About Brain-CODE

Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

Ontario’s Big Data Opportunity

The Ontario Brain Institute is a provincially‐funded, not‐for‐profit research centre seeking to maximize the impact of neuroscience and establish Ontario as a world leader in brain research, commercialization and care. Convergent partnerships are created between researchers, clinicians, industry, patients, and their advocates to foster discovery and deliver innovative products and services that improve the lives of those living with brain disorders. To help realize this goal, the OBI funds five Integrated Discovery Programs (ID Programs) spanning the areas of epilepsy, cerebral palsy, neurodegenerative disorders, depression and neurodevelopmental disorders. The creation of these programs has resulted in a big data opportunity.

big da·ta (noun): extremely large datasets that may be organized computationally to reveal patterns, trends, and associations, especially relating to human behaviour and interactions. 

The creation of these programs has resulted in a Big Data opportunity. Integrating and sharing the wealth of Ontario-based brain research data has immense potential to inspire innovative, impactful diagnostics and treatments for brain disorders. To facilitate collaboration and discovery, OBI has developed Brain-CODE. Brain-CODE is an extensible informatics platform that manages the acquisition, storage and sharing of multidimensional data collected from patients with a variety of brain disorders (Figure 1). As an ID program researcher, Brain-CODE is your data storage solution, analytics toolbox, and collaboration hub. Your commitment to data sharing will transform Brain-CODE into a platform for discovery.  

IDP Data Matrix

By collecting data elements across diseases in a standardized manner this complex matrix arises: not only can deep comparisons across data modalities be made within one single brain disorder, but so too can deep comparisons begin to be investigated across brain disorders. Brain-CODE aims to facilitate data-driven discovery in neuroscience unlike ever before. 


Brain-CODE's Guiding Principles

1) Privacy & Security

Brain-CODE adheres to high levels of data privacy and security. Encryption and de-identification tools are used to protect participant data. To federate with other databases, Brain-CODE has a high-security data transfer infrastructure using enhanced validation certificates at the Centre for Advanced Computing (CAC) facility which meets Code of Federal Regulations (CFR) Title 21, Part11 standards.

2) Open & Collaborative

Brain-CODE was designed to enable data sharing and to foster collaborations among a broader researcher community. Allowing researchers to make their data open to other researchers studying the same or different disorders is becoming a common approach that leads to ground-breaking discoveries.

3) Interdisciplinary & Integrated

Brain-CODE facilitates data sharing within and across brain disorders to further understand mechanisms of disease, commonalities, comorbidities, while promoting novel hypothesis generation. This integrated approach to research sparks collaboration between clinicians, researchers, basic scientists, industry partners, participants and patient advocacy groups.

4) Patient Centred

The fundamental purpose of data sharing and collaboration on Brain-CODE is to enable greater insights into the data and ultimately drive faster translation of the discoveries towards positive patient outcomes.

5) Standardization

Standardization is a high priority for Brain-CODE and it ensures interoperability of datasets. Standardization efforts including clinical common data elements (CDEs), MEG and EEG standardization forms, and fBIRN phantom scans, help to define and format the vast array of clinical, neuroimaging and molecular data to optimize downstream integrative analyses.  

6) Discovery for Health Impact

By facilitating collaboration on a platform of standardized neuroscience data, the stage is set for integrative big data analytics. Integration of datasets across disciplines has the potential to catalyze new discoveries which can be translated into new diagnostics and treatments for brain disorders.


At the Heart of Brain-CODE

Brain-CODE is developed by experts in research informatics

The Indoc Consortium is led by Indoc Research, who helps design and implement the technical infrastructure, working very closely with OBI on the development of the platform.  Other members are the Electronic Health Information Laboratory (EHIL) led by Dr. Khaled El-Emam, a world-leader in data privacy and security, the Centre for Advanced Computing (CAC), which hosts Brain-CODE, and the Rotman Research Institute (RRI), that  provide the neuroimaging informatics infrastructure and workflows for Brain-CODE.


Brain-CODE is currently hosted on high-performance computing nodes at the CAC which boasts a combined processing  performance of 5 Tflops. The Brain-CODE network is connected through the Orion fibre-optic network, offering a transfer bandwidth of up to 10Gbps. As the use and requirements for Brain-CODE grow, additional hardware nodes can be allocated for increased data storage, specialized data processing, added demand for federation, and intensive concurrent analytical tasks.


The Brain-CODE neuroinformatics platform is designed around five  key components: data capture, data storage, data integration, analytics, and federation. Electronic data capture software enables researchers to enter and store multi-modal data on one convenient web-based interface. REDCap and OpenClinica for clinical data, LabKey for molecular and genomics data, and SPReD (based upon XNAT) for imaging data, have been integrated within Brain-CODE to suit diverse research needs.

Integration of the diverse data sets is facilitated by a middleware application and standardized data infrastructure. IBM Infosphere enables the heterogeneous sets of research data to be regrouped and organized for analytics.

Finally, specialized software is also being developed for Brain-CODE to enable secure linking and federation with other national and international health databases.


The Brain-CODE team is working towards building a robust analytics capacity for researchers to analyze their data as well as share, collaborate, and analyze other data sets effectively and efficiently.

Customizable analytics workspaces with access to high performance computing capabilities are available to registered Brain-CODE users by request. These virtual workspaces ensure data is secure, meanwhile providing access to a host of analytics tools, including R and Python. Researchers may also bring their own software licenses into the workspace environment if additional analytics capacity is required. 

