BRISSkit - A Vision for Cloud-Based Open Source Research Applications as a Service

The marathon of updates from the NOCRI Information Systems workshops is nearly run - but we couldn't finish without covering a final champion of Open Source and caBIG resources.

Nick Holden, Systems and Database Architect at the Leicester NIHR Cardiovascular Biomedical Research Unit, gave us a vision as follows:

“The Biomedical Research Informatics Centre for Cardiovascular Science (BRICCS) uses open source applications from around the world to deliver an end-to-end informatics platform for research at the Leicester Cardiovascular BRU.

Now the BRISSkit project aims to build on BRICCS to offer the same applications in a software-as-a-service”

Nick opened by saying that though they wanted to use Open Source, they never wanted to be developers – and that there are downsides to OS in this regard – however, the positives of using open source software for Electronic Data Capture and tissue storage management (OBIBA – open-source biobanking, and caTISSUE, the most successful resource within the caBIG suite) include the potential for data sharing inherent in those platforms e.g. linking up to caGRID for federated secure data querying.

He spoke about the advantages of using these platforms on the cloud (using I2B2 for translational data management, C3PR from caBIG for participant registration) to provide cloud-based research applications as a service! We’d be interested to know if there is anyone out there who would want to take advantage of such a service...

Their project is now aligned to the JISC Managing Research Data workstream.

Application of CancerGrid Technologies to Translational Research

We're nearing the end of our summary of the day's Information Systems workshop courtesy of NOCRI but there's still plenty to cover!

Dr James Brenton, Group Leader at CRUK’sCambridge Research Institute, was one of the day’s pro-caBIG speakers. Wemanaged to jot down some of the nitty-gritty, CancerGrid SQIV integratesclinical and lab data (e.g. TMA slides) using inference rules to create XMLrepresentations of both for the purpose of modeling analytical software andinterfaces. Some of the tech used has been borrowed from Astrogrid who usejava-based tools to manipulate the vast quantities of data necessary fromresearch into the universe. From what we can recall, the CancerGrid andPathgrid softwares will be open and reusable - this is the abstract of Dr.Brenton’s talk:

“CancerGrid is an initiative involvingscientists at the Universities of Oxford and Cambridge, working together to reducethe cost of clinical research, and to increase its value through effective datasharing. It is building upon the success of a four-year project funded by theUK Medical Research Council, to address a wider range of scientific goals, withsupport from Microsoft Research. The CancerGrid team have developed standardsand tools for the automatic production of the systems needed to supportclinical studies and translational research. The vision:

· the researcher createsa model of their study or dataset, based upon standard templates, using asimple study designer tool

· the software artefacts- forms and services - needed to run the study, or interact with the dataset,are then produced automatically from the model

The production process works toimplement exactly the support required through the configuration of familiar,trusted software applications, such as Microsoft Office with SharePoint, or theopen-source eXist XML database - applications that are used throughout the UKNHS, in government, and in industry. Along with a meta-model (or modeltemplate) for clinical studies, based upon the CONSORT statement, and work onthe classification and registration of clinical trials, the project hasproduced an ISO11179-compliant metadata registry, a semantically aware trialsdesign/ management system, and a toolkit for clinical data transformation andintegration. These models and software applications have been tested throughinitial deployment on a small number of clinical studies in Oxford andCambridge. The metadata registry software has been adopted for use within theUS caBIG initiative, and is being evaluated by a number of organisations withinthe UK. Development continues at Oxford, with clinical collaboration inCambridge and London, and technical collaboration with the caBIG team in theUS.”

NIHR / NOCRI Information Systems Workshop - Part 2 - FP7 TRANSFoRm: Translational Medicine and Patient Safety in Europe

Next up, after Mike Denis, in the first session was Prof. Brendan Delaney (Guy's and St Thomas' Charity Chair in Primary Care Research, King's College London) talking about the TRANSFoRM project under FP7 – for the uninitiated, “'Framework programmes' (FPs) have been the main financial tools through which the European Union supports research and development activities covering almost all scientific disciplines.”

The project is looking to develop infrastructure supporting research and diagnostic decision support in primary care – and in the UK is working with GPRD (the primary care data-source). 

Prof. Delaney referred to the well worth reading report from the US Institute of Medicine of the National Academies DigitalInfrastructure for the Learning Health System: The Foundation for ContinuousImprovement in Health and Health Care - Workshop Series Summary 

 

Prof. Delaney’s big statement was that “Research is in crisis!”, his verdict on the recent reports (we will find the link!) on caBIG was that the lesson to be taken is, “Don’t build massive infrastructure projects! They just grow and grow and create wealth for consultants.” Interestingly, other speakers noted that they were using at least one caBIG tool in the development of their own infrastructures.

Prof. Delaney’s work on TRANSForM encompasses a data quality tool, data linkage functionality (browsing, selection, extraction) and semantic mediation – the latter facilitating the transformation of Electronic Health Records (EHRs) into research quality data (EHRs with tabs for CRFs which partially pre-populate and can ultimately be signed-off online).

This last facility is at the heart of the work, using reference ontologies, controlled vocabularies etc. to interpret the EHRs.

The first year’s deliverables (including the privacy framework, security framework and provenance framework – together creating the governance framework) are already available on the website: http://137.73.82.45/Home.html

We’d be interested to know the relative ease of navigation of the regulatory landscape for each of the involved nations.... and will the deliverables form the semantic mediation be published?

This is the abstract for Prof. Delaney’s talk:

“TRANSFoRm is an EU FP7 project that aims to develop and test a digital infrastructure for the 'learning healthcare system'. Specifically we are working to develop capacity within primary care electronic health records to manage research workflow (recruitment and follow up), data collection and record linkage, and to develop diagnostic decision support using a common infrastructure.

