BRISSkit: Biomedical Research Infrastructure Software Service kit

Transcription

1 BRISSkit: Biomedical Research Infrastructure Software Service kit Jonathan Tedds University of Leicester BRISSkit 12/10/11

2 BRISSkit: Biomedical Research Infrastructure Software Service kit prototype open source IT infrastructure for Biomedical Research Informatics Anonymised versions of patient sensitive databases are hosted for University researchers on LAMP VMware platform implemented by IT Services Collects data for consented participants, combine with NHS data Bridges UHL and university domains provide sophisticated cohort selection criteria for research e.g. 'people with existing diagnosis of A, with a family history of B, who have taken C for more than six months, have undergone procedure D and have blood sample E in our lab')

3 BRISSkit: Biomedical Research Infrastructure Software Service kit 820k from JISC University Modernisation Fund 11/12 Leicester ITS-RCS (60%), Cardiovascular (25%), Genetics (10%) & Health Sciences (5%) + UHL Trust UK e-science AstroGrid know-how inside! develop national shared service with Eduserv - VMware platform brokered by JANET host, implement, deploy biomedical research database applications Remove duplication of highly skilled development effort via Design from scratch Buy & administer

4 BRISSkit: Biomedical Research Infrastructure Software Service kit Questionnaire / elec data capture application OBiBa Onyx LCB specimen inventory catissue Cohort selection and data querying - i2b2

5 Electronic Data Capture Onyx from the OBiBa Open BioBank suite of software tools manages baseline interviews. Records participant consent, questionnaire data & primary specimen IDs. Web-based, secure data entry by research staff. Used for all recruits to BRICCS prototype mobile computing on wards and outpatient clinic Ontario/Montreal/Perth (Aus)/East Coast US Allows for integration with physical measurement devices, manages appointments, participant look-up to registry services or walk-in volunteers.

6 Electronic Data Capture REDCap allows for common data elements to be re-used in building and managing online surveys and databases. Create and design projects using your web browser using the Online Designer; and/or by constructing a 'data dictionary' template file in Microsoft Excel. Both surveys and databases (or a mixture of the two) can be built. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R).

7 Specimen Management catissue is cabig's biorepository tool for biospecimen inventory management, tracking, and annotation. This tool permits users to enter and retrieve data concerning the collection, storage, quality assurance, and distribution of biospecimens. catissue Suite is scalable and configurable for deployment across biospecimen resources of varying size and function, and that manage multiple types of biospecimens (tissue, biofluids, nucleic acid). Recording of biospecimen shipping and tracking events across repositories in a single catissue installation.

8 Translational Data Management I2b2 is a comprehensive software and methodological framework to enable clinical researchers to accelerate the translation of genomic and traditional clinical findings into novel diagnostics, prognostics, and therapeutics. Data from disparate sources can be loaded into i2b2 under a sophisticated mechanism of ontology building, allowing for complex searching and crossreferencing of data, visualisations and export. Plugins allow for natural language processing and data visualisation.

9 Central Participant Registration C3PR cabig Central Clinical Participant Registry enables efficient and streamlined registration of participants into studies. It can be used by an individual site, or by a multiinstitutional organization with many, graphically dispersed sites. C3PR helps to organize, and standardize a template for patient registration, informed consent, inclusion/exclusion criteria, stratification categories, and treatment arms. The system tracks screening failures and enrollment statistics, and can be configured to alert study personnel when accrual thresholds are met.

10 BRISSkit and clinical informatics Potential sources of clinical data for BRISSkit i2b2 Administrative Patient Master Index >1m records in UHLeics Trust alone Admissions, Discharges, Transfers Patient Pathway Clinical BRICCS interview data Pathology Prescribing Primary Care Diagnosis and Procedure Codes

11 BRISSkit and clinical informatics Potential sources of clinical data for BRISSkit i2b2 Imaging and complex data ECGs Radiology CT / MRI Echocardiography

12 BRICCS and clinical informatics What is not currently available, other than on paper/individual spreadsheets? Clinical record of inpatient and outpatient consultations Observations Findings Differential diagnoses Medical history Family history So there is a research imperative for 'clinical informatics' at UHL, whether as Electronic Patient Record or something less ambitious.

