Overview

The Brain Data Science Platform (BDSP) organizes projects into three access levels, each with its own standardized access point. Once you are granted access to a specific level, you will have access to all projects within that access level.

To request access: Go to the project page for a specific dataset and follow the required instructions. This includes:

• Open Access: No special requirements
• Restricted Access: Sign the Data Use Agreement (DUA)
• Credentialed Access: Sign the Data Use Agreement (DUA) and provide proof of CITI training

Access Points by Level

Open Access

Access Point: s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-open-access-point/

Credentialed Access

Access Point: s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/

Restricted Access

Access Point: s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/

Open Access Projects

1. The Human Burst Suppression Electroencephalogram of Deep Hypothermia

Folder: hypothermia/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-open-access-point/hypothermia/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-open-access-point/hypothermia/ /your_local_path/ --recursive

2. Assessing Risk of Health Outcomes From Brain Activity in Sleep

Data Location: Data for this project is entirely on the GitHub repository.

3. Visual EEG-Based Grading of Delirium Severity and Associations with Clinical Outcomes (VE-CAM-S)

Data Location: Data for this project is entirely on the GitHub repository.

Credentialed Access Projects

1. Harvard-Emory ECG Database

Folder: ECG/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/ECG/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/ECG/ /your_local_path/ --recursive

2. Harvard Electroencephalography Database

Folder: EEG/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/EEG/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/EEG/ /your_local_path/ --recursive

3. The Human Sleep Project (HSP) & Boston Children's Hospital Sleep Corpus

Folder: PSG/

Note: The Boston Children's Hospital Sleep Corpus data is included within The Human Sleep Project folder.

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/PSG/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/PSG/ /your_local_path/ --recursive

4. The Brain Imaging and Neurophysiology Database (BIND)

Folder: Imaging/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/Imaging/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/Imaging/ /your_local_path/ --recursive

5. Automated phenotyping of mild cognitive impairment and dementias using electronic health records - Data and Code

Folder: NAX/nax-mci-dementia/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/NAX/nax-mci-dementia/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/NAX/nax-mci-dementia/ /your_local_path/ --recursive

6. Identification of patients with epilepsy using automated electronic health records phenotyping - Data and Code

Folder: NAX/NAX-epilepsy/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/NAX/NAX-epilepsy/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/NAX/NAX-epilepsy/ /your_local_path/ --recursive

7. NIDX - Identifying Neuroinfectious Diseases in Electronic Health Records

Data Location: Data for this project is entirely in the GitHub folder described on the project page.

8. Electronic Health Records (EHR) Context Data

Folder: EHR/

Note: This contains electronic health records data available for BDSP patients across multiple projects, providing context for data in other repositories. Includes data related to Harvard-Emory ECG Database, Harvard Electroencephalography Database, The Human Sleep Project, and The Brain Imaging and Neurophysiology Database (BIND).

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/EHR/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/EHR/ /your_local_path/ --recursive

9. Patient Merge History

Folder: PatientMergeHistory/

Note: This contains the merge history for all subject IDs (BDSPIDs). Most subjects have only one BDSPID, but occasionally subjects are discovered to have multiple BDSPIDs and are merged. This table provides the merge history.

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/PatientMergeHistory/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-credentialed-access-point/PatientMergeHistory/ /your_local_path/ --recursive

Restricted Access Projects

1. I-CARE - International Cardiac Arrest Research consortium EEG Database

Folders: i-care/ and ICARE_train/

Note: ICARE_train/ is part of the I-CARE project.

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/i-care/
aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/ICARE_train/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/i-care/ /your_local_path/ --recursive

2. Cyclops - Automated detection of interictal epileptiform discharges with few EEG channels

Folder: cyclops/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/cyclops/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/cyclops/ /your_local_path/ --recursive

3. E-CAM-S - Physiological Assessment of Delirium Severity via EEG

Folder: e-cam-s/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/e-cam-s/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/e-cam-s/ /your_local_path/ --recursive

4. SPaRCNet - Seizures, Rhythmic and Periodic Patterns in ICU EEG

Folders: sparcnet/ and sparcnet_data/

Note: sparcnet_data/ is part of the SPaRCNet project.

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/sparcnet/
aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/sparcnet_data/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/sparcnet/ /your_local_path/ --recursive

5. SpikeNet 2.0 - Deep learning model for epileptiform discharges in EEG

Folder: spikenet2/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/spikenet2/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/spikenet2/ /your_local_path/ --recursive

6. TEEGLLTEEG - This EEG Looks Like That EEG

Folder: teegllteeg/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/teegllteeg/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/teegllteeg/ /your_local_path/ --recursive

7. Quantifying Loop Gain using Dynamical Modelling of Ventilatory Control

Folder: LG_estimation/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/LG_estimation/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/LG_estimation/ /your_local_path/ --recursive

8. Sleep Recordings from Wearable Devices in Meditators

Folder: meditation-bai/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/meditation-bai/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/meditation-bai/ /your_local_path/ --recursive

9. Real-Time Segmentation of Burst Suppression Patterns in Critical Care EEG Monitoring

Folder: burst-supression/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/burst-supression/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/burst-supression/ /your_local_path/ --recursive

