider humanities and arts community. The two projects are part of the European Strategy Forum on Research Infrastructures (ESFRI) programme. This initiative helps to support a coherent approach to policy-making on research infrastructures in Europe so that researchers get the resources/technologies they need.

This latest agreement cements the relationship between the 2 ESFRI projects and EGI.eu, helping all three to develop common tools and technologies while exploring further opportunities for collaboration. Connecting EGI with the infrastructures developed by these two projects will have benefits for the sites within partner countries providing the resources, benefits for the countries themselves in terms of integrating the resource centres with the EGI monitoring and support services and finally, benefits for the research communities in terms of support, advice and influence over the evolving infrastructure. The first priority however is to understand the needs of the communities that DARIAH and CLARIN represent so that they can build and manage an infrastructure for their users. The areas of greatest concern are; data storage and availability, the hosting and monitoring of services as well as authentication and authorisation issues.

Chief Community Officer, Steve Brewer said: “For EGI this is the first step in establishing and welcoming a valuable new user community onto the European grid, DARIAH and CLARIN represent a broad range of interests across the arts, humanities and social sciences with, between them, a wealth of digitally-enabled methods and tools to integrate with the infrastructure.”

Outside the agreement with EGI, CLARIN and DARIAH have also agreed to co-organise the SDH 2011 conference in Copenhagen later in the year. The meeting, the full name of which is “Supporting the Digital Humanities: Answering the unaskable”, will be held in the Danish capital on the 17th and 18th of November. It will provide a forum for discussing the benefits of the e-Infrastructures to the arts and humanities alongside how new forms of research can be facilitated and supported. 

Grid Reviewed for Nature

One particular research area that benefits hugely from easy access to computational resources is the analysis of medical images, like brain scans or x-ray images. In a paper published in this month’s Nature Reviews Neurology various infrastructures on offer to the biomedical community are compared, including EGI’s partner neuGRID.

Research into neurodegenerative diseases uses imaging techniques to help diagnose, and track the progress of, numerous illnesses including Alzheimer’s. Until recently however the image collections used by the researchers have been usually collected locally, and only being 10s or 100s of images. However thanks to a growth in the availability and accessibility of clinical and research imaging data, the area is being transformed.

The teams now working on these illnesses have access to data sets made up of literally hundreds of thousands of individual images. Traditionally only a few laboratories had the expertise and computational resources required to make use of the data. However recent developments in e-Science have changed this and there are many solutions available to the community.

The paper is a review of the three major projects helping overcome the image overload; neuGRID, LONI and CBRAIN. All three use different techniques, technologies and image sets, making them equally useful to different researchers. LONI and CBRAIN focus on using High Performance Computing resources while neuGRID is based on the technology provided by EGI as well as using the computational resources of the infrastructure.

David Manset, from the neuGRID project and Technical Coordinator of its international chapter outGRID, is one of the paper’s authors “Putting this paper together has been a great experience. neuGRID has achieved a lot in the last 3 years and it has been interesting learning about the differences between our approach and the others. I also hope that the paper raises awareness of the tools on offer to the community by the three projects”.

The paper, Virtual imaging laboratories for marker discovery in neurodegenerative diseases, is published in July’s Nature Reviews NeurologyDoi:10.1038/nrneurol.2011.99

 
neuGRID launches its new phase later this month called “neuGRID for you (N4U): expansion of neuGRID services and outreach to new user communities”, led by Giovanni Frisoni, who was also principal investigator of neuGRID, which will aim to expand the services offered by neuGRID to their end users.

Grid Reviewed for Nature

One particular research area that benefits hugely from easy access to computational resources is the analysis of medical images, like brain scans or x-ray images. In a paper published in this month’s Nature Reviews Neurology various infrastructures on offer to the biomedical community are compared, including EGI’s partner neuGRID.

Research into neurodegenerative diseases uses imaging techniques to help diagnose, and track the progress of, numerous illnesses including Alzheimer’s. Until recently however the image collections used by the researchers have been usually collected locally, and only being 10s or 100s of images. However thanks to a growth in the availability and accessibility of clinical and research imaging data, the area is being transformed.