13 Clinical informatics Not just for research Benefits for clinicians, managers, and at UHL strategic level Improve patient care no more 'missing notes' in clinics Improve accuracy of clinic letters and discharge forms Improve planning of clinics more data on attendances Improve audit compliance and data collection

14 BRISSkit: Biomedical Research Infrastructure Software Service kit Team includes JISC, Eduserv, JANET in partnership at Leicester with: Jonathan Tedds, Project Lead (IT Services / Physics & Astronomy) UoL IT Services Mary Visser, Director Research Computing Services technical team UoL Medical Sciences Profs Samani, Ng, Goodall, Squire (Cardiovascular Science & Biomedical Research Unit) Prof Brookes, Dr Tim Beck, Dr Rob Free (Genetics) Prof Burton (Health Sciences) University Hospitals Trust Leicester Biomedical Research Unit technical & management team Board representation: Peter Knight (NHS NIHR Research Capability Programme) Prof Kevin Schurer (UoL PVC Research & Enterprise) Kevin Harris (UHL Trust Medical Director) Charles Beagrie Consulting Ltd; Malcolm Newbury JISC / Eduserv / JANET

15 BRISSkit service design Primary objective: design, deliver and begin to exploit a data hosting service for researchers in the field of Biomedicine & Bioinformatics Sensitive, attributable clinical data will be hosted on infrastructure managed by UHLT De-identified versions of this data will be replicated to a cloud based infrastructure and made available to researchers establish best practice for similar initiatives both within the UoL/UHLT and nationally service delivery model and policies for supporting successful research using this approach will be established benefits of undertaking research using this service will be established strengths, weaknesses, threats and opportunities associated with using this approach will be assessed

16 BRISSkit: Biomedical Research Infrastructure Software Service kit Theme Core Components Lead Service Design Detailed & revised project plan (1.1, 1.2) Engagement with key stakeholders (UoL / UHL / NHS / JISC / JANET / Eduserv / International) Provision of Workshops (9.1, ) Sustainability OS community engagement, standards compliance and service vision Cross-enterprise Service Architecture: how to join & use service for new BRUs & partners. Definition of service vision, organisational & service components; all relevant standards & tools which Brisskit partners will be expected to use and comply with OS Community Engagement Charter: defining engagement with existing & new OS communities incl. adoption &code commitments Technical development Generic deployment infrastructure VM Test facilities (2.2) catissue API client (4.2) Data generation tools (5.4) Data warehouse application (7.3) UK customisations (7.1) Integration of catissue / i2b2 (8.1) Return on Investment Baseline NIHR BRU / BRC Baseline non NIHR Biomedical Research Groups Model cost savings and develop Business Plan Jonathan Tedds (UoL) / Chris Greengrass (UHLT) / Malcolm Newbury (Guildfoss) Jeff Lusted (UoL) / Nick Holden (UHLT) Charles Beagrie Consultants / UoL Business Development

17 BRISSkit: Biomedical Research Infrastructure Software Service kit Timing Factors to evaluate Measures of success November 2011 Detailed project plan (1.1) VM Test facilities (3.2) Artifact repository (4.2) catissue deployment mechanism (5.4) February 2011 ROI scoping report (2.2) Generic deployment infrastructure (4.3) catissue API client (5.2) Data generation tools (6.4) Data warehouse application (8.3) UK customisations (8.1) Integration of catissue / i2b2 (9.1) Provision of initial workshops (9.1) Provisional Service Design (10.1) June 2012 Revised project plan (1.2) UK customisation of catissue (5.3) Deployment of catissue (5.6) Principles of Questionnaire Design (6.2) Data capture from clinical systems (7.3) Ontology pull cell for i2b2 (8.4) Clinical deployment guide (8.2) Clinical deployment tools (8.3) Provision of final workshops ( ) Final Business Plan for Service Design (10.2) Exists Operational Exists Deployed and tested Exists Exists Available for use Data available for export Deployed Complete Available Scheduled Exists On schedule to revised plan Integrated into core code Grid available Documented Documented Accesses alternative sources Documented Underway Scheduled Exists

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19 BRISSkit sustainability & dependencies Technical service design challenge (UoL/UHLT) National engagement High Board level commitments from UoL,NIHR, UHLT, JISC, Eduserv JAT invited on to NHS-HE Forum will present BRISSkit at next meeting HEFCE benchmarking of efficiencies & expectations Define meaningful metrics: take up & cost savings Establish methodology to capture data against metrics E.g. eliminating duplication of software acquisition and/or development Modify end service design accordingly Commitment to investigate future service delivery options, e.g. JISC brokered service once a technically sustainable infrastructure in place UoL and/or UHLT provides service on behalf of JISC [Open source provision]