10. Targeted Metabolomics in the REGARDS Stroke Case-Cohort Study

Folder: regmet/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/regmet/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/regmet/ /your_local_path/ --recursive

11. Continuous EEG Predicts Delayed Cerebral Ischemia After SAH

Folder: sah/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/sah/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/sah/ /your_local_path/ --recursive

12. Morphological Prediction of CPAP Associated Acute Respiratory Instability (Self Similarity)

Folder: self-sim/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/self-sim/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/self-sim/ /your_local_path/ --recursive

13. Complete AI Sleep Report (CAISR)

Folder: caisr/

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/caisr/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/caisr/ /your_local_path/ --recursive

14. Automated EEG-based prediction of delayed cerebral ischemia after subarachnoid hemorrhage

Folder: sah/

Note: This project shares the same data folder as "Continuous EEG Predicts Delayed Cerebral Ischemia After SAH"

aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/sah/
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/bdsp-restricted-access-point/sah/ /your_local_path/ --recursive

15. Ordinal Sleep Depth - Data and Code

Status: This dataset will be uploaded soon.

16. Cerebrospinal Fluid Testing for Neuroinvasive West Nile Virus (CSF-WNV dataset)

Data Location: Data for this project is not on AWS. It can be downloaded directly from the bdsp.io project page.

General Usage Instructions

Prerequisites

1. AWS Account: Create an AWS account and add your AWS Account ID to your BDSP profile
2. Dataset Access Request: After adding your AWS ID, navigate to each dataset's page and click "Request Access"
3. AWS CLI: Install the AWS CLI on your system
4. Credentials: Configure your AWS credentials using aws configure
5. Access Approval: Complete the Data User Agreement (DUA) for your desired access level

Verify Your AWS Profile

Before attempting to access data, verify you are using the correct AWS profile/credentials:

# Verify your current AWS identity
aws sts get-caller-identity

This command will display your AWS Account ID, User ARN, and User ID. Make sure these match the credentials you expect to use. If you have multiple AWS profiles configured, you can set the active profile using:

# Set your AWS profile
export AWS_PROFILE=profilename

# Then verify again
aws sts get-caller-identity

Basic Commands

# List folders at the top level of your access point
aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/[ACCESS-POINT-NAME]/

# List contents of a specific project folder
aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/[ACCESS-POINT-NAME]/[PROJECT-FOLDER]/

# Download a single file
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/[ACCESS-POINT-NAME]/[PROJECT-FOLDER]/[FILE-NAME] /your_local_path/

# Download an entire project folder
aws s3 cp s3://arn:aws:s3:us-east-1:184438910517:accesspoint/[ACCESS-POINT-NAME]/[PROJECT-FOLDER]/ /your_local_path/ --recursive

# List files recursively (shows all files in all subfolders)
aws s3 ls s3://arn:aws:s3:us-east-1:184438910517:accesspoint/[ACCESS-POINT-NAME]/[PROJECT-FOLDER]/ --recursive

Listing Data from Access Point

To access data from an access point, use: aws s3 ls <access_point> to see the list of directories available from the specific access point.

Basic Command Examples:

# List Folders:
$ aws s3 ls s3://<<accesspointname>>/<<project_folder>>

# Copy a file:
$ aws s3 cp s3://<<accesspointname>>/<<project_folder>>/<<file_name>> /<<your_local_path>>/

# Copy a folder:
$ aws s3 cp s3://<<accesspointname>>/<<project_folder>> /<<your_local_path>> --recursive

Access Point Format:

s3://arn:aws:s3:us-east-1:184438910517:accesspoint/<<access-point-name>>/<<project-folder>>/

AWS Configuration Reference

If you need to reconfigure your AWS credentials:

aws configure
# Enter your credentials:
# AWS Access Key ID: [your access key]
# AWS Secret Access Key: [your secret access key]  
# Default region name: us-east-1
# Default output format: json

Step 1: Sign in to AWS

1. Go to the AWS Management Console: https://console.aws.amazon.com/
2. Log in with your AWS account.

Step 2: Open IAM

1. In the search bar at the top of the AWS console, type IAM.
2. Click IAM (Identity and Access Management).

Step 3: Select Your User or Role

1. If you are using an IAM User: click Users from the left menu, then select your username.
2. If you are using an IAM Role: click Roles from the left menu, then select the role you use.

Step 4: Attach S3 Permissions

1. Go to the Permissions tab.
2. Click Add permissions → Attach policies directly.
3. Search for and select AmazonS3FullAccess.
4. If your organization requires limited access, create a custom policy with at least the following permissions:

   {
     "Version": "2012-10-17",
     "Statement": [
       {
         "Effect": "Allow",
         "Action": [
           "s3:GetObject",
           "s3:ListBucket"
         ],
         "Resource": "*"
       }
     ]
   }

5. Click Add permissions.

Troubleshooting Access Issues

If you still receive "Access Denied" errors after completing the steps above:

1. Ensure you've clicked "Request Access" on the specific dataset page (not just added your AWS ID to your profile)
2. Try multiple times: Click "Request Access" multiple times if needed - permissions may take a few attempts to propagate due to caching (up to 3 attempts)
3. Wait between attempts: Wait a few minutes between attempts for the system to update
4. Verify IAM permissions: Double-check that your IAM user or role has the required S3 permissions (GetObject and ListBucket at minimum)