Blogs

BRISSKit Technical Description paper published, Aug 2016

An important milestone for the project. The Biomedical Research Infrastructure Software as a Service Kit (BRISSKit): technical description paper has been published in the open access and open peer reviewed F1000 Research journal. The full citation for the article is: Oliver W. Butters, Shajid Issa, Jeff Lusted, Malcolm Newbury, Russ Parsloe, Nick Holden, Robert C. Free, Tim Beck, Rebecca C. Wilson, Paul R. Burton and Jonathan A. Tedds: "The Biomedical Research Infrastructure Software as a Service Kit (BRISSKit): technical description" [version 1; referees: awaiting peer review]. F1000Research 2016, 5:1905 (doi: 10.12688/f1000research.8736.1).

We hope this is useful in interpreting the software and reusing it - as ever, contact us via brisskit@le.ac.uk with any queries.

BRISSKit short animated explainer!

Along with the full software and documentation release just announced, please see the short BRISSKit animated explainer to help explain what the platform can do, who might want to use it and how! We acknowledge Moving Studio Ltd in Leicester for a great job on the animation for what is quite a complex suite of software :)

BRISSKit Team, University of Leicester

Full Software and Documentation Release, July 2016

Hi everyone

I'm excited to announce that the full suite of BRISSKit software, with versioned source code hosted on github, and including demo tools and all associated documentation is now available. Please contact us at brisskit@le.ac.uk with any questions and see the updates to use cases for ongoing work using the platform. Do let us know if you are adapting or reusing the code and you never know, we may be able to help!

Thanks
Jonathan Tedds (Project Lead), Saj Issa (Technical Lead) and the BRISSKit team

Update from Leicester Cardiovascular Biomedical Research Unit on use of i2b2, civiCRM, RedCap in Cardiovascular Research

Part 4 of our series of updates from BRISSKit collaborators and users was presented at the Feb 2015 community and hack event by Nick Holden of the Leicester Cardiovascular Biomedical Research Unit on their use of i2b2, civiCRM, RedCap in Cardiovascular Research

Nick Holden gave a whistle stop tour of the software used by the NIHR funded Leicester Cardiovascular Biomedical Research Unit (BRU), which has been using web based open source applications included in BRISSKit since before the BRISSKit project began. The BRU adopted i2b2, Open Specimen, CiviCRM, Obiba Onyx and latterly RedCap to address various parts of the research process across 16 different research projects with over 19,000 participants. They started out on this road precisely because commercial alternatives were too expensive to procure and sustain while writing everything from scratch in-house would have been much too demanding, and too expensive to resource. They chose to adopt existing open source tools that they could adapt and integrate as needed - exactly the BRISSKit philosophy! They see BRISSKit as a way of integrating and sustaining their solutions longer term e.g. if dedicated informatics expertise is no longer resourced or available in-house.

Although the vast majority of their recruitment is happening within the hospital, the tools are set up to allow recruitment and work to be carried out over a wider area. Nick illustrated this by describing their RedCap set up, which includes three different servers: one located behind the hospital firewall for projects on site; one visible on the NHS private internet backbone, N3, allowing data to be collected at other NHS sites; and one that is publicly visible but only used in survey mode, allowing study participants to complete questionnaires offsite.

Nick gave an overview of the data flow, explaining how the BRU uses CiviCRM to monitor every engagement with participants (including their consent), RedCap to complete questionnaires, then pipes this data into i2b2 each night together with data from their clinical data warehouse. This allows them to create cohorts with data from a range of sources.

You can watch Nick Holden’s presentation in full at: https://youtu.be/NRpkAv71oJ8

Update on BRISSKit and University of Bristol / ALSPAC Synergies - Dr Olly Butters

This is Part 3 of a series of updates from BRISSKit collaborators and related projects at the Feb 2015 BRISSKit community and hack event in Leicester

Dr Olly Butters, ALSPAC Senior Data Manager at the University of Bristol, gave an overview of the ALSPAC project, which is a population-based birth cohort study led by the School of Community Medicine at Bristol. ALSPAC originally included 14,000 women who were pregnant in 1991-1992, but has since expanded to include the extended family of those participants and many subsequent studies and associated datasets.

The study, one of the largest and best known of it's type in the world, produces a large volume of data from paper questionnaires, electronic questionnaires, blood and tissue samples from their clinic, and linkage data derived from other sources, such as the DWP and HMRC.

