Translational Bioinformatics

 

Overview

The strategic purpose of Translational Bioinformatics ("TBI") projects is to develop an 'integrated translational research infrastructure in biomedicine' that is broadly accessible to all UNSW researchers.

Initially, will focus on cancer, but over time it will expand to support other clinical issues. This infrastructure is anticipated to greatly improve the access to large clinical datasets (i.e. ClinCR, NSW BD&M, NSW Cancer Registry).

Having access to these datasets, which relate directly to individuals with tissues already stored at UNSW, will greatly facilitate the translational work of UNSW researchers. TBI projects will enable researchers at UNSW to easily access and analyze research data simplifying data management.  

In its application to the Cancer Institute NSW ("CINSW") the TCRN highlighted data integration and accessibility as a goal to meet the CINSW program objectives:

  • Facilitate the generation of practice improving research and its more rapid adoption for improved patient outcomes
  • Facilitate evidence into practice research

 

Translational Bioinformatics Projects

 

 


 

Surgical Oncology Quality Registry 

 

The objective of this projec is to establish high quality system for surgical data collection by tumour specific data fields with key clinical indicators and also Introduce  structured operating reports.  The first part of the project will be led by Gynaecological Cancer Centre at Royal Hospital for Woman and St George and will then move to Hepatic, Pancreatico-bilary and Upper GI surgery. 

 


 

 

REDCap

REDCap is a mature, secure web application for building and managing online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a 'data dictionary' template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides automated export procedures for seamless data downloads to Excel and common statistical packages (SPSS, SAS, Stata, R), as well as a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields.


OpenClinica  

OpenClinica is an open source software that allows electronic data capture (EDC) and clinical data management (CDM) in clinical research. TCRN has made OpenClinica available to all TCRN members. Currently, OpenClinica is being used in various research studies including  the Lymphoma Lifestyle, Environment, and Family ‘LEAF’ StudyAustralian Genomics and Clinical Outcomes of Glioma 'AGOG' Study, and the Molecular and Cellular Oncology 'MCO' Study.

 


OpenSpecimen  

OpenSpecimen is a free and open source biobank management system that link biospecimens to respective clinical data. This software simplifies biospecimen management throughout collection, distribution and more. OpenSpecimen is currently being used for managing biospecimens collected for various biobanks within the UNSW Biorepository.


 

SHMi Appliance V3

SHMi stands for Secure Health Messaging Interface. SHMi is mirth connect (community version) wrapped in a virtual appliance with additional security layers. It is a useful middleware tool to integrate or exchange healthcare data using HL7 standard in a secure and compliant manner. SHMi interprets HL7 messages according to user-specified rules, transforms it into a form that receiving system (ex: OpenSpecimen) can understand and finally passes the transformed messages downstream. SHMi supports interfacing with HL7 feeds over HTTP which are clear-text and unsecured protocols. The key-differentiator with SHMi however is the support for HL7 over HTTPS. HTTPS encrypts traffic between the communicating endpoints using a strong, mutually-negotiated cipher suite such as AES or 3DES. This additional security is highly recommended when endpoints connect over public networks such as the Internet and to protect PHI data thereby complying with regulations and laws governing the healthcare industry. 


 

UNSW Secure Health Grade Infrastructure

TCRN TBI projects team and UNSW central IT has developed a capability to provide secure hosting for research activities that need to store, transmit or process Protected Health Information (PHI). Working with grant recipients and system owners we can ensure that hosted data and systems are secured appropriately to meet the requirements of Australian Commonwealth and state legislation, relevant institutions, granting bodies and study protocols. Specifically, our hosting capability is designed to comply with the 'Privacy Act 1988' and provide a capability for the encrypted transmission, storage and backup of data. The secure health grade infrastructure is used in all TCRN TBI projects. 


 Biogrid Australia - AustralianSarcoma Study Group

BioGrid Australia Limited is a secure research platform and infrastructure that provides access to real-time clinical, imaging and biospecimen data from the Australian Sarcoma Study Group across different institutions and jurisdictions. The web-based platform provides ethical access while protecting both privacy and intellectual property.