The teams now working on these illnesses have access to data sets made up of literally hundreds of thousands of individual images. Traditionally only a few laboratories had the expertise and computational resources required to make use of the data. However recent developments in e-Science have changed this and there are many solutions available to the community.

The paper is a review of the three major projects helping overcome the image overload; neuGRID, LONI and CBRAIN. All three use different techniques, technologies and image sets, making them equally useful to different researchers. LONI and CBRAIN focus on using High Performance Computing resources while neuGRID is based on the technology provided by EGI as well as using the computational resources of the infrastructure.

David Manset, from the neuGRID project and Technical Coordinator of its international chapter outGRID, is one of the paper’s authors “Putting this paper together has been a great experience. neuGRID has achieved a lot in the last 3 years and it has been interesting learning about the differences between our approach and the others. I also hope that the paper raises awareness of the tools on offer to the community by the three projects”.

The paper, Virtual imaging laboratories for marker discovery in neurodegenerative diseases, is published in July’s Nature Reviews NeurologyDoi:10.1038/nrneurol.2011.99

 
neuGRID launches its new phase later this month called “neuGRID for you (N4U): expansion of neuGRID services and outreach to new user communities”, led by Giovanni Frisoni, who was also principal investigator of neuGRID, which will aim to expand the services offered by neuGRID to their end users.

The grid on a cloud

Stratus Lab logo

Last week the StratusLab project launched a production release of their eponymous software, StratusLab 1.0. This first stable distribution makes it even easier to turn available computing resources into a cloud environment, and in the process lowers one of the barriers to providing resources to the European grid.

The team at StratusLab has spent the last 12 months working with users and system administrators to provide a set of tools for creating and managing a private cloud-based infrastructure. For users still unsure about moving to the cloud the project also provide a reference infrastructure running their latest tools. This allows potential users to see what they can do with the system before investing time and effort in setting one up.

One of the clear benefits of this work for the European grid, however, is the ability to create and run a grid site on a StratusLab cloud. In fact the Greek National Grid already has one of their sites up and running like this using a previous version of the software. This makes it easier for institutes with limited resources to join and contribute to the European Grid Infrastructure (EGI).

Dr Charles Loomis, the Project coordinator, has been very happy with the progress: "thanks to everyone pulling together we have been able to ship four beta releases and this production release in our first year, which is brilliant. Alongside the speed of development is the quality of our product, demonstrated by the Greek NGI using our software to run a certified EGI grid site in the cloud. I'm looking forward to the next 12 months, which will bring a series of incremental releases featuring improvements to existing services and added functionality."

It is not only the developers who are happy with StratusLab, researchers from various disciplines have been interested in the benefits that this work could have for them. One of these, Christophe Blanchet of the Institut de Biologie et Chimie des Protéines (IBCP) France, hopes to see the work become a standard tool for bioinformatics research: “French bioinformatics platforms are planning to use StratusLab to help the deployment of their site inside our national grid infrastructure. This will also allow them to use the flexibility and elasticity of the cloud to provide bioinformaticians and biologists with a simple way to access the bioinformatics services and applications needed to analyse the massive biological datasets normal in modern research."

Currently the software offers the benefits of both systems, from cloud’s ease of adding new resources to grid’s openness and wealth of applications. The team are not finished yet though. They will continue to add more functionality to StratusLab, including the ability to interface with commercial cloud services.

The key features of StratusLab v1.0 are:

  • It is a full production-ready release with many bug-fixes and enhancements

  • Uses the OpenNebula 2.2 virtual infrastructure manager

  • includes the Claudia platform service management toolkit for dynamic service provisioning and scalability

  • has a marketplace allowing user communities to create, search for and share customised digitally-signed virtual machine images

  • numerous Base OS images are available in the Marketplace as well as grid and bioinformatics appliances

  • persistent storage allows users to create and access disks on remote cloud storage resources

  • provides a sophisticated web-monitoring tool

  • has easy-to-use command line tools for system administrators and users

  • uses an authentication proxy service which allows cloud authentication via X509 grid certificates

  • provides both manual and Quattor installation options


Try out StratusLab and find out the full technical details and downloads