NIHR / NOCRI Information Systems Workshop - updates to come

We'll be blogging in greater depth on the NOCRI Information Systems workshop this afternoon - but just to tantalise... it was a really inspirational day which showcased a great deal of talent and achievement in the bioinformatics arena - and arrived at some concrete actions which the NIHR will be taking forward - watch this blog later today...

So what tools are European Bioinformaticians using? Part 1

We blogged at the end of September about an article in ecancermedicalscience covering a paper which documented usage of caBIG tools and technologies by European researchers - the basic findings of the repot were that the tools are not widely used (these are tools designed to produce "an integrated informatics grid to incorporate open source, open access tools to collect, analyse and share data, enabling everyone to use the same methods and language for these tasks") but that where they are, they are very highly rated.

The feedback we had when we spoke to some friends at caBIG was that this was no big surprise as their efforts had been directed at the US biomedical enterprise and they had not made any serious investment in promoting their offering in Europe...

We thought the headline of the article ("European cancer researchers failing to use research tools") might raise a few eyebrows with other friends of ours at research institutes across the UK who most certainly are using research tools - so we thought we'd set about finding out what tools are available in Europe and who is using what.

First stop, the European Bioinformatics Institute - OK, so they don't focus on cancer, but the tools they offer clearly have an application in various aspects of cancer research - in their own words, the most popular of them "include tools for the analysis and comparison of nucleotide and protein sequences, data from functional genomics experiments, text mining of the scientific literature and tools for determination and visualisation of macromolecular structures. All these tools can be accessed over the web and most provide Web Services interfaces using SOAP orREST APIs."


For more detail, see the EBI tools page - but in summary, they offer tools covering:

• Nucleotide sequence searches x2 (across various database including EMBL-Bank, Coding Sequences, immunoglobulins and High throughput cDNA)
• Protein sequence searches x2 (across database including UniProtKB, sequences derived from macro molecular structures, immunoglobulins and sequences from patents)
• Multiple sequence alignment tools x5!
• Pairwise sequence alignment tools x2
• Functional genomics tools x3
• Potein function analysis tools x4
• Molecular structural analysis tools x2
• Scientific literature text mining tools x2
• And five data retrieving and ID mapping services:
• • dbfetch
  • ENA / SRA
  • ENA / EMBL-SVA
  • UniProt / UniSave
  • SRS
  • PICR

Over the next week we are going to look in more detail at some of the tools being used in the UK from micro-array technologies to clinical data management systems - including those from the EBI listed above - and how these are being linked to derive new insights...  use any yourself which you particularly rate? Then let us know!

Cloud computing speeds up biomedical data analysis

We came across this story in Medical Technology Business Europe

In summary:

Biomedical informatics scientists at The Ohio State University have created a system that uses cloud computing to enable researchers around the world to access and analyze biomedical data.

Funding has been provided by the National Institute of Health and the creators of the TRIAD system are making some pretty big claims:

“With the current technology, a researcher might dedicate more than 100 hours to connect the dots between a set of tissue samples, the individual medical histories for the patients who provided those tissues, and then analyzing the group as a whole. With the TRIAD platform, researchers can now execute this type of search and analysis in minutes,” says Philip RO Payne, chair of the department of biomedical informatics at The Ohio State University Medical Center.

Having been one of those researchers, I have reservations – in that the issues we encountered on a weekly basis (trying to link tissue analysis outputs to clinical records and from that assess correlations) were less to do with processing power and more to do with conceptual and data entry issues.

The kind of issues we encountered were as banal as ‘when looking at Acute Leukaemia relapse scenarios, what constitutes a sample taken at relapse before treatment when we can only be confident that dates entered on the tissue storage and clinical data systems are accurate to around a fortnight and outcome assessment is carried out a fortnight after the start of treatment?’.

To be fair, the aims of the developers of TRIAD (which, incidentally uses caGRID technology for all those denigrators of caBIG) are directed at interoperability between data encoded using different standards:

“When it comes to biomedical research, you have the digital equivalent of the Tower of Babel. One piece is written in French. And another is written in Russian. And maybe a third component is in Chinese,” explains Payne. “TRIAD acts like the ultimate interpreter between all the different “languages” that biomedical data comes in so that researchers spend time figuring out how the information could improve the way we treat a disease rather than spend time finding and translating various data sets.”

NCRI / NCI - Cancer Informatics - Joint Conference slides available

The fifth Joint Conference of the U.S. National Cancer Institute cancer Biomedical Informatics Grid® caBIG® and the U.K. National Cancer Research Institute (NCRI) Informatics Initiative took place in London at the Wellcome Trust on June 13-14, 2011.

This annual event is the result of a close international collaboration founded on the sharing of open-source tools, infrastructure, and data. This year, the meeting had a different format from those of previous years.

Conscious of the fact that these conferences present a unique opportunity to formulate concrete collaborations (bringing together as they do, a wealth of expertise and knowledge from around the world) the conference moved away from the open registration format of the past, to being an 'invitation-only' event, with international representatives invited to contribute to one of five key themes.

The hope was that the small size of the groups working on each theme would facilitate the quick and easy exchange of ideas between key international players, and, hopefully, the generation of actual collaborations which would help to address key, unresolved issues in the respective themes.

In this regard the conference was a success with each of the groups producing recommendations, commitments and collaborative proposals which will be taken forward in the coming months. These experiences will form the basis for a number of peer reviewed papers and, it is hoped, submissions to Nature Precedings.

A summary of the discussions and the slide-shows presented are now available on the UK's National Cancer Research Institute Informatics Initiative pages