Olly identified a number of synergies between ALSPAC and BRISSKit, including using the Bristol Data2Knowledge developed DataSHIELD to make their data more accessible to others by making DataSHIELD become part of BRISSKit via integration of the Obiba Opal BioBanking Database solution. There is a shared interest in utilising the SAIL Secure Anonymised Information Linkage databank platform provided at the Swansea node of the UK Farr Institute in order to make solutions and datasets available to UK wide biomedical researchers.

Finally, Olly discussed the information security aspects of ALSPAC’s work, which is currently being carried out in isolation. The ALSPAC team are keen to explore opportunities to work with other groups in this area, including via BRISSKit.

You can watch Olly Butters’ presentation in full at: https://youtu.be/Hk9uv6kFypE

Feb 2015 Hack Event - Part 2: The Importance of Health Informatics Data and Software, Prof Paul Burton, University of Bristol

Paul Burton discussed how academic health science should respond to the challenges of big data, and the potential role for BRISSKit in this space.

He began by emphasising that the term ‘big data’ is a misnomer, as the size of the data is only one part of the issue and can often obscure some of the other characteristics of the data that need to be considered. BRISSKit can play a role in addressing some of the areas that are being obscured.

To illustrate this point, Paul used the analogy of describing a city as a big village. He pointed out that the infrastructure and integration systems (both internal and external) required by a city are very different from those required by a village. Cities are complex, integrative systems that are qualitatively different from villages. They also happen to be larger than villages, but size is not the sole defining difference. Paul acknowledged that the accepted definition of ‘big data’ has evolved to reflect this, and now encompasses this issue of complexity, but this is not always fully communicated.

In a recent strategic review for the University of Bristol, Paul and his team concluded that universities responding to the real challenges of big data in the health sciences need to have:

• Good involvement in at least some methodological development, particularly in niche areas;
• An effective and sustainable support infrastructure, including facilities, equipment and staff for the leading applied research groups in the university;
• An adequate investment in an effective, up to date, multipurpose IT infrastructure across the university.

He discussed some of the ways in which the University of Bristol and the ALSPAC Longitudinal Birth Cohort Study he co-directs has been responding to these challenges, including the introduction of a university-wide institute for data science to help integrate existing efforts.

Paul argued that universities need to allow access to integrated data, including horizontally and vertically partitioned data. He suggested a data pipeline, including:

• Effective ways to generate data;
• Physical infrastructure to pull data together;
• Effective, well-governanced data access systems;
• Adequate security, appropriate for the level of problem;
• Quality assessment and data harmonisation;
• Valid, efficient and scaleable approaches to analysis;
• Effective visualisation approaches;
• Archiving and curation.

Each of these steps requires integration of a range of specialist activities. Paul advocated a bottom-up approach, allowing users to work with a range of different software and hardware, with funders performing a central enabling role by offering guidance and investment in the communications between different systems to allow greater flexibility for researchers to use appropriate functionality from different systems to suit their needs. This ‘plugin’ approach could go right across the data pipeline and gradually enhance it over time. This reflects the philosophy underpinning BRISSKit, with Jisc potentially playing the central enabling role.

To conclude, Paul gave a brief overview and demonstration of his team’s current project - DataSHIELD - which is incorporated in Opal. There are plans to integrate Opal into BRISSKit, so DataSHIELD will soon form part of the BRISSKit stack. DataSHIELD allows users to combine data from multiple sources and co-analyse it by taking the analysis to the data, rather than the data to the analysis. This provides a non-disclosive way of pulling together the data from multiple studies, which will add an extra dimension to BRISSKit.

You can watch Paul Burton’s presentation in full here.

Quick update + Part 1: What we did at the Feb 2015 Hack Event - Overview and Service Vision

Hi everyone,

We've been pulling out all the stops to complete a range of technical tasks on the software, including Puppet provisioning and work to improve patient cohort management using CiviCRM and integrate DataShield for biobanking with the Bristol Data2Knowledge group, among the highlights. We've also been completing a range of sustainability planning, audits and market research for the Jisc Business Case being considered for a proposed Jisc service in future.