Federation with National and International Databases

Brain-CODE is designed to seamlessly link with autonomous databases to leverage existing resources, augment data holdings and provide for richer analytics. This enables researchers to link their data with data that was previously difficult to access, making new discoveries possible.

  • ICES - Brain-CODE Linkage:
    • OBI and the Institute for Clinical and Evaluative Sciences (ICES) are currently working towards piloting a secure linkage which would allow researchers to augment the data collected from research participants with administrative health data.
    • The linkage of data from ICES with an external database such as Brain-CODE is unprecedented.
  • LORIS-Brain-CODE Federation:
    • This federation effort is aimed at two-way data access between both databases, and will help large national initiatives like Canadian Consortium for Neurodegeneration and Aging (CCNA).
  • NDAR - Brain-CODE Federation:
    • OBI and the National Database of Autism Research (NDAR) are working towards a federation effort which aims to provide two-way data access to researchers through both the Brain-CODE portal and the NDAR database.

Brain-CODE was designed with best-practice privacy strategies at the forefront to enable secure capture of sensitive participant data in a manner that abides by government legislation while fostering data sharing and linking opportunities. Privacy and security features have been incorporated into the foundation of Brain-CODE’s infrastructure, and are reinforced by comprehensive guidelines and state-of-the-art approaches to keep participant data safe. As a result, OBI has been named a “Privacy by Design” Ambassador by the Office of the Information and Privacy Commissioner of Ontario. By embedding the 7 foundational principles of Privacy by Design into the core of Brain-CODE, we can ensure that researchers have the information they need, and that participants are protected.

Access to Data

OBI is a supporter of the international open data movement. As such, it aims to make brain related research datasets available to a broader research community for greater outcomes with positive impact on patient care. To achieve this goal, data on Brain-CODE will be available to recognized academic and non-academic researchers. While Public Data will be immediately available to registered individuals, Controlled Data will require a formal data access request and committee review. More information is available in our Data Sharing Policy which can be accessed at www.braincode.ca/content/governance.

Participant Privacy

The number one priority when sharing data on Brain-CODE is ensuring participant privacy. The safe-guarding of participant identity begins before any data sharing on Brain-CODE. Brain-CODE will only share data in accordance with participant informed consent and adequate research ethics board approval. Through Brain-CODE, inter-institutional collaborators can share their raw study data. Further sharing with external researchers takes place after all data are stripped of identifying information to the extent possible using advanced de-identification tools. These tools are designed to both assess and consequently minimize the risk posed to a participant’s privacy.  The tiered approach to data organization on Brain-CODE enables granular access permissions to ensure only authorized users may access sensitive datasets.

All technical staff working with Brain-CODE are trained on how to respond to any unauthorized attempts at accessing data. Should any such attempts occur, procedures have been put in place to identify, report and manage any threats to data in Brain-CODE. More information on this can be found in our Privacy Breach Policy at available at www.braincode.ca/content/governance

Security Practices

To ensure that data in Brain-CODE are safe and secure, a number of measures have been implemented:

  • Continuous monitoring of software tools to identify any unauthorized attempt to access or interfere with data in Brain-CODE
  • Systematic user role validation and data de-identification before release to parties requesting data for analysis
  • A strict containment process as defined in the Brain-CODE governance policy
  • Regular Privacy Impact Assessment and Threat Risk Assessments to ensure that the infrastructure and data manipulation abide by high security standards
  • Regular meetings of a Brain-CODE Information Security Committee that oversees the privacy and security practices for all Data on Brain-CODE

If you have any questions, please contact governance@braincode.ca

Governance Structure

A robust governance structure has been developed to ensure that Brain-CODE maintains a high level of quality and security that is consistent with OBI’s vision and mandate. The following committees were formed to ensure the success of Brain-CODE:


Brain-CODE Informatics Steering Committee: provides insight on all issues relating to the establishment and management of Brain-CODE, ensuring that all progress is timely, of high quality and remains in line with the vision of OBI.

Brain-CODE Advisory Committee: advises on the direction and progress of Brain-CODE, ensuring the platform meets international best practices for data organization, sharing and analysis.

Brain-CODE Data Access Committee: develops data access and sharing policies and make recommendations to the Informatics Steering Committee regarding the release of data to third parties.

Brain-CODE Information Security Committee: recommends appropriate information security framework for the Brain-CODE platform, and work with the service group to implement and maintain privacy standards for all data and infrastructure in the platform. 

Brain-CODE Analytics Advisory Committee: advises on the analytics direction of Brain-CODE, ensuring the platform meets international best practices on data curation and integrated data analysis for discovery and sharing. 


Governance Policies

The Ontario Brain Institute has worked with a team of experts to develop clear and comprehensive guidelines on privacy and the use of participant research data. Our governance documents outline how the data are collected, stored, and accessed by Brain-CODE users.

To ensure clarity for study participants, we have developed standard informed consent language outlining how sensitive data will be collected, entered, de-identified, and shared using Brain-CODE.    

QUESTIONS: contact governance@braincode.ca




One of OBI’s key goals is to enable researchers to collaborate across disciplines, across institutions and across diseases. Efficient comparison of data (analysis) can only be done when data are in the same format. To properly analyze the vast array of clinical, neuroimaging, and molecular data that will be stored in Brian-CODE, it has to be standardized. Common Data Elements (CDEs) help define and format the different types of variables that researchers analyze . They allow for consistency in data collection across studies, improved quality of the data collected, and they increase opportunities for sharing and cross-study analysis. CDEs also optimize researchers’ ability to analyze large pools of data as well as facilitate its linking with external databases.

Learn more about Brain-CODE CDEs, including links to Brain-CDEs and resources