WP3 - VPH ToolKit PDF | Print | E-mail

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.

This page describes the strategy taken in developing the ToolKit and its design, and recounts recent activities. The main interface to the ToolKit is through a web portal. Also, find out more about how you can get involved.

ToolKit Development Strategy and Design

The Virtual Physiological Human (VPH) ToolKit is intended to be a technical and methodological framework to support and enable VPH research – the collaborative investigation of the human body as a single complex system. The aim is to achieve this goal through the creation, accumulation, and curation of VPH research-related ‘capacities’ – the integration of existing work, and its further development towards greater interoperability.

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” (practical and user-friendly) solutions for clinicians and biomedical researchers, 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 ToolKit beyond the lifetime of the VPH-NoE.

The ToolKit is being developed with currently available key resources and ongoing initiatives in this area in mind, and is designed to provide solutions which tie in with the activities of WP2 VPH Exemplar Projects and the wider VPH Initiative projects. 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.

Particular technological foci for development are:

• 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;
• libraries of open source computational routines and graphical user interfaces (GUIs) that, via the APIs, can access the data and model repositories.

The evolving approach to constructing the VPH ToolKit has been set out in two recent documents. Firstly, we have written a paper describing the central role of standards in ensuring that components within the ToolKit can interoperate. The second document describes the steps being taken to achieve long-term sustainability of the ToolKit.

The VPH ToolKit Portal

The ToolKit will be developed through the creation, accumulation, and curation of VPH research-related 'capacities' - the integration of existing work, and its further development towards greater interoperability. A companion website, the VPH ToolKit portal, plays a central role in this effort. It provides a knowledge base of the 'capacities' available, whether these be specific tools, methods for conducting VPH research in an integrative fashion, or services available to researchers. It thus enables researchers easily to find technologies that may be of relevance to them, rather than re-inventing the wheel. It also provides a structure that can help to place individual activities in their correct context within the VPH initiative as a whole.

Researchers are invited to submit tools, methods, and services for inclusion in the database. You may submit items that you have developed, or that you have found to be useful for your research. There is also the facility to provide feedback on the technologies listed, and so share knowledge with the community. Find out more about how you can get involved.

Guideline documents are now available to assist groups preparing content for submission to the ToolKit in ensuring that their submissions are of the highest quality. The eight key topics cover optimising the submission of tools, models and data (separately), understanding and respecting ethical constraints, approaches to licensing, improving interoperability, maximising usability, and the use of ontological annotation. The first release of all eight documents took place in March 2011 and an update with worked examples will follow in early 2012.

WP3 Activities

A variety of work has been done thus far, including development of individual ToolKit resources, all of which are listed on the ToolKit portal. Some joint activities and deliverables are particularly worthy of note, however, and are discussed here.

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 and a related overview paper have also been published.

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

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.

VPH NoE WP2/WP3/VPH-I Meeting (March 2011)

The next meeting in this series was held in the splendid setting of the European Bioinformatics Institute’s facilities just outside Cambridge. It aimed to allow partners to meet and exchange ideas, but also to open to the wider community the opportunity of sharing in the NoE’s technical developments. This year WP3 had its most successful meeting yet, with almost 100 participants, primarily from the many VPH projects, drawn together for a two-day process of discussion, debate and mutually-didactic discourse. There are currently almost 30 live VPH-I projects and many of them sent representatives to the Technical meeting.  Each project is in routine contact with the NoE to ensure that the maximum possible transfer of re-usable tools, models and data is made to the ToolKit.

After a rousing introduction from NoE leader Prof Coveney, sessions focused on updating the developing stories of each of the VPH-I projects, the use of ontologies, the importance of the Guidance documents and, in a particularly timely session, the emergence of infrastructure as a key step in the maturing of the VPH community as it establishes the need for workflows to be comprehensively supported as the basis for meeting future need.

The final Technical Meeting will take place in Spring 2012, so if you are interested in keeping up with the growing catalogue of NoE technical activity, make a diary entry now. Details will appear here in due course.

ToolKit Hands-on Workshops

The first workshop on ToolKit hands-on training took place from 6^th to 8^th September 2010 in Barcelona. The main objective of this workshop was to start to deliver training activities that bring together researchers from different backgrounds and institutions, promoting the consolidation of a VPH community whilst providing valuable information on these experiences to direct and inform future training activities; on the other hand, a need has been identified for tuition on critical aspects of VPH expertise, for example, training on the VPH ToolKit.

The ToolKit Workshop focused on the identification of ‘gaps’ in existing tools used by the VPH Community and promoted the use and re-use of these tools in problem-solving activities, and will ultimately encourage the collaborative improvement of such tools. Potential attendees were asked to submit problem descriptions in advance to be worked on during the workshop, and problems for which ToolKit tools could be beneficial were selected from these proposals. Proposers then worked with tool developers to address their problems, which included visualization of the myocardial strain tensor over time, aortic valve segmentation, and wall segmentation in abdominal aortic aneurysms. The workshop was well received by the 6 experts and 5 problem providers who attended, and a further hands-on workshop is being organised for 21^st-23^rd November 2011 at INRIA, Sophia Antipolis, France, which will focus on interoperability between medical imaging toolkits.

VPH ToolKit - how can you get involved?

VPH NoE Repository