More news on all that when we have it but in the meantime here's part 1 of a series of summaries which includes embedded videos from our February 2015 community event and hack. Special thanks to all who participated and to Kirsty Pitkin at EventAmplifier who helped us capture it all :)

BRISSKit Community Event and Hack, February 2015: Part 1 - Overview and Service Vision

The BRISSKit Data Meet and Hack Event gathered together 49 researchers, data managers, software engineers, doctors, trainers and consultants to encourage collaboration in the provision and use of open source software tooling for health research data management.

Attendees’ interests included putting i2b2 into a clinical context, introducing environmental variables into i2b2 alongside clinical data, helping non-technical users to use the BRISSKit tools, improving BRISSKit’s data input tools, and getting a general view of BRISSKit. The event featured a range of presentations and opportunities for attendees to work together to on projects to explore or extend BRISSKit’s functionality.

This is the first of a series of write-ups on the formal and informal presentations that took place throughout the event, and captures the results of the collaborative hack projects undertaken by attendees.

1. Presentation of BRISSKit Service Vision

Dr Jonathan Tedds, BRISSKit Principal Investigator, opened the event with an overview of the BRISSKit platform, which is designed to provide a stack of generic but integrated web applications that apply to many areas of the biomedical research process.

Jonathan introduced the main components, including CiviCRM, which provides patient cohort management; OpenSpecimen, which is used for sample management; Redcap and Onyx, which provide web-based, secure questionnaire data entry and survey management; and i2b2, which provides data warehousing and querying.

He explained that the unique selling points for BRISSKit include integrated support for the core research process and a stack of open source applications. It is very easy to set up, use and administer through a browser, and is transportable, so can be hosted locally or externally. It offers a much more secure approach to data management than the use of ad hoc spreadsheets, project by project. The project is currently exploring offering BRISSKit through the Jisc Shared Data Centre over the Janet academic network and with direct links in to the NHS N3 network, having appropriate Information Governance.

Jonathan detailed the BRISSKIt team’s co-design approach, working with the community to explore how BRISSKit can be made sustainable for the community going forward. This means the vision the BRISSKit project team chooses can and will change in response to feedback from the community.

Jonathan concluded by highlighting key collaborations, including work with the University of Bristol through the ALSPAC Birth Cohort Studies, DataShield and the Swansea SAIL-Farr node; University Hospitals Leicester NHS Trust including the NIHR funded Cardiovascular, Respiratory and Lifestyle Biomedical Research Units; the Leicester Cancer Research Biobank and the University of Leicester Data to Knowledge for Practice strategic theme. Links to further details on these collaborations can be found here.

You can watch Jonathan Tedds’ presentation in full.

Malcolm Newbury's picture

NHSHACKDAY - BRISSKIT+HEALTHKIT = ?

Another hackday appearance for the myself, Saj and Russ this weekend as we travel to London's Guys Hospital for another NHSHackday bash.
This time we'll be trying to make a useful connection between tools in the BRISSKit suite and Apple's HealthKit. There seems to be a lot in common between the underlying data models, and who knows we might be able to come up with a useful personal fitness research application at the end of it. - Lets hope so!

Malcolm

Final agenda for community meet + hack Feb 23-24th 2015!

We're excited to announce the final agenda for the community meet + hack on Feb 23rd - 24th at College Court, Leicester. See the event link for details: https://www.brisskit.le.ac.uk/civicrm/event/info?reset=1&id=9

We can squeeze in a last handful if you're quick!

Cheers
Jonathan

Malcolm Newbury's picture

QRcodes for Research administrators : NHSHackday Cardiff

Interesting project at NHShackday Cardiff 24/25 January.

Problem: Carers have no access to patient data
Solution : Paper's Got Data / WISDAM
Produce secure ODF catalogues of patient data
Give patient a summary printout of catalogue with QR codes
Each QR code can be scanned on phone to get latest up to date data of each dataset.
Restrict data access to patient and carers
Build Libreoffice plugin to create QRcodes in ODF
NO PRINTOUT – NO ACCESS
WITH PRINTOUT – SECURE ACCESS TO OWN DATA

The 2 day project managed to deliver a lot of discussion and argument between myself, Helga Perry and Rupert Fawdry, plus a plugin to Libreoffice to insert a QRcode into a word processing file - courtesy Michael Meeks of Collabra. https://people.gnome.org/~michael/blog/2015-01-25.html

QRcodes are of significant use to research administrators who have to handle lots of letters and consent forms as part of the interaction with the patient, so this open source plugin may come in useful to Brisskit - we'll wait and see.

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