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Overview

Coordinator: UOXF

Participants: UCL, USFD, IMIM, UOA, INRIA, UPF, EBI-EMBL, CNRS

The VPH NoE aims to develop, evolve and promote standardised markup languages which permit interoperability of models and, where this is appropriate, interoperable codes which may be coupled both horizontally and vertically. Standards developed will need to be suitable for, adopted by, and adhered to not only within the European VPH initiative, but also on a global basis, e.g. via interaction with the international Physiome Project. The VPH ToolKit provides a means to ensure that, in the first instance, all VPH-funded projects are able to work towards this common aim.

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Detail

The ToolKit will be developed with currently available key resources and ongoing initiatives in this area in mind, and will be designed to provide solutions which tie in with the activities of WP2 VPH Exemplar Projects (EPs). The end result will be products that are tailored to address existing needs, that are efficient and usable and, hence, that are adopted by the VPH Community.

In particular, the VPH NoE will develop:

• open markup language (XML) standards for describing data and models at spatial scales that range from proteins to the human organ;
• application programming interfaces (APIs) and libraries for implementing these VPH standards;
• workflows that use existing middleware for facilitating grid-enabled VPH research;
• web-accessible repositories for data, models and workflows based on the VPH standards and including annotation and tutorials for non-expert biologist users;
• a library of open source computational routines and graphical user interfaces (GUIs) that, via the APIs, can access the data and model repositories.

It should be noted that the VPH ToolKit is not intended to be merely a collection of individual tools used by VPH researchers and clinicians, nor a monolithic entity fulfilling all the needs of the VPH. The latter is impossible, and the former has little impact or utility. Rather, it must evolve into a curated set of tools that are sufficiently usable, flexible, and interoperable that they can be configured and connected by researchers to provide a range of “shrink-wrapped” solutions for clinicians, instead of starting from scratch for each new use-case. This goal imposes requirements on VPH ToolKit development, and on the approaches taken in designing VPH tools, in order to achieve long-term sustainability of the outputs of WP3.

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VPH ToolKit Requirements and Technology Assessment Exercise (RTAE)

A key requirement across WP3 is to ensure that standards and policies, and the infrastructure and tools implementing those policies and utilising those standards, are not only adopted within the VPH NoE but are also accepted and implemented across the VPH programme. This will ensure the interoperability of models and modelling approaches that is essential to the success of the entire VPH concept, allowing routine sharing of models, data and resources across the VPH community. In order to ensure that the approach adopted in WP3 will meet the requirements of the entire VPH community, a comprehensive requirements exercise was undertaken during the first six months of the project, during which all projects funded under the VPH call, and other VPH-related projects, were consulted and a detailed requirements document developed. At the same time a comprehensive technology review was undertaken, to determine which existing technologies meet these VPH community requirements. This initial exercise will be repeated over the life of the project to ensure that the documents created are evolved and that the team act on current information.

The full version of this initial RTAE document may be found in the document repository. A summary document of the RTAE findings has also recently been published.

We would welcome comments on these documents - please contact us if you wish to contribute.

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VPH ToolKit - development milestones

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VPH ToolKit - how can you get involved?

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VPH NoE WP2/WP3/VPH-I Meeting (February 2010)

On the 4^th and 5^th of February, delegates from workpackages 2 and 3 of the VPH-NoE, and from almost all of the current VPH-I projects, met in Brussels for a technical workshop to develop a strategy for the sustainability of the VPH. The aims of this workshop were fourfold: to communicate the strategy being adopted by the WP3 ToolKit team, to agree the key sustainability principles for VPH tools, to learn from the NoE Exemplar Projects about their contributions to the ToolKit, and to build a solid foundation for collaboration within the VPH-I. The outputs from this meeting will feed into the second release of the VPH ToolKit, and the corresponding deliverable to the EC in April 2010.

The meeting went very well, with in-depth discussions on a variety of topics despite the time constraints, and has provided us with much useful feedback. Many of the slide sets presented are publicly available here on the VPH-NoE website.

In discussions around the issues of long-term sustainability for the VPH ToolKit, 5 key criteria were identified.

1. Standards – these are crucial to enable tools to interoperate, and for researchers to be able to share their data and models.

2. Ontologies – a sub-theme of standards, but so important as to merit its own focus. Ontological annotation of models and data ensures that resources can be connected together reliably.

3. Certification – ToolKit content needs to be demonstrably high standard, well documented, and properly validated.

4. Interoperability & workflow – tools should not exist in isolation, but be used in tandem to achieve clinical goals.

5. User friendliness – essential to uptake of tools by users!

The focus of NoE effort will be on tasks such as developing the core standards, training in the use of ontologies, and working with the VPH-I and Exemplar projects to bring their outputs to the ToolKit, increasing interoperability between VPH tools.

Several key needs of the VPH community were also identified during the meeting.

• Provision of a data sharing infrastructure for clinical data, and high volume data storage.

• The utility of ontologies is beginning to be widely recognised, but there is still much uncertainty about how to best make use of them. There is thus a need for both training, and exemplification of best practice.

• VPH modellers need access to good quality models in standard forms, so that they can be used by modelling groups wishing to integrate models of different systems.

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VPH NoE Repository